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Protein subunit interfaces: heterodimers versus homodimers.

(2005) Bioinformation 1

PubMed: 17597849 | PubMedCentral: PMC1891636 | DOI: null

References 1 Jones S Thornton JM Proc Natl Acad Sci 1996 93 13 8552589 2 Xu D Protein Engineering 1997 10 999 9464564 3 Tsai CJ Protein Science 1997 6 53 9007976 4 Conte L Lo J Mol Biol 1999 285 2177 ... 925793 5 Chakrabarti P Janin J Proteins 2002 47 334 11948787 6 Brinda KV Protein Eng 2002 15 265 11983927 7 Bahadur RP Proteins 2003 53 708 14579361 8 Nooren IM Thornton JM J Mol Biol 2003 325 991 12527304 9 Caffrey DR Protein Sci 2004 13 190 14691234 10 Zhanhua C Frontiers in Bioscience 2005 10 844 15569623 11 Jones S Thornton JM Prog Biophys Mol Biol 1995 63 31 7746868 12 Lijnzaad P Argos P Proteins 1997 28 333 9223180 13 Dasgupta S Proteins 1997 28 494 9261866 14 Valdar WS Thornton JM J Mol Biol 2001 313 399 11800565 15 Li L Frontiers in Bioscience 2005 10 1977 15769678 16 Lee B Richard EM J Mol Biol 1971 55 379 5551392 17 Rodriguez R Bioinformatics 1998 14 523 9694991 18 Jones S Thornton JM J Mol Biol 1997 272 121 9299342 Figures and Tables Table 1 Dataset Creation Hetero-dimers PDB code Resolution n (Å) Chain one Name of chain one Length Chain two Name of chain two Length 1YCS 2.2 B 53BP2 193 A P53 191 1ABR 2.1 B Abrin-A 267 A Carbohydrate 251 1KU6 2.5 A Acetylcholinesterase 535 B Fasciculin 2 61 1LFD 2.1 B Active ras protein 167 A Ras-interacting domain of ralgds 87 1JIW 1.7 P Alkaline metalloproteinase 470 I Proteinase inhibitor 105 1BPL 2.2 B Alpha-amylase 290 A Alpha-amylase 179 1KXV 1.6 A Alpha-amylase 496 C Camelid VHH domain cab10 119 1TMQ 2.5 A Alpha-amylase 470 B Ragi bifunctional inhibitor 117 1BVN 2.5 P Alpha-amylase 496 T Tendamistat 71 1ACB 2.0 E Alpha-chymotrypsin 241 I Eglin C 63 1CHO 1.8 E Alpha-chymotrypsin 238 I Turkey ovomucoid third domain 53 1CGI 2.3 E Alpha-chymotrypsinogen 245 I Trypsin inhibitor 56 1SLU 1.8 B Anionic trypsin 216 A Ecotin 131 1RE0 2.4 B ARF guanine-nucleotide exchange factor 1 195 A ADP-ribosylation factor 1 162 1KSH 1.8 A ARF-like protein 2 164 B Cyclic phosphodiesterase delta-subunit 141 1MG9 2.3 B ATP dependent CLP protease 143 A Protein YLJA 84 1BRL 2.4 A Bacterial luciferase 340 B Bacterial luciferase 319 1AVA 1.9 A Barley alpha-amylase 2 403 C Barley alpha-amylase/subtilisin inhibitor 181 1B27 2.1 A Barnase 110 D Barstar 90 1LUJ 2.5 A Beta-catenin 501 B Beta-catenin-interacting protein ICAT 71 1S0W 2.3 A Beta-lactamase tem 263 C Beta-lactamase inhibitory protein 165 1BND 2.3 A Brain derived neurotrophic factor 109 B Neurotrophin 3 108 1D4X 1.8 A C. Elegans actin 1/3 368 G Gelsolin 124 1G4Y 1.6 R Calmodulin 147 B Calcium-activated potassium channel RSK2 81 1DTD 1.7 A Carboxypeptidase A2 303 B Metallocarboxypeptidase inhibitor 61 1NW9 2.4 B Catalytic domain of caspase-9 238 A Inhibitor of apoptosis protein 3 91 1OKK 2.1 D Cell division protein 265 A Signal recognition particle protein 290 1H1S 2.0 A Cell division protein kinase 2 296 B Cyclin A2 258 1OHZ 2.2 A Cellulosomal scaffolding protein A 140 B Endo-1 4-beta-xylanase Y 56 1HL6 2.5 A CG8781 protein 119 B Mago nashi protein 137 1P5V 1.7 A Chaperone protein CAF1M 191 B F1 capsule antigen 136 1PDK 2.4 A Chaperone protein PAPD 296 B Protein PAPK 258 1N0L 2.3 A Chaperone protein PAPD 212 B Mature fimbrial protein PAPE 116 1FFG 2.1 B Chemotaxis protein chea 68 A Chemotaxis protein chey 128 1EAY 2 A Chey 128 C Chea 67 1P2M 1.8 A Chymotrypsinogen A 238 B Pancreatic trypsin inhibitor 58 1HCG 2.2 A Coagulation factor 236 B Coagulation factor 51 1V74 2.0 A Colicin D 107 B Colicin D immunity protein 87 1E44 2.4 B Colicin E3 96 A Immunity protein 84 1FR2 1.6 B Colicin E9 131 A Colicin E9 immunity protein 83 1F5Q 2.5 A Cyclin dependent kinase 2 296 B Gamma herpesvirus cyclin 247 1FIN 2.3 A Cyclin-dependent kinase 298 B Cyclin A 260 1BLX 1.9 A Cyclin-dependent kinase 6 305 B P19ink4D 160 1M9E 1.7 A Cyclophilin A 164 D HIV-1 capsid 135 1S6V 1.9 A Cytochrome C peroxidase 294 B Cytochrome C 108 1R8S 1.5 E Cytohesin 2 187 A ADP-ribosylation factor 1 160 1UJZ 2.1 B Designed colicin E7 dnase 127 A Designed colicin E7 immunity protein 87 1NLV 1.8 A Dictyostelium discoideum actin 364 G Gelsolin 123 1H31 1.5 A Diheme cytochrome C 260 B Cytochrome C 138 1EM8 2.1 A DNA polymerase III CHI subunit 147 B DNA polymerase III PSI subunit 110 1JQL 2.5 A DNA polymerase III beta chain 366 B DNA polymerase III delta subunit 140 1EAI 2.4 A Elastase 240 C Chymotrypsin isoinhibitor 1 61 1EFV 2.1 A Electron transfer flavoprotein alpha chain 312 B Electron transfer flavoprotein beta chain 252 1F60 1.7 A Elongation factor EEF1A 440 B Elongation factor EEF1BA 90 1TA3 1.7 B Endo-1 4-beta-xylanase 301 A Xylanase inhibitor protein I 274 1TE1 2.5 B Endo-1 4-xylanase 190 A Xylanase inhibitor protein I 274 3FAP 1.9 A FK506-binding protein 107 B FKBP12-rapamycin associated protein 94 1FCD 2.5 A Flavocytochrome C sulfide dehydrogenase 401 C Flavocytochrome c sulfide dehydrogenase 174 1NF3 2.1 A G25k GTP-binding protein 194 C PAR-6B 123 1NQI 2 B Galactosyltransferase 272 A Alpha lactalbumin 123 1WQ1 2.5 G Gapette 320 R Harvey-RAS 166 1OR0 2.0 B Glutaryl acylase beat subunit 510 A Glutaryl acylase alpha subunit 152 1AXI 2.1 B Growth hormone receptor 191 A Growth hormone 175 2NGR 1.9 B Gtpase activating protein 196 A GTP binding protein 191 1TX4 1.7 A Gtpase-activating protein rhogap 196 B Transforming protein RHOA 174 1AY7 1.7 A Guanyl-specific ribonuclease SA 96 B Barstar 89 1HX1 1.9 A Heat shock cognate 71 KDA 377 B Bag-family molecular chaperone regulator-1 112 1USU 2.2 A Heat shock protein HSP82 246 B AHA1 132 2HBE 2.0 B Hemoglobin 146 A Hemoglobin 141 1GPW 2.4 A Hisf protein 253 B Amidotransferase HISF 200 1CXZ 2.2 A His-tagged transforming protein RHOA 182 B PKN 86 1US7 2.3 B HSP90 chaperone protein kinase 194 A Heat shock protein HSP82 207 1KXP 2.1 D Human vitamin D-binding protein 438 A Actin alpha skeletal muscle 349 1H2A 1.8 L Hydrogenase 534 S Hydrogenase 267 1KA9 2.3 F Imidazole glycerol phosphtate synthase 251 H Imidazole glycerol phosphtate synthase 195 1IBR 2.3 B Importin beta-1 subunit 458 A GTP-binding nuclear protein ran 169 1PVH 2.5 A Interleukin 6 signal transducer 201 B Leukemia inhibitory factor 169 1IAR 2.3 B Interleukin-4 receptor alpha chain 188 A Interleukin 129 1I1R 2.4 A Interleukin-6 receptor beta chain 301 B Viral IL-6 167 1O6S 1.8 A Internalin A 461 B E-cadherin 105 1KI1 2.3 B Intersectin long form 342 A G25k GTP-binding protein 178 2KIN 1.9 A Kinesin 238 B Kinesin 100 1PPF 1.8 E Leukocyte elastase 218 I Ovomucoid inhibitor 56 1OP9 1.9 B Lysozyme C 130 A Hl6 camel VHH fragment 121 1UUZ 1.8 D Lysozyme C 129 A Inhibitor of vertebrate lysozyme 130 1OO0 1.9 A Mago nashi protein 144 B Drosophila Y14 92 1SVX 2.2 B Maltose-binding periplasmic protein 369 A Ankyrin repeat protein OFF7 157 1PQZ 2.1 A MCMV M144 238 B Beta-2-microglobulin 99 1MEE 2.0 A Mesentericopeptidase 275 I Eglin-C 64 1JW9 1.7 B Molybdopterin biosynthesis moeb protein 240 D Molybdopterin converting factor 81 1Q40 2.0 B Mrna export factor MEX67 180 A Mrna transport regulator MTR2 163 1SHW 2.2 B Neural kinase 181 A Ephrin-A5 138 1QAV 1.9 B Neuronal nitric oxide synthase 115 A Alpha-1 syntrophin 90 1E96 2.4 B Neutrophil cytosol factor 2 185 A Ras-related C3 botulinum toxin substrate 1 178 1NPE 2.3 A Nidogen 263 B Laminin gamma-1 chain 164 1GL4 2.0 A Nidogen-1 273 B Proteoglycan core protein 89 1M4U 2.4 A Noggin 199 L Osteogenic protein 1 112 1FYH 2.0 A Nterferon-gamma 242 B Interferon-gamma receptor alpha chain 201 1STF 2.4 E Papain 212 I Stefin B 98 1F34 2.5 A Pepsin A 325 B Major pepsin inhibitor PI-3 138 1UBK 1.2 L Periplasmic hydrogenase large subunit 534 S Periplasmic hydrogenase small subunit 267 1JLT 1.4 B Phospholipase A2 122 A Phospholipase A2 inhibitor 122 1L4Z 2.3 A Plasminogen 248 B Streptokinase 125 1DHK 1.9 A Porcine pancreatic alpha-amylase 495 B Bean lectin-like inhibitor 195 3YGS 2.5 P Procaspase 9 97 C Apoptotic protease activating factor 1 95 1FT1 2.3 B Protein farnesyltransferase 416 A Protein farnesyltransferase 315 1G4U 2.3 S Protein tyrosine phosphatase SPTP 360 R Ras-related C3 botulinum toxin substrate 1 180 1CT4 1.6 E Proteinase 185 I Ovomucoid inhibitor 51 1VG0 2.2 A Rab escort protein 1 481 B Ras-related protein rab-7 182 1F2T 1.6 A Rad50 abc-atpase N-terminal domain 145 B Rad50 abc-atpase C-terminal domain 143 1GUA 2.0 A Rap1A 167 B C-raf1 76 1HE1 2.0 C Ras-related C3 botulinum toxin substrate 1 176 A Exoenzyme S 135 1DS6 2.4 A Ras-related C3 botulinum toxin substrate 2 181 B RHO GDP-dissociation inhibitor 2 179 1C1Y 1.9 A Ras-related protein 167 B Proto-onkogene serine 77 1DFJ 2.5 E Ribonuclease A 124 I Ribonuclease inhibitor 456 1DZB 2.0 A SCFV fragment 1F9 224 X Turkey egg-white lysozyme C 129 1H2S 1.9 A Sensory rhodopsin II 225 B Sensory rhodopsin II transducer 60 1P57 1.8 B Serine protease hepsin heavy chain 247 A Serine protease hepsin light chain 110 4SGB 2.1 E Serine proteinase B 185 I Potato inhibitor 51 1SMP 2.3 A Serratia metallo proteinase 468 I Erwinia chrysanthemi inhibitor 100 1NRJ 1.7 B Signal recognition particle receptor 191 A Docking protein 147 1RJ9 1.9 A Signal recognition protein 277 B Signal recognition particle protein 282 1JTP 1.9 A Single-domain antibody 135 L Lysozyme C 129 1SGD 1.8 E Streptogrisin B 185 I Ovomucoid 51 1LW6 1.5 E Subtilisin BPN 281 I Ubtilisin-chymotrypsin inhibitor-2A 63 2SIC 1.8 E Subtilisin BPN 275 I Streptomyces subtilisin inhibitor 107 1SPB 2.0 S Subtilisin BPN 264 P Subtilisin BPN prosegment 71 1R0R 1.1 E Subtilisin carlsberg 274 I Ovomucoid 51 1CSE 1.2 E Subtilisin carlsberg 274 I Eglin-C 63 1SCJ 2.0 A Subtilisin E 275 B Subtilisin E 71 2SNI 2.1 E Subtilisin novo 275 I Chymotrypsin inhibitor 2 64 1EUC 2.1 B Succinyl-coa synthetase beta chain 393 A Succinyl-coa synthetase alpha chain 306 1ONQ 2.2 A T-cell surface glycoprotein CD1A 274 B Beta-2-microglobulin 99 1JTD 2.3 A Tem-1 beta-lactamase 262 B Beta-lactamase inhibitor protein II 273 1KTZ 2.2 B TGF-beta type II receptor 106 A Transforming growth factor beta 3 82 2TEC 2.0 E Thermitase 279 I Eglin-C 63 1JKG 1.9 B Tip associating protein 180 A NTF2-related export protein 1 139 1D4V 2.2 B TNF-related apoptosis inducing ligand 163 A Death receptor 5 117 1AVW 1.8 A Trypsin 223 B Trypsin inhibitor 171 1BRB 2.1 E Trypsin 223 I BPTI 51 1F5R 1.7 A Trypsin II 216 I Pancreatic trypsin inhibitor 57 1K9O 2.3 E Trypsin II anionic 223 I Alaserpin 376 1D6R 2.3 A Trypsinogen 223 I Bowman-birk proteinase inhibitor 58 1OPH 2.3 B Trypsinogen 223 A Alpha-1 protease inhibitor 375 1P2J 1.4 A Trypsinogen 220 I Pancreatic trypsin inhibitor 56 1S1Q 2.0 A Tumor susceptibility gene 101 protein 137 B Ubiquitin 71 1ITB 2.5 B Type 1 interleukin-1 receptor 310 A Interleukin-1 beta 153 1J7D 1.9 B Ubiquitin-conjugating enzyme E2-17 KDA 149 A MMS2 140 1EUV 1.3 A ULP1 protease 221 B Ubitqutin-like protein SMT3 79 1UGH 1.9 E Uracil-dna glycosylase 223 I Uracil-DNA glycosylase inhibitor 82 1UZX 1.9 A Vacuolar protein sorting-associated protein 135 B Ubiquitin 75 1JTT 2.1 A VH single-domain antibody 133 L Lysozyme 129 1RKE 2.4 A Vinculin 262 B VCL protein 176 1MA9 2.4 A Vitamin D-binding protein 442 B Actin alpha skeletal muscle 356 1YVN 2.1 A Yeast actin 372 G Gelsolin 125 1OXB 2.3 A YDP1P 166 B Osmolarity two-component system protein 124 Homodimers PDB code Resolution(Å) Name of Homodimer Scientific source Chain one Length Chain two Length 1CNZ 1.8 3-isopropylmalate dehydrogenase Salmonella typhimurium A 363 B 363 1AFW 1.8 3-ketoacetyl-coa thiolase Saccharomyces cerevisiae A 390 B 393 1M4I 1.5 Acetyltransferase Escherichia coli A 181 B 176 1LQ9 1.3 Actva-orf6 monooxygenase Streptomyces coelicolor A 112 B 112 1ADE 2 Adenylosucinate synthetase Escherichia coli A 431 B 431 1M7H 2 Adenylylsulfate kinase Penicillium chrysogenum A 203 B 200 1NA8 2.3 ADP-ribosylation binding protein Homo sapiens A 151 B 145 1OR4 2.2 Aerotactic transducer hemat Bacillus subtilis A 169 B 158 1BD0 1.6 Alanine racemase Bacillus stearothermophilus A 381 B 380 1A4U 1.9 Alcohol dehydrogenase Drosophila lebanonensis A 254 B 254 1ALK 2 Alkaline phosphatase Escherichia coli A 449 B 449 1LK9 1.5 Alliin lyase Allium sativum A 425 B 427 1HSS 2.1 Alpha-amylase inhibitor Triticum aestivum A 111 B 111 1S2Q 2.1 Amine oxidase B Homo sapiens A 499 B 494 1EKP 2.5 Amino acid aminotransferase Homo sapiens A 365 B 365 2GSA 2.4 Aminotransferase Synechococcus SP A 427 B 427 1DQT 2 Antigen Mus musculus A 117 B 117 1BJW 1.8 Aspartate aminotransferase Thermus thermophilus A 381 B 381 1JFL 1.9 Aspartate racemase Escherichia coli A 228 B 228 1MJH 1.7 Atp-binding protein Methanococcus jannaschii A 143 B 144 1IRI 2.4 Autocrine motility factor Homo sapiens A 557 B 557 1LR5 1.9 Auxin binding protein Zea mays A 160 B 160 1N80 2.5 Baseplate structural protein Bacteriophage T4 A 328 B 328 1EWZ 2.4 Beta lactamase oxa-10 Pseudomonas aeruginosa A 243 C 243 1EBL 1.8 Beta-ketoacyl-acp Synthase III Escherichia coli A 309 B 309 1N1B 2 Bornyl diphosphate synthase Salvia officinalis A 516 B 519 1KSO 1.7 Calcium-binding protein A3 Homo sapiens A 93 B 93 1JD0 1.5 Carbonic anhydrase Homo sapiens A 260 B 259 1AUO 1.8 Carboxylesterase Pseudomonas fluorescens A 218 B 218 1CDC 2 CD2 Rattus norvegicus A 96 B 96 1F13 2.1 Cellular coagulation factor Homo sapiens A 722 B 719 1NW1 2 Choline kinase Caenorhabditis elegans A 365 B 357 1R5P 2.2 Circadian oscillation regulator Anabaena SP A 90 B 93 1G64 2.1 Cob(I) alamin adenosyltransferase Salmonella typhimurium A 169 B 190 1OTV 2.1 Coenzyme pqq synthesis protein C Klebsiella pneumoniae A 254 B 254 1I0R 1.5 Conserved hypothetical protein Archaeoglobus fulgidus A 161 B 168 1OAC 2 Copper amine oxidase Escherichia coli A 719 B 722 1EAJ 1.4 Coxsackie virus Homo sapiens A 124 B 120 1CHM 1.9 Creatinase Pseudomonas putida A 401 B 401 1S44 1.6 Crustacyanin A1 subunit Homarus gammarus A 180 B 180 1GD7 2 CSAA protein Thermus thermophilus A 109 B 109 1L5B 2 Cyanovirin-N Nostoc ellipsosporum A 101 B 101 1SO2 2.4 Cyclic Phosphodiesterase B Homo sapiens A 363 B 363 1P3W 2.1 Cysteine desulfurase Escherichia coli A 385 B 385 1COZ 2 Cytidylyltransferase Bacillus subtilis A 126 B 126 1P6O 1.1 Cytosine deaminase Saccharomyces cerevisiae A 156 B 161 2DAB 2 D-amino acid aminotransferase Thermophilic bacillus A 280 B 282 1F17 2.3 Dehydrogenase Homo sapiens A 293 B 291 2NAC 1.8 Dehydrogenase Methylotrophic bacterium pseudomonas A 374 B 374 1NFZ 2 Delta-isomerase Escherichia coli A 176 B 180 1D1G 2.1 Dihydrofolate reductase Thermotoga maritima A 164 B 164 1DOR 2 Dihydroorotate dehydrogenase A Lactococcus lactis A 311 B 311 1AD1 2.2 Dihydropteroate synthetase Staphylococcus aureus A 264 B 251 1NU6 2.1 Dipeptidyl peptidase Homo sapiens A 728 B 728 1PE0 1.7 DJ-1 Homo sapiens A 187 B 187 1G1A 2.5 DTDP-D-glucose 4,6-Dehydratase Salmonella enterica A 352 B 352 1BBH 1.8 Electron transport Chromatium vinosum A 131 B 131 1Q8R 1.9 Endodeoxyribonuclease rusa Escherichia coli A 118 B 109 1RVE 2.5 Endonuclease Escherichia coli A 244 B 244 1M9K 2 Endothelial nitric-oxide synthase Homo sapiens A 400 B 401 1P43 1.8 Enolase 1 Saccharomyces cerevisiae A 436 B 436 1JR8 1.5 Erv2 protein mitochondrial Saccharomyces cerevisiae A 105 B 105 1V26 2.5 Fatty-acid-coa synthetase Thermus thermophilus A 489 B 510 1LBQ 2.4 Ferrochelatase Saccharomyces cerevisiae A 356 B 354 1RYA 1.3 Gdp-mannose mannosyl hydrolase Escherichia coli A 160 B 160 1QFH 2.2 Gelation factor Dictyostelium discoideum A 212 B 212 1JV3 2.2 Glcnac1p uridyltransferase Homo sapiens A 490 B 484 1DPG 2 Glucose 6-phosphate dehydrogenase Leuconostoc mesenteroides A 485 B 485 1QXR 1.7 Glucose-6-phosphate isomerase Pyrococcus furiosus A 187 B 187 1EOG 2.1 Glutathione S-transferase Escherichia coli A 208 B 208 1N2A 1.9 Glutathione S-transferase Escherichia coli A 201 B 187 1M0W 1.8 Glutathione synthetase Saccharomyces cerevisiae A 481 B 479 1R9C 1.8 Glutathione transferase Mesorhizobium loti A 125 B 118 1F4Q 1.9 Grancalcin Homo sapiens A 161 B 165 1DQP 1.8 Guanine phosphoribosyltransferase Giardia lamblia A 230 B 230 3SDH 1.4 Hemoglobin Scapharca inaequivalvis A 145 B 145 1IPI 2.2 Holliday junction resolvase Pyrococcus furiosus A 114 B 114 1FWL 2.3 Homoserine kinase Methanococcus jannaschii A 296 B 296 2HHM 2.1 Hydrolase Homo sapiens A 272 B 272 1PP2 2.5 Hydrolase Crotalus atrox R 122 L 122 1FJH 1.7 Hydroxysteroid dehydrogenase Comamonas testosteroni A 236 B 236 1G0S 1.9 Hypothetical Protein Escherichia coli A 201 B 202 1JOG 2.4 Hypothetical protein Haemophilus influenzae A 129 B 129 1PT5 2 Hypothetical protein Escherichia coli A 415 B 415 1QYA 2 Hypothetical Protein Escherichia coli A 293 B 307 1FUX 1.8 Hypothetical protein Escherichia coli A 164 B 163 1J30 1.7 Hypothetical rubrerythrin Sulfolobus tokodaii A 141 B 137 1LHZ 2.3 Immunoglobulin lambda Homo sapiens A 213 B 213 1AA7 2.1 Influenza virus matrix mrotein Influenza virus A 158 B 157 8PRK 1.9 Inorganic pyrophosphatase Saccharomyces cerevisiae A 282 B 282 1R8J 2 Kaia Synechococcus elongatus A 272 B 264 1CQS 1.9 Ketosteroid isomerase Pseudomonas putida A 124 B 124 1AQ6 2 L-2-haloacid dehalogenase Xanthobacter autotrophicus A 245 B 245 1I2W 1.7 Lactamase Bacillus licheniformis A 255 B 256 1BH5 2.2 Lactoylglutathione lyase Homo sapiens A 177 B 182 1QMJ 2.2 Lectin Gallus gallus A 132 B 132 1K75 1.8 L-histidinol dehydrogenase Escherichia coli A 425 B 425 1EHI 2.4 Ligase Leuconostoc mesenteroides A 360 B 347 1NWW 1.2 Limonene-1,2-epoxide hydrolase Rhodococcus erythropolis A 145 B 146 1UC8 2 Lysine biosynthesis enzyme Thermus thermophilus A 240 B 239 1EN5 2.3 Manganese superoxide dismutase Escherichia coli A 205 B 205 1A4I 1.5 Methylenetetrahydrofolate Homo sapiens A 285 B 295 1FC5 2.2 Molybdopterin biosynthesis Escherichia coli A 397 B 396 1JYS 1.9 Mta/sah nucleosidase Escherichia coli A 226 B 226 1LNW 2.1 Multidrug resistance operon repressor Pseudomonas aeruginosa A 137 B 135 1FP3 2 N-acyl-d-glucosamine Sus scrofa A 402 B 402 1FYD 2.3 NAD(+) Synthetase Bacillus subtilis A 271 B 246 1HJ3 1.6 Nitrite reductase Paracoccus pantotrophus A 544 B 542 1G1M 2.3 Nitrogenase iron protein Azotobacter vinelandii A 287 B 289 1G8T 1.1 Nuclease SM2 isoform Seratia marcencsens A 241 B 241 1EYV 1.6 N-utilizing substance protein Mycobacterium tuberculosis A 131 B 133 1M98 2.1 Orange carotenoid protein Arthrospira maxima A 316 B 314 1ORO 2.4 Orotate phosphoribosyltransferase Escherichia coli A 213 B 206 1DVJ 1.5 Orotidine 5'-phosphate decarboxylase Methanobacterium thermoautotrophicum A 239 B 211 1GGQ 2.5 Outer surface protein C Borrelia burgdorferi A 162 B 162 1AOR 2.3 Oxidoreductase Pyrococcus furiosis A 605 B 605 1BMD 1.9 Oxidoreductase Thermus flavus A 327 B 327 1HDY 2.5 Oxidoreductase Homo sapiens A 374 B 374 1N2O 2.1 Pantothenate synthetase Mycobacterium tuberculosis A 279 B 279 1RN5 2.2 Peptide deformylase Leptospira interrogans A 177 B 177 1PN2 2 Peroxisomal hydratase Candida tropicalis A 269 B 267 1PN0 1.7 Phenol 2-monooxygenase Trichosporon cutaneum A 652 C 656 1BXG 2.3 Phenylalanine dehydrogenase Rhodococcus SP A 349 B 347 1M6P 1.8 Phosphate receptor Bos Taurus A 146 B 146 1RQL 2.4 Phosphonoacetaldehyde hydrolase Bacillus cereus A 257 B 257 1O4U 2.5 Phosphoribosyltransferase Thermotoga maritima A 265 B 266 1EZ2 1.9 Phosphotriesterase Pseudomonas diminuta A 328 B 328 1EXQ 1.6 Pol polyprotein Escherichia coli A 147 B 145 1MNA 1.8 Polyketide synthase Streptomyces venezuelae A 276 B 278 1C6X 2.5 Protease Escherichia coli A 99 B 99 1FL1 2.2 Protease Escherichia coli A 192 B 207 1F89 2.4 Protein YLC351C Saccharomyces cerevisiae A 271 B 271 1LHP 2.1 Pyridoxal kinase Ovis aries A 306 B 309 1CBK 2 Pyrophosphokinase Haemophilus influenzae A 160 B 160 1QR2 2.1 Quinone reductase type 2 Homo sapiens A 230 B 230 1EN7 2.4 Recombination endonuclease Bacteriophage T4 A 157 B 157 1EV7 2.4 Restriction endonuclease naei Nocardia aerocolonigenes A 295 B 293 1H8X 2 Ribonuclease Homo sapiens A 125 B 125 1I4S 2.2 Ribonuclease III Aquifex aeolicus A 147 B 147 1KGN 1.9 Ribonucleotide reductase protein Corynebacterium ammoniagenes A 296 B 296 1TLU 1.6 S-adenosylmethionine decarboxylase Thermotoga maritima A 117 B 117 1K6Z 2 Secretion chaperone syce Yersinia pestis A 120 B 119 1K3S 1.9 Sige Salmonella enterica A 106 B 104 1PJQ 2.2 Siroheme synthase Salmonella typhimurium A 447 B 454 1HJR 2.5 Site-specific recombinase Escherichia coli A 158 C 158 3LYN 1.7 Sperm lysine Haliotis fulgens A 122 B 124 2SQC 2 Squalene-hopene Cyclase Alicyclobacillus acidocaldarius A 623 B 623 1SCF 2.2 Stem cell factor Homo sapiens A 116 B 118 1OX8 2.2 Stringent starvation protein B Escherichia coli A 105 B 105 1M3E 2.5 Succinyl-coa Sus scrofa A 459 B 460 1R7A 1.8 Sucrose phosphorylase Bifidobacterium adolescentis A 503 B 503 1SOX 1.9 Sulfite oxidase Gallus gallus A 463 B 458 1L5X 2 Survival protein E Pyrobaculum aerophilum A 270 B 272 1REG 1.9 T4 rega Bacteriophage T4 X 122 Y 120 1MKB 2 Thiol ester dehydrase Escherichia coli A 171 B 171 1QHI 1.9 Thymidine kinase Herpes simplex virus A 304 B 308 1HSJ 2.3 Transcription/sugar binding protein Escherichia coli A 487 B 487 1NY5 2.4 Transcriptional regulator Aquifex aeolicus A 384 B 385 1ON2 1.6 Transcriptional regulator Bacillus subtilis A 135 B 135 1SMT 2.2 Transcriptional repressor Synechococcus A 98 B 101 1TRK 2 Transferase Saccharomyces cerevisiae A 678 B 678 7AAT 1.9 Transferase Gallus gallus A 401 B 401 1KIY 2.4 Trichodiene synthase Fusarium sporotrichioides A 354 B 354 1I8T 2.4 Udp-galactopyranose mutase Escherichia coli A 367 B 367 1F6D 2.5 Udp-n-acetylglucosamine Escherichia coli A 366 B 363 1JP3 1.8 Undecaprenyl pyrophosphate synthase Escherichia coli A 210 B 207 1JMV 1.9 Universal stress protein A Haemophilus influenzae A 140 B 137 1HQO 2.3 URE2 protein Saccharomyces cerevisiae A 221 B 217 9WGA 1.8 Wheat germ agglutinin Triticum vulgaris A 170 B 170 1MI3 1.8 Xylose reductase Candida tenuis A 319 B 319 Figure 1 Difference between heterodimer and homodimer interface properties is shown.

Publication Year: 2005


Recognizing protein-protein interfaces with empirical potentials and reduced amino acid alphabets.

(2007) BMC Bioinformatics 8

PubMed: 17662112 | PubMedCentral: PMC2034607 | DOI: 10.1186/1471-2105-8-270

Blind heterodimer set a TS1, TS2 sets b PDB ID 20Cl Bastolla 6Cl PDB ID 20Cl Bastolla 6Cl 1ai7 1 1 1 1abr 4 2 3 1as4 1 1 1 1aui 1 1 1 1bpl 1 1 1 1ay7 3 3 2 1clv 2 1 2 1blx 3 6 3 1dj7 4 4 4 1c1y 3 4 3 ... dow 1 1 1 1dkf 2 47 1 1eud 8 9 7 1ugh 1 3 1 1f0c 1 1 1 1efv 1 1 1 1ksg 5 3 5 1ezq 1 1 1 1ku6 3 2 4 1f3v 67 145 36 1lot 1 1 1 1fle 19 4 9 1lpb 20 8 16 1hdm 1 1 1 1mhm 1 1 1 1itb 1 1 3 1mtp 1 1 1 1phn 1 1 1 1mzw 3 3 4 1qav 1 2 1 1npe 4 4 2 1smp 14 69 2 1nw9 1 10 1 1stf 2 5 1 1n52 10 1 9 D c 8/17 6/17 9/17 1o5m 3 1 2 D 3 13/17 9/17 15/17 1qge 1 1 1 1rke 1 1 1 1rtj 1 2 1 1ubt 1 2 1 4sgb 5 6 5 D c 13/24 13/24 13/24 D 3 17/24 18/24 16/24 Decoys constructed by other methods: Sternberg and Vakser decoys Limited series of protein–protein structures have been made available by Sternberg (ten series) and Vakser (five series) and coworkers, along with 99 high-quality decoys each.

Publication Year: 2007


Atomic analysis of protein-protein interfaces with known inhibitors: the 2P2I database.

(2010) PLoS One 5

PubMed: 20231898 | PubMedCentral: PMC2834754 | DOI: 10.1371/journal.pone.0009598

Class # Family Complex a Number of Inhibitors b Source c Affinity d (nM) Ref I 1 BclX L /Bak 1bxl 8 PubMed 340 [27] I 2 MDM2/p53 1ycr 1ycq 3 PubMed 600 [28] I 3 XIAP BI... 3/CASPASE 9 1nw9 2 PubMed 20 [29] I 4 XIAP BIR3/SMAC 1g73 5 PubMed 420 [29] I 5 ZipA/FtsZ 1f47 4 PubMed 20,000 [30] II 6 Chagasin/Papain 3e1z 1 PDB 0.036 e [31] II 7 E2/E1 1tue 1 PubMed na [32] II 8 FKBP12/TGFR 1b6c 17 PDB na [33] II 9 IL-2/IL-2R 1z92 8 PubMed 10 [34] II 10 MMP1/TIMP1 2j0t 1 PDB 0.40 e [35] II 11 MMP3/TIMP1 1oo9 1 PDB 0.22 e [36] II 12 Subtilisin/Eglin C 1cse 1r0r 1to2 1 PDB 0.029 [37] – [39] II 13 Thrombin/Protein C inhibitor 3b9f 1 PDB na [40] II 14 Trypsin/Trypsin inhibitor 2uuy 3 PDB 0.02 [41] PPIs were subdivided into class I that correspond to protein/peptide interactions with less than six segments at the interface (families 1–5) and class II that represent more globular interacting domains with more segments (families 6–14).

In the case of the XIAP/Caspase complex (PDB code: 1nw9) the high number of hydrogen bonds and the absence of charged residues were responsible for its different behavior.

Publication Year: 2010


Computational protein design: validation and possible relevance as a tool for homology searching and fold recognition.

(2010) PLoS One 5

PubMed: 20463972 | PubMedCentral: PMC2864755 | DOI: 10.1371/journal.pone.0010410

SKIs __________ Chemokines __________ PDZ domains __________ Caspases __________ PDB code Identity PDB code Identity PDB code Identity PDB code Identity 4pti 37.4 1ilq 30.3 1pdr 36.0 1nme 31.0 2knt 42... 2 1plf 31.3 1kwa 22.8 1m72 31.6 1tfx 41.8 1msg 25.6 2fe5 36.3 1pyo 37.5 1aap 42.6 1hum 32.4 1be9 32.5 1i51 32.1 1bik 42.6 1vmp 32.2 1qav 29.7 1qdu 28.7 1dtx 37.3 1rto 40.1 1nte 24.2 1nw9 41.9 1bun 37.1 1dom 26.0 1l6o 31.7 1dem 41.9 1eig 27.9 1qau 30.3 1g2s 26.5 1g9o 35.4 1j9o 18.2 1ihj 28.6 1nr2 38.7 1n7f 30.5 1nap 30.7 2h3l 36.2 1n7e 30.9 1q3o 35.6 2f5y 35.6 2fne 35.2 2byg 36.5 Mean 40.4 30.3 32.3 33.8 a Mean identity of the 8.000 lowest-energy designed sequences relative to each corresponding native template.

Publication Year: 2010


Benchmarking and analysis of protein docking performance in Rosetta v3.2.

(2011) PLoS One 6

PubMed: 21829626 | PubMedCentral: PMC3149062 | DOI: 10.1371/journal.pone.0022477

PDB Difficulty | type N 5 µ (N 5 ) [σ(N 5 )] P success Irmsd Classification PDB Difficulty | type N 5 µ (N 5 ) [σ(N 5 )] P success Irmsd Classification 1K74 rigid-body ... O 2 2.5 [1.1] 0.20 1.63 RB sampling 1EER difficult | O 1 0.9 [1.0] 0.02 2.23 BB sampling 1Z5Y rigid-body | O 2 2.4 [1.1] 0.16 1.14 BB sampling 1FAK difficult | O 1 0.9 [0.9] 0.01 3.30 discrimination 1WEJ rigid-body | A 2 2.2 [1.1] 0.14 2.60 discrimination 1TMQ rigid-body | E 1 0.8 [0.9] 0.01 1.47 RB sampling 1HE8 medium | O 2 2.2 [1.1] 0.13 3.19 BB sampling 1I4D rigid-body | O 1 0.8 [0.9] 0.01 3.13 RB sampling 1ATN difficult | O 2 2.1 [1.2] 0.12 1.53 RB sampling 1RLB rigid-body | O 1 0.8 [0.9] 0.01 3.88 RB sampling 2HQS rigid-body | O 2 2.1 [1.2] 0.13 2.69 BB sampling 1Z0K rigid-body | O 1 0.7 [0.8] 0.00 3.56 BB sampling 1JMO difficult | O 2 2.1 [1.2] 0.11 2.82 BB sampling 1EFN rigid-body | O 1 0.7 [0.8] 0.00 3.58 BB sampling 2O8V rigid-body | E 2 2.1 [1.2] 0.12 3.62 BB sampling 1I9R rigid-body | AB 1 0.6 [0.8] 0.00 0.52 RB sampling 1J2J rigid-body | O 2 2.0 [1.4] 0.14 1.10 BB sampling 1AZS rigid-body | O 0 0.5 [0.9] 0.01 5.41 RB sampling 1NSN rigid-body | AB 2 2.0 [1.2] 0.10 1.15 discrimination 2B42 rigid-body | E 0 0.4 [0.6] 0.00 5.85 RB sampling 1K5D medium | O 2 2.0 [1.1] 0.09 2.87 BB sampling 2BTF rigid-body | O 0 0.3 [0.6] 0.00 4.44 BB sampling 1FQ1 difficult | E 2 1.7 [1.3] 0.08 2.18 RB sampling 1KKL medium | E 0 0.2 [0.5] 0.00 4.60 RB sampling 2AJF rigid-body | O 2 1.7 [1.1] 0.06 1.23 RB sampling 1F51 rigid-body | O 0 0.2 [0.5] 0.00 12.35 BB sampling 1E96 rigid-body | O 1 1.6 [1.1] 0.05 3.38 BB sampling 1KAC rigid-body | O 0 0.1 [0.5] 0.00 4.01 BB sampling 1I2M medium | O 1 1.5 [1.0] 0.03 2.68 BB sampling 1MLC rigid-body | A 0 0.1 [0.4] 0.00 4.31 BB sampling 1QFW rigid-body | AB 1 1.5 [1.1] 0.03 1.93 RB sampling 1S1Q rigid-body | O 0 0.1 [0.3] 0.00 4.37 BB sampling 1GLA rigid-body | O 2 1.5 [1.1] 0.05 2.98 BB sampling 1M10 medium | E 0 0.0 [0.0] 0.00 4.46 BB sampling 1AKJ rigid-body | O 1 1.2 [1.0] 0.02 1.48 BB sampling 1A2K rigid-body | O 0 0.0 [0.0] 0.00 5.20 BB sampling 1EZU rigid-body | E 1 1.2 [1.0] 0.02 2.82 RB sampling 1R8S difficult | O 0 0.0 [0.0] 0.00 5.21 BB sampling 1F34 rigid-body | E 1 1.2 [1.0] 0.02 4.00 RB sampling 1GP2 medium | O 0 0.0 [0.0] 0.00 5.23 BB sampling 1GRN medium | O 1 1.1 [1.0] 0.02 1.24 BB sampling 1IBR difficult | O 0 0.0 [0.0] 0.00 5.46 RB sampling 1NW9 medium | E 1 1.1 [1.0] 0.02 2.33 BB sampling 1BKD difficult | O 0 0.0 [0.0] 0.00 5.62 BB sampling 2H7V medium | O 1 1.1 [1.0] 0.02 3.65 BB sampling 2OT3 difficult | O 0 0.0 [0.0] 0.00 6.00 BB sampling 1GHQ rigid-body | O 1 1.0 [1.0] 0.01 2.69 BB sampling 1FQJ rigid-body | O 0 0.0 [0.0] 0.00 6.48 RB sampling 2NZ8 medium | O 1 1.0 [1.0] 0.02 3.91 BB sampling 1PXV difficult | E 0 0.0 [0.0] 0.00 9.49 BB sampling 1IB1 medium | O 1 1.0 [1.0] 0.01 3.95 discrimination 1H1V difficult | O 0 0.0 [0.0] 0.00 9.96 BB sampling 1K4C rigid-body | AB 1 1.0 [1.1] 0.02 2.15 BB sampling 1Y64 difficult | O 0 0.0 [0.0] 0.00 13.70 discrimination 1EWY rigid-body | E 1 1.0 [1.1] 0.02 3.01 BB sampling 1DQJ rigid-body | A 0 0.0 [0.2] 0.00 6.15 BB sampling 2PCC rigid-body | E 1 1.0 [0.9] 0.01 3.38 discrimination 1ACB medium | E 0 0.0 [0.1] 0.00 4.56 RB sampling 1KLU rigid-body | O 0 0.0 [0.1] 0.00 8.16 BB sampling Unsuccessful docking predictions are classified as cases for which the five lowest-energy decoys did not contain at least three near-native structures.

Publication Year: 2011


Visualisation of variable binding pockets on protein surfaces by probabilistic analysis of related structure sets.

(2012) BMC Bioinformatics 13

PubMed: 22417279 | PubMedCentral: PMC3359218 | DOI: 10.1186/1471-2105-13-39

Table 4 Structures used in protein-ligand and protein-protein pocket analysis Target protein (PDB id of apo structure) Inhibitor (PDB id) Protein partner (PDB id) Bcl-X L ) acyl sulfonamide derivative... Bak (1LXL) (1YSI) (1BXL) MDM2 benzodiazapine derivative p53 (1Z1M) (1T4E) (1YCR) Xiap apoptosis inhibitor naphthalenamide derivative Caspase 9 Bir3 domain (1F9X) (1TFQ) (1NW9) Xiap apoptosis inhibitor Smac peptidomimetic SMAC caspase activator Bir3 domain (1F9X) (2JK7) (1G73) ZipA indoloquinolizin inhibitor 1 FtsZ (1F46) (1S1J) (1F47) HPV11 E2 protein tetrahydrofuran derivative HPV11 E1 protein (1RK6) (1R6N) (1TUE) (1R6N) Interleukin 2 diphenyl derivative IL2-Receptor (1M47) (1M48) (1Z92) HIV-1 Integrase chlorophenyl-dihydroquinolin acetic acid LEDGF (3L3U) (3LPT) (2B4J) TNFa subunit A chromen-4-one derivative TNFa subunit B (1TNF) (2AZ5) (1TNF) TNF receptor 1a thiazolidin-4-one derivative TNF-beta (1EXT) (1FT4) (1TNR) MDM4 subunit A chlorobenzyl-phenyl-imidazol derivative p53 (3DAB) (3LBJ) (3DAB) Structures used in comparative analyses (detailed in Tables 1 and 2) are taken from the 2P2I database of protein-protein complexes with known inhibitors of the protein-protein interaction.

Publication Year: 2012


The E. coli effector protein NleF is a caspase inhibitor.

(2013) PLoS One 8

PubMed: 23516580 | PubMedCentral: PMC3597564 | DOI: 10.1371/journal.pone.0058937

E. Superimposition of the NleF-bound caspase-9 dimer presented in this study and the previously described caspase-9 crystal structure (light blue) in complex with the BIR3 domain of the XIAP inhibitor... shown as red cartoon (PDB entry 1NW9).

Publication Year: 2013


Monoubiquitination and activity of the paracaspase MALT1 requires glutamate 549 in the dimerization interface.

(2013) PLoS One 8

PubMed: 23977204 | PubMedCentral: PMC3747146 | DOI: 10.1371/journal.pone.0072051

Model of the MALT1 protease domain, calculated based on the crystal structures of caspase-9, -3 and -8 (PDB codes 1NW9, 1CP3 and 2C2Z, respectively) and the dimeric structure of caspase-8 (1F9E).

The model of the monomeric MALT1 protease domain was calculated based on the crystal structures of caspase-9, -3 and -8 (PDB codes 1NW9, 1CP3 and 2C2Z) sharing 19%, 18% and 18% sequence identity, respectively, with the MALT1 caspase-like domain.

Publication Year: 2013


IAP proteins as targets for drug development in oncology.

(2013) Onco Targets Ther 9

PubMed: 24092992 | PubMedCentral: PMC3787928 | DOI: 10.2147/OTT.S33375

( B–D ) Comparison of the XIAP-BIR3 (blue) bound to the IBM of caspase-9 (ATPFQ) (orange) (pdb 1nw9): ( B ) The IBM (AVPI tetrapeptide) of Smac (red) (pdb 2opz); ( C ) The monovalent Smac mime... ic SM-130 (green) (pdb 2 jk7); and ( D ) The BIR domains of IAPs are organized in four α-helices and three β-strand sheets maintained by a zinc ion (yellow).

Publication Year: 2013


HADDOCK(2P2I): a biophysical model for predicting the binding affinity of protein-protein interaction inhibitors.

(2014) J Chem Inf Model 54

PubMed: 24521147 | PubMedCentral: PMC3966529 | DOI: 10.1021/ci4005332

Table 1 K i and K d Binding Affinity Data Set of Protein–Protein Interaction Inhibitors a   interaction biological role PDB (complex) K d (complex) (M)   Bcl-x L /Bak programme... cell death 1bxl 3.4 × 10 –7   modulator (common name) PubChem compound identifier (CID) binding partner PDB (complex) K i ∥ K d (modulator) (M) 1 N3B 4369509 Bcl-x L 1ysi 1.2 × 10 –7 2 ABT-737 11228183 Bcl-x L 2yxj 5.0 × 10 –10 3 4FC 2782689 Bcl-x L 1ysg 3.0 × 10 –5 4 TN1 68258 Bcl-x L 1ysg 4.3 × 10 –3 5 LIU 15991562 Bcl-2 2o22 6.7 × 10 –8 6 W1191542 44182311 Bcl-x L 3inq 1.1 × 10 –8   interaction biological role PDB (complex) K d (complex) (M)   MDM2/p53 transcription regulation 1ycr 6.0 × 10 –7   modulator (common name) PubChem compound identifier (CID) binding partner PDB (complex) K i ∥ K d (modulator) (M) 7 HDM2 656933 MDM2 1t4e 8.0 × 10 –8 8 WK23 44825260 MDM2 3lbk 9.2 × 10 –7 9 MI-63 72200152 MDM2 3lbl 3.6 × 10 –8   interaction biological role PDB (complex) K d (complex) (M)   XIAP-BIR3/CASPASE-9 programmed cell death 1nw9 2.0 × 10 –8   modulator (common name) PubChem compound identifier (CID) binding partner PDB (complex) K i ∥ K d (modulator) (M) 10 998 4369343 XIAP-BIR3 1tfq 1.2 × 10 –8 11 997 5388929 XIAP-BIR3 1tft 5.0 × 10 –9 12 9JZ 72199974 XIAP-BIR3 3hl5 3.4 × 10 –5   interaction biological role PDB (complex) K d (complex) (M)   XIAP-BIR3/SMAC programmed cell death 1g73 4.2 × 10 –7   modulator (common name) PubChem compound identifier (CID) binding partner PDB (complex) K i ∥K d (modulator) (M) 13 BI6 72199334 XIAP-BIR3 2jk7 6.7 × 10 –8 14 AoxSPW 24916924 XIAP-BIR3 2opy 3.0 × 10 –5 15 Smac005 25011737 XIAP-BIR3 3clx 1.2 × 10 –7 16 Smac005 25011737 XIAP-BIR3 3cm7 1.2 × 10 –7 17 Smac010 25011738 XIAP-BIR3 3cm2 4.2 × 10 –7 18 Smac037 25058143 XIAP-BIR3 3eyl 2.2 × 10 –7 19 CZ3 72199333 XIAP-BIR3 3g76 2.3 × 10 –7   interaction biological role PDB (complex) K d (complex) (M)   ZipA/FtsZ cell cycle regulation/cellular structure 1f47 2.0 × 10 –5   modulator (common name) PubChem compound identifier (CID) binding partner PDB (complex) K i ∥ K d (modulator) (M) 20 WAI 656967 ZipA 1y2f 1.2 × 10 –5 21 CL3 5287936 ZipA 1y2g 8.3 × 10 –5   interaction biological role PDB (complex) K d (complex) (M)   HPV-E2/E1 viral infection 1tue n/d   modulator (common name) PubChem compound identifier (CID) binding partner PDB (complex) K i ∥ K d (modulator) (M) 22 BILH 434 5287508 HPV-E2 1r6n 4.0 × 10 –8   interaction biological role PDB (complex) K d (complex) (M)   IL-2/IL-2R immune system regulation 1z92 1.0 × 10 –8   modulator (common name) PubChem compound identifier (CID) binding partner PDB (complex) K i ∥ K d (modulator) (M) 23 FRG 5288250 IL-2 1m48 2.2 × 10 –5 24 FRB 23586028 IL-2 1pw6 7.0 × 10 –6 25 SP-1985 5287951 IL-2 1m49 7.5 × 10 –6 26 FRH 5288251 IL-2 1py2 1.0 × 10 –7 27 SP-4160 656989 IL-2 1qvn 1.4 × 10 –6 a Original references for the affinity data are provided in the Supporting Information (Table S1).

Table 2 IC50 Binding Affinity Data Set of Protein–Protein Interaction Inhibitors a   interaction biological role PDB (complex) K d (complex) (M)   Bcl-x L /Bak programmed cell death 1bxl 3.4 × 10 –7   modulator (common name) PubChem compound identifier (CID) binding partner PDB (complex) IC50 (modulator) (M) 28 HI0 24798804 Bcl-x L 3qkd 3.0 × 10 –09 29 0Q5 56973540 Bcl-x L 4ehr 1.3 × 10 –08   interaction biological role PDB (complex) K d (complex) (M)   LEDGF/75-integrase programmed cell death 2b4j 1.1 × 10 –8   modulator (common name) PubChem compound identifier (CID) binding partner PDB (complex) IC50 (modulator) (M) 30 723 921795 75-integrase 3lpt 1.2 × 10 –5 31 976 45281242 75-integrase 3lpu 1.4 × 10 –6 32 TQ2 44199170 75-integrase 4e1m 2.2 × 10 –7 33 TQX 44198672 75-integrase 4e1n 1.9 × 10 –8   interaction biological role PDB (complex) K d (complex) (M)   MDM2/p53 transcription regulation 1ycr 6 × 10 –7   modulator (common name) PubChem compound identifier (CID) binding partner PDB (complex) IC50 (modulator) (M) 34 IMY 49867154 MDM2 1ttv 1.6 × 10 –7 35 YIN 5594130 MDM2 3jzk 1.2 × 10 –6 36 0R2 56591324 MDM2 4ere 4.2 × 10 –9 37 0R3 56965957 MDM2 4erf 1.1 × 10 –9 38 BLF 56951871 MDM2 4dij 3.0 × 10 –8   interaction biological role PDB (complex) K d (complex) (M)   TNF/TNF receptor inflammation n/d n/d   modulator (common name) PubChem compound identifier (CID) binding partner PDB (complex) IC50 (modulator) (M) 39 703 4470566 TNF receptor 1ft4 2.7 × 10 –7   interaction biological role PDB (complex) K d (complex) (M)   bromodomain/histone inflammation n/d n/d   modulator (common name) PubChem compound identifier (CID) binding partner PDB (complex) IC50 (modulator) (M) 40 P9M 53054259 BRD2 4a9m 5.0 × 10 –7 41 A9N 72200779 BRD2 4a9n 1.5 × 10 –6 42 JQ1 46907787 BRD2 3oni 1.3 × 10 –7 b 43 JQ1 46907787 BRDT 4flp 1.9 × 10 –7 b 44 JQ1 46907787 BRD4 3mxf 4.9 × 10 –8 b 45 EAM 46943432 BRD4 3p5o 5.1 × 10 –8 b 46 I-BET151 52912189 BRD4 3zyu 1.0 × 10 –7 b   interaction biological role PDB (complex) K d (complex) (M)   integrin α-L/ICAM1 (CD-54) host–virus interaction 1nw9 2.0 × 10 –8   modulator (common name) PubChem compound identifier (CID) binding partner PDB (complex) IC50 (modulator) (M) 47 LA1 5326914 integrin α-L 1xuo 6.9 × 10 –8 48 2O7 16040268 integrin α-L 2o7n 1.5 × 10 –8 49 BQM 11712628 integrin α-L 3bqm 1.7 × 10 –9 50 E2M 24875322 integrin α-L 3e2m 0.4 × 10 –10 51 BJZ 11699447 integrin α-L 3m6f 2.5 × 10 –9 a Original references for the IC50 data were retrieved from the relevant PDB entries in the Protein Data Bank ( www.pdb.org ).

Publication Year: 2014


Highly precise protein-protein interaction prediction based on consensus between template-based and de novo docking methods.

(2013) BMC Proc 7

PubMed: 24564962 | PubMedCentral: PMC4044902 | DOI: 10.1186/1753-6561-7-S7-S6

Table 1 Protein and PDB ID list of human apoptosis pathway dataset Protein Name PDB ID (_Chain) AIF 1M6I _A AKT1 1UNQ _A 3CQW _A 3O96 _A AKT2 1MRV _A 1O6K _A 1O6L _A 1P6S _A AKT3 2X18 _A APAF1 1CY5 _A... 1Z6T _A 2YGS _A 3IZA _A 3YGS _C BCL-2 2W3L _A 2XA0 _A BCL-XL 2B48 _A 3FDL _A BID 2BID _A 2KBW _B Bax 1F16 _A 2G5B _I 2XA0 _C 3PK1 _B CASP3 1RHQ _A 1RHQ _B 2DKO _A 2DKO _B 2J32 _A CASP6 2WDP _A CASP7 1F1J _A 1I4O _A 1I51 _A 1I51 _B 2QL9 _A 2QL9 _B CASP8 1QTN _A 1QTN _B 2FUN _B 3H11 _B CASP9 1JXQ _A 1NW9 _B 3D9T _C 3YGS _P Calpain1 1ZCM _A Calpain2 1KFU _L 2NQA _A Cn(CHP) 2E30 _A Cn(CHP2) 2BEC _A Cn(PPP3CA) 1AUI _A 1MF8 _A 2R28 _C 3LL8 _A Cn(PPP3R1) 1AUI _B 1MF8 _B 3LL8 _B CytC 1J3S _A DFF40 1IBX _A DFF45 1IBX _B 1IYR _A FADD 1A1W _A 2GF5 _A 3EZQ _B FLIP 3H11 _A Fas 3EWT _E 3EZQ _A IAP(BIRC2) 3D9T _A 3M1D _A 3MUP _A IAP(BIRC3) 2UVL _A 3EB5 _A 3EB6 _A 3M0A _D 3M0D _D IAP(BIRC4) 1G73 _C 1I4O _C 1I51 _E 1NW9 _A 2ECG _A 2KNA _A 2POI _A 3CM7 _C IκBα 1IKN _D 1NFI _E IKK 2JVX _A 3BRT _B 3BRV _B 3CL3 _D 3FX0 _A IL-1(A) 2ILA _A IL-1(B) 1ITB _A 2NVH _A 3O4O _A IL-1R(1) 1ITB _B IL-1R(RAP) 3O4O _B IL-3 1JLI _A IL-3R 1EGJ _A IRAK2 3MOP _K IRAK4 2NRU _A 3MOP _G MyD88 2JS7 _A 3MOP _A NF-κB(NFKB1) 1IKN _C 1NFI _B 1SVC _P 2DBF _A NF-κB(RELA) 1IKN _A 1NFI _A NGF 1WWW _V 2IFG _E PI3K(PIK3CA) 2ENQ _A 2V1Y _A 3HHM _A PI3K(PIK3CG) 1E8Y _A PI3K(PIK3R1) 1A0N _A 1H9O _A 1PBW _A 2IUG _A 2V1Y _B 3HHM _B 3I5R _A PI3K(PIK3R2) 2KT1 _A 2XS6 _A 3MTT _A PRKACA 3AGM _A PRKAR2A 2IZX _A TNFα 1A8M _A 4TSV _A TNF-R1 1EXT _A 1ICH _A TP53 1AIE _A 1OLG _A 1XQH _B 1YC5 _B 2B3G _B 2FOO _B 2GS0 _B 2K8F _B 2VUK _A 3D06 _A 3DAB _B 3LW1 _P TRADD 1F3V _A TRAF2 1CZZ _A 1D00 _A 1F3V _B 3KNV _A 3M0A _A 3M0D _A TRAIL 1D4V _B 1DG6 _A 1DU3 _D TRAIL-R 1D4V _A 1DU3 _A TrkA 1HE7 _A 1SHC _B 1WWW _X 2IFG _A The abbreviations used are: AIF, apoptosis-inducing factor, mitochondrion-associated, 1 (AIFM1); AKT1, RAC-alpha serine/threonine-protein kinase; AKT2, RAC-beta serine/threonine-protein kinase; AKT3, RAC-gamma serine/threonine-protein kinase; APAF1, apoptotic peptidase activating factor 1; BCL-2, B-cell lymphoma 2; BCL-XL, BCL extra-large; BID, BH3 interacting domain death agonist; Bax, BCL-2-associated × protein; CASP3/6/7/8/9, caspase-3/6/7/8/9; Cn(CHP), calcineurin B homologous protein 1; Cn(CHP2), calcineurin B homologous protein 2; Cn(PPP3CA), protein phosphatase 3 catalytic subunit alpha isoform; Cn(PPP3R1), protein phosphatase 3 regulatory subunit 1; CytC, cytochrome C; DFF40, DNA fragmentation factor, 40kDa, beta polypeptide; DFF45, DNA fragmentation factor, 45kDa, alpha polypeptide; FADD, Fas-associated via death domain; FLIP, FLICE/CASP8 inhibitory protein (CASP8 and FADD-like apoptosis regulator, CFLAR); Fas, tumor necrosis factor receptor (TNF) superfamily member 6; IAP, inhibitor of apoptosis; BIRC2/3/4, baculoviral IAP repeat-containing protein 2/3/4; IκBα, nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor alpha; IKK, inhibitor of nuclear factor kappa-B kinase; IL-1(A), interleukin-1 alpha; IL-1(B), interleukin-1 beta; IL-1R(1), type 1 interleukin-1 receptor; IL-1R(RAP), interleukin-1 receptor accessory protein; IL-3, interleukin-3; IL-3R, interleukin-3 receptor; IRAK2/4, interleukin-1 receptor-associated kinase 2/4; MyD88, myeloid differentiation primary response protein MyD88; NF-κB(NFKB1), nuclear factor of kappa light polypeptide gene enhancer in B-cells; NF-κB(RELA), nuclear factor of kappa light polypeptide gene enhancer in B-cells 3; NGF, nerve growth factor (beta polypeptide); PI3K, phosphatidylinositide 3-kinase; PIK3CA, PI3K subunit alpha; PIK3CG, PI3K subunit gamma; PIK3R1, PI3K regulatory subunit alpha; PIK3R2, PI3K regulatory subunit beta; PRKACA, cyclic adenosine monophosphate (cAMP)-dependent protein kinase catalytic subunit alpha; PRKAR2A, cAMP-dependent protein kinase type II-alpha regulatory subunit; TNFα, tumor necrosis factor; TNF-R1, TNF receptor superfamily member 1A; TP53, cellular tumor antigen p53; TRADD, TNF receptor type 1-associated death domain protein; TRAF2, TNF receptor-associated factor 2; TRAIL, TNF receptor superfamily member 10; TRAIL-R, TNF receptor superfamily member 10B; TrkA, neurotrophic tyrosine kinase receptor type 1.

Publication Year: 2013