Citations in PubMed

PubMed ID is not available.

PDB ID Mentions in PubMed Central Article count: 9

Citations in PubMed

This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.

PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

  • 3 per page
  • 5 per page
  • 10 per page
  • view all
  • Publication Year
  • Ascending
  • Descending

LIGSITEcsc: predicting ligand binding sites using the Connolly surface and degree of conservation.

(2006) BMC Struct Biol 6

PubMed: 16995956 | PubMedCentral: PMC1601958 | DOI: 10.1186/1472-6807-6-19

Complex Unbound RMSD (Å) 1 Protein Description Ligand Description 2 1bid 3tms 0.24 Thymidylate synthase CBX, UMP 1cdo 8adh 1.17 Alcohol dehydrogenase NAD 1dwd 1hxf 0.44 Alpha thrombin + hirudi... MID 1fbp 2fbp 0.89 Phosphohydrolase AMP, F6P 1gca 1gcg 0.32 Galactose-binding protein GAL 1hew 1hel 0.21 Acetylchitotriose NAG 1hyt 1npc 0.87 Thermolysin DMS, BZS 1inc 1esa 0.21 Elastase ICL 1rbp 1brq 0.54 Retinol binding protein RTL 1rob 8rat 0.28 Ribonuclease A C2P 1stp 1swb 0.33 Streptavidin BTN 1ulb 1ula 0.61 Purine nucleoside phosphorylase GUN 2ifb 1ifb 0.37 Fatty acid binding protein PLM 3ptb 3ptn 0.26 Beta trypsin BEN 2ypi 1ypi 0.57 Triose phosphate isomerase PGA 4dfr 5dfr 0.80 Dihydrofolate reductase MTX 4phv 3phv 1.28 HIV 1 protease VAC 5cna 2ctv 0.44 Concanavalin A MMA 7cpa 8adh 2.17 Carboxypeptidase FVF 1a6w 1a6u 0.35 B1-8 FV fragment NIP 1apu 3app 0.36 Penicillopepsin MAN, OET, IVA, STA 1acj 1qif 0.34 Acetylcholinesterase THA 1blh 1djb 0.23 Methyl]phosphonate FOS 1byb 1bya 0.26 Beta amylase GLC 1hfc 1cge 0.37 Fibroblast collagenase HAP 1ida 1hsi 1.41 HIV 2 protease QND, HPB, PY2, PPL 1ivd 1nna 1.00 Sialidase FUC, ST1, NAG, MAN 1mrg 1ahc 0.30 Alpha momorcharin AND 1mtw 2tga 0.31 Trypsin DX9 1okm 4ca2 0.34 carbonic anhydrase II SAB 1pdz 1pdy 0.54 Enolase PGA 1phd 1phc 0.17 Camphor 5-monoxygenase HEM, PIM 1pso 1psn 0.33 Pepsin 3a IVA, STA 1qpe 3lck 0.25 Lck kinase PP2, PTR 1rne 1bbs 0.60 Renin NAG, C60 1snc 1stn 0.52 Staphylococcal nuclease PTP 1srf 1pts 0.45 Streptavidin MTB 1stp 2rta 0.62 Streptavidin BTN 2ctc 2ctb 0.15 Carboxypeptidase LOF 2h4n 2cba 0.33 Carbonic anhydrase II AZM 2pk4 1krn 0.63 Plasminogen kringle ACA 2sim 2sil 0.25 Sialidase (neuraminidase) DAN 2tmn 1l3f 0.62 Thermolysin PHO, NH2 3gch 1chg 0.91 Gamma chymotrypsin CIN 3mth 6ins 1.00 Methylparaben insulin MPB 5p2p 3p2p 0.62 Phosphilipase DHG 1imb 1ime 1.45 Inositol monophosphatase LIP 6rsa 7rat 2.08 Ribonuclease UVC 1 RMSD: Root mean square deviation of C α atoms after superimposing unbound structures on bound structures.

Complex Unbound LIGSITE csc 1 LIGSITE 2 PASS 3 SURFNET 4 CAST PDB Hits 5 D Near 6 Hits D Near Hits D Near Hits 7 D Near Hits D Near 1bid 3tms 1 3.4 1 2.0 1 3.9 1 3.9 1 3.1 1cdo 8adh 1 0.8 1 0.6 1 0.2 1 1.3 1 0.8 1dwd 1hxf 1 1.7 1 2.3 1 0.7 1 2.3 1 0.9 1fbp 2fbp 1 0.5 1 0.6 (2) 0.8 - - 1 1.5 1gca 1gcg 1 0.8 1 0.8 1 0.5 1 3.4 1 0.5 1hew 1hel 1 1.8 1 1.8 1 1.0 1 2.6 1 1.6 1hyt 1npc 1 1.2 1 1.1 1 1.7 1 1.0 1 0.7 1inc 1esa 1 2.9 3 0.8 - - 1 1.9 (10) 2.1 1rbp 1brq 1 0.9 1 0.9 1 0.9 (2) 1.6 1 1.0 1rob 8rat 1 0.9 2 1.0 1 0.3 1 1.7 1 1.6 1stp 1swb 1 0.6 1 0.3 1 0.8 1 2.4 1 1.4 1ulb 1ula - - (20) 3.2 - - 1 3.6 1 3.3 2ifb 1ifb 1 2.2 1 2.2 1 2.5 1 2.3 1 2.1 3ptb 3ptn 1/2 1.1 2 1.0 (2) 0.5 (2) 1.7 1 0.9 2ypi 1ypi - 3.0 2 3.0 (3) 2.2 - - (2) 2.7 4dfr 5dfr 1 1.9 1 3.5 1 2.3 - - 1 4.5 4phv 3phv 1 2.7 1 2.6 - - 1 2.9 1 2.6 5cna 2ctv 1/11 1.0 (13) 1.0 (2) 0.8 (6) 1.1 (6) 1.0 7cpa 5cpa 1 1.0 1 1.1 1 1.3 1 1.6 (3) 1.0 1a6w 1a6u 1/3 0.5 (4) 1.4 - - - - 1 1.4 1acj 1qif - 3.5 - 3.6 1 1.9 - - (40) 3.9 1apu 3app - 1.2 - 1.9 - - 1 3.7 -(2) -(4.1) 1blh 1djb 1 0.7 2 1.2 1 2.4 (2) 3.9 (5) 0.8 1byb 1bya 1 2.5 1 2.8 (4) 1.1 -1 -(4.2) 1 2.4 1hfc 1cge 1 0.7 1 0.9 (3) 0.8 (3) 1.2 1 0.5 1ida 1hsi 1 3.4 1 2.9 (3) 1.0 1 1.0 1 1.6 1igj 1a4j /4 0.8 -(19) 2.9 - - - - - - 1imb 1ime 1 1.7 1 1.0 1 1.7 1 4.0 1 1.3 1ivd 1nna 1 1.4 1 1.1 1 3.5 (2) 0.9 1 1.9 1mrg 1ahc 1 1.9 1 1.9 - - 1 3.3 1 0.8 1mtw 2tga 1/5 2.8 -(7) 1.2 - - (7) 3.2 (8) 1.6 1okm 4ca2 1 2.2 1 1.6 - - (3) 2.2 1 2.1 1pdz 1pdy 1 2.6 1 3.1 1 1.7 - - (5) 1.0 1phd 1phc 1 0.7 1 1.2 1 1.8 (2) 1.4 1 1.3 1pso 1psn 1 0.8 1 1.6 1 1.6 -1 -(4.3) 1 2.1 1qpe 3lck 2 1.5 2 1.2 1 0.7 - - - - 1rne 1bbs 1 1.0 1 1.2 1 1.4 1 2.2 1 1.0 1snc 1stn 1 1.5 1 1.5 1 1.3 1 1.9 1 1.3 1srf 1pts 1 1.5 1 0.5 1 1.2 (5) 0.8 1 1.1 2ctc 2ctb 1 0.6 1 1.1 (2) 0.8 1 2.2 1 1.2 2h4n 2cba 1/2 1.0 2 1.0 - - (3) 1.2 (2) 1.2 2pk4 1krn 1/2 0.7 2 0.8 - - (2) 2.2 1 1.9 2sim 2sil 1/2 0.7 2 0.6 - - (2) 2.3 (2) 0.8 2tmn 1l3f - 2.1 - - - - 1 0.7 1 3.9 3gch 1chg 10 2.2 -(10) 2.2 1 0.9 (11) 1.5 (2) 2.5 3mth 6ins 9 3.8 -(9) 1.8 - - -(3) -(4.7) - - 5p2p 3p2p 1 1.3 1 1.6 1 1.8 (2) 1.6 (2) 1.5 6rsa 7rat 1/4 0.9 -(5) 1.1 1 1.1 1 0.6 1 0.9 1 Grid resolution: 1.0 Å; probe radius: 1.6 Å.

Publication Year: 2006


PocketPicker: analysis of ligand binding-sites with shape descriptors.

(2007) Chem Cent J 1

PubMed: 17880740 | PubMedCentral: PMC1994066 | DOI: 10.1186/1752-153X-1-7

Complex Unbound Protein Description Pocket Ligand 1 Other Ligands 2 1bid 3tms Thymidylate synthase UMP CBX 1cdo 8adh Alcohol dehydrogenase NAD zn 1dwd 1hxf Alpha thrombin MID chains i, l 1fbp 2fbp Fru... tose 1,6-bisphosphatase AMP F6P, mg 1gca 1gcg Glucose/galactose-binding protein GAL ca 1hew 1hel Hen egg white lysozyme NAG - 1hyt 1npc Thermolysin BZS DMS, ca, zn 1inc 1esa Elastase ICL ca, so4 1rbp 1brq Retinol binding protein RTL - 1rob 8rat Ribonuclease A C2P - 1stp 1swb Streptavidin BTN - 1ulb 1ula Purine nucleoside phosphorylase GUN so4 2ifb 1ifb Fatty acid binding protein PLM - 3ptb 3ptn Beta trypsin BEN ca 2ypi 1ypi Triose phosphate isomerase PGA - 4dfr 5dfr Dihydrofolate reductase MTX ca, cl 4phv 3phv HIV 1 protease VAC - 5cna 2ctv Concanavalin A MMA ca, cl, mn 7cpa 5cpa Carboxypeptidase A FVF zn 1a6w 1a6u B1-8 FV fragment NIP - 1acj 1qif Acetylcholinesterase THA - 1apu 3app Penicillopepsin [IVA-VAL-VAL-STA-OET] MAN 1blh 1djb Beta-lactamase FOS - 1byb 1bya Beta amylase GLC so4 1hfc 1cge Fibroblast collagenase HAP ca, zn 1ida 1hsi HIV 2 protease [QND-VAL-HPB-PPL-PY2] - 1igj 1a4j Immunoglobulin DGX chain y 1imb 1ime Inositol monophosphatase LIP gd 1ivd 1nna Hydrolase ST1 FUC, NAG, MAN, ca 1mrg 1ahc Alpha momorcharin ADN - 1mtw 2tga Trypsin DX9 ca 1okm 4ca2 Carbonic anhydrase II SAB hg, zn 1pdz 1pdy Enolase PGA ace, mn 1phd 1phc Camphor 5-monoxygenase PIM HEM 1pso 1psn Pepsin 3a [IVA-VAL-VAL-STA-ALA-STA] - 1qpe 3lck Lck kinase PP2 PTR, so4 1rne 1bbs Renin C60 NAG 1snc 1stn Staphylococcal nuclease PTP ca 1srf 1pts Streptavidin MTB - 2ctc 2ctb Carboxypeptidase A LOF zn 2h4n 2cba Carbonic anhydrase II AZM zn 2pk4 1krn Plasminogen kringle ACA - 2sim 2sil Sialidase DAN - 2tmn 1l3f Thermolysin [PHO-LEU-NH2] ca, zn 3gch 1chg Gamma chymotrypsin CIN - 3mth 6ins Methylparaben insulin MPB cl, zn 5p2p 3p2p Phosphilipase DHG ca 6rsa 7rat Ribonuclease A UVC dod 1 Considered ligand defining the active site.

Complex Hits 1 D near /Å) 2 Unbound Hits 1 D near /Å) 2 1bid 1 2.7 3tms 1 2.3 1cdo 1 2.3 8adh 1 1.9 1dwd 1 0.5 1hxf 1 0.3 1fbp 1 1.3 2fbp 4 1.2 1gca 1 2.4 1gcg 1 1.4 1hew 1 1.4 1hel 1 1.2 1hyt 1 1.3 1npc 1 1.7 1inc 1 0.5 1esa (1) 4.1 1rbp 1 0.8 1brq 1 1.0 1rob 1 1.7 8rat 1 1.9 1stp 1 2.4 1swb 1 1.0 1ulb 1 1.0 1ula (1) 4.4 2ifb 1 1.7 1ifb 1 2.5 3ptb 1 0.4 3ptn 3 1.0 2ypi 5 1.0 1ypi (1) 4.8 4dfr (1) 7.8 5dfr 1 1.8 4phv 2 2.7 3phv 2 3.5 5cna - - 2ctv - - 7cpa 1 1.0 5cpa 1 1.1 1a6w 2 1.4 1a6u 3 1.2 1acj 1 0.8 1qif 2 1.2 1apu 1 0.6 3app 1 0.5 1blh 1 1.0 1djb 1 0.8 1byb 1 3.3 1bya 1 3.6 1hfc 1 1.2 1cge 1 1.0 1ida 1 1.5 1hsi 1 3.2 1igj 4 1.6 1a4j 3 1.4 1imb (1) 5.5 1ime 1 3.4 1ivd 2 1.7 1nna 1 1.5 1mrg (1) 5.8 1ahc (1) 5.2 1mtw 2 0.8 2tga 4 0.6 1okm 2 1.2 4ca2 1 1.6 1pdz 1 2.2 1pdy 1 2.7 1phd 1 1.1 1phc 1 0.9 1pso 1 0.4 1psn 1 1.1 1qpe 1 0.9 3lck 1 1.1 1rne 1 1.7 1bbs 1 0.7 1snc 1 2.1 1stn 1 0.3 1srf 1 0.5 1pts 1 0.6 2ctc 1 1.2 2ctb 1 1.5 2h4n 1 0.8 2cba 1 2.1 2pk4 2 0.7 1krn 1 0.7 2sim 2 0.6 2sil 2 0.4 2tmn 1 1.3 1l3f 1 1.1 3gch 1 0.8 1chg 2 1.5 3mth 2 0.8 6ins 2 1.3 5p2p 1 1.0 3p2p 1 0.8 6rsa 1 3.0 7rat 1 0.9 1 Rank of pocket centers within 4 Å of the considered ligand (brackets indicate hits exceeding the 4 Å criterion).

Publication Year: 2007


DOVIS 2.0: an efficient and easy to use parallel virtual screening tool based on AutoDock 4.0.

(2008) Chem Cent J 2

PubMed: 18778471 | PubMedCentral: PMC2542995 | DOI: 10.1186/1752-153X-2-18

PDB code Receptor-ligand complex All-atom model Polar-hydrogen model RMSD (Å) Score a RMSD (Å) Score a 186L Lysozyme(L99A)/n-butylbenzene 0.59 3.33 0.80 4.03 1ABE Arabinose-binding pro... ein/α-L-arabinose 2.64 4.58 2.33 4.08 1BR6 Ricin A chain/pteroid acid 0.62 5.40 0.75 5.27 1KIM Thymidine kinase/deoxythymidine 1.17 3.87 0.73 4.31 1RBP Retinol-binding protein/retinol 1.98 -18.88 1.54 5.92 1STP Streptavidin/biotin 0.83 5.16 0.81 5.31 3PTB Trypsin/benzamidine 0.48 3.37 0.48 3.54 4DFR Dihydrofolatereductase/methotrexate 5.06 4.59 5.03 4.23 Root mean square deviation (RMSD) values were calculated between the docked ligand poses and the X-ray ligand based on heavy atoms.

Publication Year: 2008


Application of the PM6 semi-empirical method to modeling proteins enhances docking accuracy of AutoDock.

(2009) J Cheminform 1

PubMed: 20150996 | PubMedCentral: PMC2820493 | DOI: 10.1186/1758-2946-1-15

PDB code of the complex RMSD of the first rank result as compared to the X-ray (Å) Energy rank of the lowest RMSD hit Frequency rank/frequency of the best geometry Lowest RMSD (Å) Esti... ated free energy of binding (kcal/mol) Experimental binding energy (kcal/mol) 1AI5 1.21 1 1/48 0.65 -5.11 -5.08 1AJP 2.56 2 1/47 1.09 -4.40 -3.05 1AMW 1.68 1 1/21 1.59 -5.62 -6.19 1BGQ 1.03 1 1/48 0.71 -6.27 -11.69 1CBR 1.00 1 1/51 0.92 -7.94 -10.58 1D3Q 2.68 2 2/19 1.23 -10.33 -8.88 1D3T 2.29 2 2/20 1.08 -10.08 -8.73 1DWB 9.59 3 1/51 0.53 -6.24 -3.98 1FLR 0.60 1 1/100 0.53 -10.76 -10.98 1GNI 1.56 1 1/49 1.10 -7.73 -11.01 1HVJ 3.12 - -10.03 -14.27 1HVR 0.65 1 1/26 0.54 -14.74 -12.97 1K4G 2.82 4 1/30 1.66 -6.98 -7.99 1KV1 0.64 1 1/98 0.56 -8.91 -8.10 1LIF 2.33 4 1/21 1.08 -5.47 -9.65 1M0N 3.91 - -8.22 -3.03 1M0Q 2.24 5 33/1 1.46 -5.99 -5.30 1OLU 1.34 1 4/10 0.74 -6.96 -6.01 1Q8T 1.88 1 1/77 1.41 -8.29 -6.49 1RBP 0.84 1 1/100 0.56 -9.15 -9.17 1S39 4.29 2 2/11 0.32 -5.29 -10.50 1U33 2.49 1 2/14 1.73 -8.14 -6.28 1ULB 1.88 1 1/100 1.83 -4.66 -7.20 1UWT 2.36 1 1/89 0.87 -6.77 -8.14 1X8R 1.24 1 1/80 0.87 -4.17 -8.36 1XD1 2.92 - -11.12 -10.80 1YDT 2.2 2 1/30 0.74 -10.14 -9.98 1ZC9 2.71 - -4.00 -4.39 2ACK 3.96 8 8/1 1.07 -4.72 -8.97 2BAJ 0.68 1 1/74 0.42 -12.40 -11.46 2BAK 1.28 1 16/2 1.28 -13.78 -10.14 2CEQ 7.14 - -4.66 -9.92 2CET 4.86 - -7.06 -10.94 2CGR 0.87 1 1/43 0.50 -10.68 -9.89 2CPP 1.56 1 1/100 1.21 -6.35 -8.28 2D3U 0.87 1 1/58 0.83 -9.43 -9.44 2D3Z 4.68 3 2/20 0.69 -8.89 -9.06 2FDP 2.35 5 73/1 1.68 -13.67 -10.35 2G94 3.13 - -7.57 -12.99 2GBP 0.99 1 1/90 0.92 -4.18 -10.37 2IFB 2.03 2 1/45 1.10 -6.03 -7.41 2IWX 0.88 1 1/68 0.55 -6.66 -9.11 2J77 1.9 1 1/100 1.85 -7.52 -6.67 2J78 0.83 1 2/11 0.83 -6.41 -8.75 2QFU 2.75 3 3/1 1.02 -6.29 -5.70 2QWB 4.38 13 6/5 1.17 -5.40 -3.74 2QWD 1.36 1 1/54 0.97 -6.80 -6.62 2R04 2.06 2 3/21 1.02 -8.97 -8.87 2XIS 1.20 1 1/95 1.15 -5.43 -7.94 2YPI 4.73 - -3.09 -6.57 3PTB 1.35 1 1/100 0.51 -5.66 -6.47 4HMG 1.82 1 1/22 1.02 -4.78 -3.48 7ABP 2.15 2 2/13 1.64 -4.58 -8.78 Average: 2.34 without outliers (rmsd above 4 Å): 1.83 28 first hits 30 first hits Average: 1.00 The average value of the RMSD between the lowest energy result and experimental structure and the total number of successful first rank predictions (based on lowest energy and highest cluster population, respectively) are indicated at the bottom of the table.

1AI5 Penicillin acylase 2.4 m-nitrophenylacetic acid [ 24 ] 1AJP Penicillin acylase 2.3 2,5-dihydroxyphenylacetic acid [ 24 ] 1AMW Heat shock protein 90 1.9 ADP [ 25 ] 1BGQ Heat shock protein 90 2.5 radicicol [ 26 ] 1CBR Retionic acid binding protein 2.9 retinoic acid [ 27 ] 1D3Q Human thrombin 2.9 benzo [ b ]thiophene derivative [ 28 ] 1D3T Human thrombin 3.0 benzo [ b ]thiophene derivative [ 28 ] 1DWB a-Thrombin 3.2 benzamidine [ 29 ] 1FLR Immunoglobulin 1.9 fluorescein [ 30 ] 1GNI Human serum albumin 2.4 oleic acid [ 31 ] 1HVJ HIV-1 Protease 2.0 A78791 [ 32 ] 1HVR HIV-1 Protease 1.8 XK263 [ 33 ] 1K4G tRNA-guanine transglycosylase 1.7 quinazoline derivative [ 34 ] 1KV1 p38 MAP kinase 2.5 pyrazol derivative [ 35 ] 1LIF Adipocyte lipid-binding protein 1.6 stearic acid [ 36 ] 1M0N Dialkylglycine decarboxylase 2.2 1-aminocyclo-pentanephosphonate [ 37 ] 1M0Q Dialkylglycine decarboxylase 2.0 S-1-amino-ethanephosphonate [ 37 ] 1OLU Branched-chain alpha-ketoacid dehydrogenase kinase 1.9 thiamin diphosphate [ 38 ] 1Q8T cAMP-dependent protein kinase 2.0 (R)-trans-4-(1-aminoethyl)-n-(4-pyridyl) cyclohexanecarboxamide [ 39 ] 1RBP Retinol-binding protein 2.0 retinol [ 40 ] 1S39 tRNA-guanine transglycosylase 2.0 2-aminoquinazolin-4(3H)-one [ 41 ] 1U33 Alpha-amylase 2.0 5-trihydroxy-6-hydroxymethyl-piperidin-2-one [ 42 ] 1ULB Purine nucleoside phosphorylase 2.8 guanine [ 43 ] 1UWT Beta-glycosidase 2.0 D-galactohydroximo-1,5-lactam [ 44 ] 1X8R 3-Phosphoshikimate 1-carboxyvinyltransferase 1.5 phosphonate analogue [ 45 ] 1XD1 Alpha-amylase 2.2 acarbose derived hexasaccharide [ 46 ] 1YDT cAMP-dependent protein kinase 2.3 n-[2-(4-bromocinnamylamino)ethyl]-5-isoquinoline [ 47 ] 1ZC9 Dialkylglycine decarboxylase 2.0 pyridoxamine 5-phosphate [ 48 ] 2ACK Acetylcholinesterase 2.4 edrophonium ion [ 49 ] 2BAJ p38alpha Map kinase 2.3 pyrazol derivative [ 50 ] 2BAK p38alpha Map kinase 2.2 nicotinamid derivative [ 50 ] 2CEQ Beta-glycosidase 2.1 glucoimidazole [ 51 ] 2CET Beta-glycosidase 2.0 phenethyl-substituted glucoimidazole [ 51 ] 2CGR Immunoglobulin 2.2 N-trisubstituted guanidine [ 52 ] 2CPP Cytochrome P-450cam 1.6 camphor [ 53 ] 2D3U RNA-dependent RNA polymerase 2.0 non-nucleoside analogue inhibitor I [ 54 ] 2D3Z RNA-dependent RNA polymerase 1.8 non-nucleoside analogue inhibitor II [ 54 ] 2FDP Beta-secretase 2.5 amino-ethylene inhibitor [ 55 ] 2G94 Beta-secretase 1.9 valinamide derivative [ 56 ] 2GBP D-galactose/D-glucose binding protein 1.9 glucose [ 57 ] 2IFB Fatty-acid-binding protein 2.0 palmitic acid [ 58 ] 2IWX Heat shock protein 82 1.5 synthetic macrolactone [ 59 ] 2J77 Beta-glycosidase 2.1 deoxynojirimycin [Gloster, to be published] 2J78 Beta-glycosidase 1.7 gluco-hydroximolactam [Gloster, to be published] 2QFU 3-Phosphoshikimate 1-carboxyvinyltransferase 1.6 shikimate-3-phosphate [ 60 ] 2QWB Neuraminidase 2.0 sialic acid [ 61 ] 2QWD Neuraminidase 2.0 4-amino-Neu5Ac2en [ 61 ] 2R04 Rhinovirus 14 coat protein 3.0 W71, antiviral agent [ 62 ] 2XIS Xylose isomerase 1.6 D-xylitol [ 63 ] 2YPI Triose phosphate isomerase 2.5 2-phosphoglycolic acid [ 64 ] 3PTB b-Trypsin 1.8 benzamidine [ 65 ] 4HMG Hemagglutinin 3.0 sialic acid [ 66 ] 7ABP Arabinose-binding protein 1.7 fucose [ 67 ] Estimation of binding energies Figure 1 shows the correlation between experimentally determined and predicted binding energies as calculated by AutoDock 4.

PDB code of the complex RMSD of the first rank result as compared to the X-ray (Å) Energy rank of the lowest RMSD hit Frequency rank/frequency of the best geometry Lowest RMSD (Å) Estimated free energy of binding (kcal/mol) Experimental binding energy (kcal/mol) 1AI5 1.22 1 1/100 0.65 -5.06 -5.08 1AJP 2.73 2 1/97 1.07 -4.82 -3.05 1AMW 2.13 1 1/35 0.87 -5.67 -6.19 1BGQ 1.03 1 1/100 0.70 -6.50 -11.69 1CBR 1.01 1 1/93 0.77 -7.42 -10.58 1D3Q 2.77 2 2/40 0.85 -11.47 -8.88 1D3T 2.09 3 1/60 0.99 -10.37 -8.73 1DWB 0.72 1 1/100 0.54 -4.87 -3.98 1FLR 0.39 1 1/100 0.39 -8.54 -10.98 1GNI 3.01 2 1/69 1.01 -6.80 -11.01 1HVJ 1.61 1 1/5 1.61 -10.45 -14.27 1HVR 1.21 1 1/96 1.00 -11.67 -12.97 1K4G 2.83 4 1/89 1.42 -7.78 -7.99 1KV1 0.6 1 1/100 0.58 -9.33 -8.10 1LIF 3.1 4 3/17 0.93 -4.51 -9.65 1M0N 1.18 1 1/86 1.02 -7.65 -3.03 1M0Q 1.03 1 1/80 0.95 -7.15 -5.30 1OLU 0.89 1 1/89 0.61 -9.14 -6.01 1Q8T 1.9 1 1/100 1.41 -7.58 -6.49 1RBP 0.85 1 1/100 0.56 -8.46 -9.17 1S39 4.29 2 1/95 0.33 -4.65 -10.50 1U33 0.86 1 1/43 0.80 -9.82 -6.28 1ULB 0.7 1 1/100 0.64 -5.09 -7.20 1UWT 2.35 1 1/53 0.71 -6.47 -8.14 1X8R 1.26 1 1/100 0.96 -3.10 -8.36 1XD1 1.81 1 2/10 1.30 -15.97 -10.80 1YDT 0.79 1 1/93 0.45 -8.05 -9.98 1ZC9 2.7 14 2/26 0.96 -6.76 -4.39 2ACK 3.98 4 2/22 0.94 -5.25 -8.97 2BAJ 0.66 1 1/100 0.55 -12.50 -11.46 2BAK 1.21 1 1/98 0.64 -14.20 -10.14 2CEQ 0.85 1 1/44 0.83 -6.23 -9.92 2CET 2.61 1 2/15 0.96 -7.76 -10.94 2CGR 0.9 1 1/100 0.68 -10.05 -9.89 2CPP 1.21 1 1/100 1.21 -6.26 -8.28 2D3U 0.68 1 1/100 0.54 -7.11 -9.44 2D3Z 3.86 3 1/88 0.63 -7.60 -9.06 2FDP 0.75 1 1/89 0.68 -14.80 -10.35 2G94 1.75 1 3/5 1.45 -8.64 -12.99 2GBP 0.89 1 1/100 0.87 -5.60 -10.37 2IFB 2.05 2 1/55 1.03 -4.99 -7.41 2IWX 0.87 1 1/100 0.55 -6.76 -9.11 2J77 2.01 1 1/93 1.60 -7.62 -6.67 2J78 0.83 1 2/27 0.73 -6.13 -8.75 2QFU 2.74 4 2/37 0.94 -6.29 -5.70 2QWB 4.35 12 2/15 0.90 -6.64 -3.74 2QWD 2.57 2 1/67 0.91 -7.37 -6.62 2R04 1.99 2 2/8 0.92 -8.84 -8.87 2XIS 1.17 1 1/100 1.14 -6.93 -7.94 2YPI 1.19 1 1/61 0.78 -2.62 -6.57 3PTB 1.31 1 1/100 0.74 -5.06 -6.47 4HMG 1.04 1 1/98 0.85 -6.92 -3.48 7ABP 2.09 1 1/97 1.16 -5.58 -8.78 Average: 1.71 without outliers (rmsd above 4 Å): 1.61 38 first hits 42 first hits Average: 0.87 QASP parameter was modified from 0.01097 to 0.00679 in AutoGrid and AutoDock.

Publication Year: 2009


Sanjeevini: a freely accessible web-server for target directed lead molecule discovery.

(2012) BMC Bioinformatics 13 Suppl 17

PubMed: 23282245 | PubMedCentral: PMC3521208 | DOI: 10.1186/1471-2105-13-S17-S7

PDBID a Ligand (Molecular formula) EXBFE (kcal/mol)# PBFE (kcal/mol) b PBFE (kcal/mol) c 1 1BRA C 7 H 8 N 2 -2.496 -4.92 -4.59 2 1F0T C 19 H 19 N 5 O 4 S 2 -8.29 -6.92 -7.35 3 1F0U C 27 H 30 N 4 O 3 -... .89 -8.98 -6.96 4 1MTW C 26 H 28 N 4 O 3 -10.076 -7.84 -6.64 5 1PPC C 27 H 31 N 5 O 4 S -8.8 -8.46 -6.85 6 1TNH C 7 H 9 FN -4.59 -4.49 -4.28 7 1TNI C 10 H 15 N -2.32 -3.74 -3.53 8 1TNJ C 8 H 12 N -2.67 -3.72 -3.77 9 1TNK C 9 H 14 N -2.03 -3.81 -3.51 10 1TNL C 9 H 12 N -2.56 -3.56 -3.99 11 1TPP C 10 H 12 N 2 O 3 -7.95 -6.05 -5.55 12 3PTB C 7 H 8 N 2 -6.46 -5.36 -5.27 13 1S0R / 1S0Q C 8 H 10 N 3 O 1 -5.71 -5.25 -5.59 14 1S0R / 1S0Q C8H11N2O1 -6.04 -5.37 -5.51 15 1S0R / 1S0Q C7H10N3 -6.95 -5.16 -5.99 16 1S0R / 1S0Q C7H9N2 -6.35 -5.26 -5.12 17 1S0R / 1S0Q C8H11N2 -6.59 -5.33 -5.56 18 1S0R / 1S0Q C9H13N2 -6.07 -5.01 -5.41 19 1S0R / 1S0Q C10H15N2 -6.14 -5 -5.55 20 1S0R / 1S0Q C 10 H 15 N 2 (iso) -5.42 -5.26 -5.79 21 1S0R / 1S0Q C 11 H 17 N 2 -6.26 -5 -6.08 22 1S0R / 1S0Q C 12 H 19 N 2 -6.5 -5.45 -6.55 23 1S0R / 1S0Q C 13 H 21 N 2 -6.97 -5.82 -6.53 # Experimental binding free energies of trypsin binding molecules.

Publication Year: 2012


A rule-based algorithm for automatic bond type perception.

(2012) J Cheminform 4

PubMed: 23113939 | PubMedCentral: PMC3557220 | DOI: 10.1186/1758-2946-4-26

The first data set collected by Ricketts et al. [ 15 ] has 17 ligands extracted from the PDB files (PDB entries are 1cla, 1fcb, 1fx1, 1gox, 2aat, 2dhf, 2gbp, 2trm, 3cpp, 3ptb, 4dfr, 4xia, 5xia, 7dfr, ... atc, and 8rsa), and it has been extensively used for testing the algorithms of bond assignment.

Publication Year: 2012


Statistical estimation of the protein-ligand binding free energy based on direct protein-ligand interaction obtained by molecular dynamics simulation.

(2012) Pharmaceuticals (Basel) 5

PubMed: 24281257 | PubMedCentral: PMC3816655 | DOI: 10.3390/ph5101064

PDB ID Protein 1abe L-ARABINOSE-BINDING PROTEIN 1abf L-ARABINOSE-BINDING PROTEIN 1apu ACID PROTEINASE (PENICILLOPEPSIN) 1dbb FAB' FRAGMENT 1dbj FAB' FRAGMENT 1dog GLUCOAMYLASE 1dwb THROMBIN 1epo ENDOT... IA ASPARTIC PROTEINASE 1etr THROMBIN 1ets THROMBIN 1ett THROMBIN 1hpv HIV-1 PROTEASE 1hsl HISTIDINE-BINDING PROTEIN 1htf HIV-1 PROTEASE 1hvr HIV-1 PROTEASE 1nsd NEURAMINIDASE 1pgp 6-PHOSPHOGLUCONATE DEHYDROGENASE 1phg CYTOCHROME P450 1ppc TRYPSIN 1pph TRYPSIN 1rbp RETINOL-BINDING PROTEIN 1tng TRYPSIN 1tnh TRYPSIN 1ulb PURINE NUCLEOSIDE PHOSPHORYLASE 2cgr IGG2B (KAPPA) FAB FRAGMENT 2gbp D-GALACTOSE/D-GLUCOSE-BINDING PROTEIN 2ifb INTESTINAL FATTY ACID BINDING 2phh P-HYDROXYBENZOATE HYDROXYLASE 2r04 RHINOVIRUS 14 (HRV14) 2tsc THYMIDYLATE SYNTHASE 2ypi TRIOSE PHOSPHATE ISOMERASE 3ptb TRYPSIN 4dfr DIHYDROFOLATE REDUCTASE 5abp L-ARABINOSE-BINDING PROTEIN The structural ensembles generated from the PDB structure given by MD in explicit water were prepared as follows.

Publication Year: 2012


Integration of ligand-based drug screening with structure-based drug screening by combining maximum volume overlapping score with ligand docking.

(2012) Pharmaceuticals (Basel) 5

PubMed: 24281339 | PubMedCentral: PMC3816669 | DOI: 10.3390/ph5121332

Thrombin (PDB IDs: 1dwb, 1etr, 1ets and 1ett) and trypsin (PDB IDs: 1ppc, 1pph, 1tng, 1tnh and 3ptb) were selected as targets.

Publication Year: 2012


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4506540

The magenta Trypsin conformation corresponds to its wild-type structure in PDB 3PTB.

The classification is found in Fig. 1a : S1 pocket opening and closing ( Fig. 1b and bullets with ‘1' in Fig. 1a ): S1 is the Benzamidine-binding pocket found in PDB 3PTB that allows access and hydrogen bonding of Benzamidine to the recognition site Asp189.

The different X-ray structures have been compared with the metastable states by aligning them to PDB 3PTB on the basis of the backbone atoms of the conserved three loops forming the S1 pocket: residues 188–196, 214–220 and 226–230.

Figure 2 shows the binding site of these aligned structures together with structures of each metastable state (colours like in Fig. 1 ) that were aligned to PDB 3PTB in the same way.

The Trp215 loop is found in various conformations: in PDB 3PTB (Trypsin wild type) and the magenta Trypsin conformation it is parallel to the Asp189 loop with Trp215 placed outside the S1 pocket.

The set-up was based on the X-ray structure of a Trypsin–Benzamidine complex (PDB 3PTB).

As the crystal structure 3PTB contains Benzamidine, all of the Trypsin apo conformations deviate from the crystal structure.

However, the magenta structure is very similar to 3PTB and only differs by the open conformation of a peripheral loop (top right) that is likely affected by crystal contacts in the periodic cell.

This binding mode is most similar to the crystal structure 3PTB and has the highest conditional binding affinity, although it is not the overall most stable bound state.

Three representative structures for each conformation are shown, superimposed on the crystal structure 3PTB (in black) for comparison.

The simulation contained one calcium ion as found in crystal structure 3PTB coordinated by residues Glu70, Glu77 and Glu80.

Publication Year: 2015