Citations in PubMed

Primary Citation PubMed: 3057628 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 6

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.

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Molecular tuning of an EF-hand-like calcium binding loop. Contributions of the coordinating side chain at loop position 3.

(1997) J Gen Physiol 110

PubMed: 9236210 | PubMedCentral: PMC2233790 | DOI: null

The relevant PDB identification codes are GBP = 2gbp, sarcoplasmic Ca 2+ binding protein = 2scp, parvalbumin = 4cpv.

Publication Year: 1997


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

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 r... dicicol [ 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.

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 1.21 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.

Publication Year: 2009


A method to enhance the hit ratio by a combination of structure-based drug screening and ligand-based screening.

(2008) Adv Appl Bioinform Chem 1

PubMed: 21918604 | PubMedCentral: PMC3169939 | DOI: null

Appendix B The protein databank (PDB) identifier list of the basic protein set is: 1a28, 1a42, 1a4g, 1a4q, 1abe1, 1abe2, 1abf1, 1abf2, 1aco, 1ai5, 1aoe, 1apt, 1apu, 1aqw, 1atl, 1b58, 1b9v, 1bma, 1byb,... 1byg, 1c1e, 1c5c, 1c83, 1cbs, 1cbx, 1cdg, 1ckp, 1com, 1coy, 1cps, 1cvu, 1d0l, 1d3h, 1dd7, 1dg5, 1dhf, 1dog, 1dr1, 1ebg, 1eed, 1ejn, 1epb, 1epo, 1ets, 1f0r, 1f0s, 1f3d, 1fen, 1fkg, 1fki, 1fl3, 1glp, 1hdc, 1hfc, 1hos, 1hpv, 1hsb, 1hsl, 1htf1, 1htf2, 1hyt, 1ida, 1ivb, 1jap, 1lah, 1lcp, 1lic, 1lna, 1lst, 1mdr, 1mld, 1mmq, 1mrg, 1mts, 1mup, 1nco, 1ngp, 1nis, 1okl, 1pbd, 1phd, 1phg, 1poc, 1ppc, 1pph, 1pso, 1qbr, 1qbu, 1qpq, 1rds, 1rne, 1rnt, 1rob, 1snc, 1srj, 1tlp, 1tmn, 1tng, 1tnh, 1tni, 1tnl, 1tyl, 1xid, 1xie, 1yee, 2aad, 2ack, 2ada, 2cht, 2cmd, 2cpp, 2ctc, 2fox, 2gbp, 2ifb, 2pk4, 2qwk, 2tmn, 3cla, 3cpa, 3erd, 3ert, 3tpi, 4lbd, 4phv, 5abp1, 5abp2, 5cpp, 5er1, 6rnt, and 7tim.

Publication Year: 2008


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


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4215909

(A) Native GBP with glucose in the ligand-binding pocket and Ca 2+ present in the Ca 2+ -binding pocket (PDB ID: 2GBP).

Publication Year: 2014