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PDB ID Mentions in PubMed Central

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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 1.22 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.

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.

Publication Year: 2009


Binding-site assessment by virtual fragment screening.

(2010) PLoS One 5

PubMed: 20404926 | PubMedCentral: PMC2852417 | DOI: 10.1371/journal.pone.0010109

Figure S5 Chemical structures of a ligand co-crystallized with P38 MAPK (1kv2), binders identified in experimental screening, and high-ranking fragment hits identified from virtual fragment screening ... sing two different crystal structures, 1kv2 and 1kv1 (fragments bound to ATP site colored in green, lipophilic pocket colored in cyan, and allosteric site in magenta).

We focus on the crystal structure (1kv2) bound with most potent MAPK inhibitor, BIRB796 ( Figure 5A ), and the crystal structure (1kv1) bound with a micomolar diaryl urea type of inhibitor ( Figure 5B ).

Drug Target PDB ID RMSD ave (Å) RMSD max (Å) Log (Hit Rate) Drug Target PDB ID RMSD ave (Å) RMSD max (Å) Log (Hit Rate) ACE 1uze 0.60 HIVRT 1vrt 1.66 1o86 0.17 0.37 0.45 1rt1 1.51 2.45 1.75 1uzf 0.35 0.79 0.69 1c1c a 1.88 3.12 1.61 Alr2 1ah0 1.42 1rth a 1.62 2.28 1.61 1ah3 a 1.06 3.19 1.27 HMGR 1hw8 1.39 2acr a , b 0.88 1.72 1.10 1hwk 0.61 1.49 1.31 CDK2 1aq1 a 1.32 NA 1a4g 0.57 1buh a , b 1.77 3.20 1.44 1a4q a 0.48 2.11 0.52 1dm2 a 1.75 4.49 1.62 1nsc a 0.34 1.49 0.52 COX-2 1cvu 1.51 P38 MAPK 1a9u 1.00 1cx2 a 1.24 3.78 1.53 1kv1 3.84 10.41 1.16 3pgh a 1.11 3.96 1.64 1kv2 3.54 11.26 1.61 DHFR 3dfr 1.01 PDE5 1xoz 1.18 6dfr b 1.47 1.96 1.02 1xp0 0.79 2.23 1.24 ER 1l2i 1.69 PPARg 1fm6 1.46 3ert a 2.61 4.47 1.55 1fm9 a 1.47 4.64 1.62 1err a 2.01 4.39 1.61 2prg a 0.71 1.27 1.43 Fxa 1f0r 1.64 Thrombin 1ba8 1.53 1fjs 1.09 2.57 1.59 1hgt b 0.69 1.85 1.55 1ksn a 0.67 1.65 1.59 TK 1kim a 1.58 1xka a 1.27 2.46 1.56 1ki4 a 1.78 2.90 1.40 RMSD ave was defined as the sidechain RMSD based on binding site residues within a cutoff distance of 4.5 Å from crystallographic ligands; RMSD max is defined as the largest sidechain RMSD value among all the binding site residues.

(B) A low-affinity ligand BMU (stick) is shown bound to the allosteric pocket (1kv1).

Publication Year: 2010


Dynamic clustering threshold reduces conformer ensemble size while maintaining a biologically relevant ensemble.

(2010) J Comput Aided Mol Des 24

PubMed: 20499135 | PubMedCentral: PMC2901495 | DOI: 10.1007/s10822-010-9365-1

For the goal of comparing different tools in their ability to reproduce the conformation of ligands in their bound states, conformers generated by OMEGA were subsequently clustered and the information... in the smaller number of cluster centers was compared to the information contained in the original OMEGA output Table 1 The protein data bank IDs from which the ligands were extracted, the number of rotatable bonds, the number of conformers Ligand Rotors omega a nmrclust b rms c rms_avg d Ligand Rotors omega a nmrclust b rms c rms_avg d 1CIM 1 8 4 4 4 1UVT 8 500 57 66 253 1QPE 2 2 2 2 1 1YDT 8 500 44 52 121 1YDR 2 25 7 11 12 2CGR 8 500 55 68 66 2PCP 2 5 5 5 3 3ERT 8 500 92 102 8 1F4E 3 26 6 6 5 1M48 9 500 48 48 54 1FCX 3 111 21 23 27 1NHU 9 500 47 54 104 1H1P 3 378 47 50 44 1NHV 9 500 88 99 113 1H9U 3 32 5 8 8 2QWI 9 500 35 35 15 1 JSV 3 68 16 18 24 1K1 J 10 500 57 64 142 1BR6 4 79 16 20 23 1KV2 10 500 72 72 44 1DLR 4 109 16 17 19 1MQ6 10 500 62 66 76 1FCZ 4 135 19 20 24 7DFR 10 500 78 84 28 1L2S 4 34 7 7 8 1EZQ 11 500 68 69 88 2CSN 4 88 10 10 11 1FKG 11 500 78 84 92 1K7E 5 75 19 23 10 1K22 11 500 54 60 33 1KV1 5 38 6 8 6 1QBU 11 500 66 69 118 1QL9 5 500 54 60 198 1HFC 12 500 54 59 50 1YDS 5 319 22 22 11 1MNC 12 500 55 55 57 5STD 5 331 48 54 29 1OHR 12 500 44 44 47 1EVE 6 500 37 46 31 1UVS 12 500 58 60 83 1F0T 6 500 64 68 262 7EST 12 500 62 68 29 1H1S 6 500 61 69 88 1ELA 13 500 39 45 25 1HDQ 6 45 9 12 6 1GWX 13 500 110 120 274 1K7F 6 500 75 80 52 1HPV 13 500 41 47 115 1A42 7 500 63 67 33 1O86 13 500 33 34 27 1IF7 7 500 70 82 179 1F4G 14 500 49 49 35 1L8G 7 500 36 36 50 1HTF 15 500 58 59 149 1LQD 7 500 60 65 182 1MMB 15 500 37 37 63 966C 7 500 52 56 45 Average 7.7 366.8 43.8 47.7 65.0 The number of conformers generally increased with the number of rotors for each method a Enumerated with recommended settings in OMEGA Generated by: b  Clustering the OMEGA conformers employing the NMRCLUST algorithm c Adjusting the rms parameter of OMEGA to generate similar numbers of conformers as the number of clusters identified by the NMRCLUST algorithm d Partitioning the dataset into low, medium and large numbers of rotatable bonds, averaging the rms values in each group and using the averaged rms values Next, the computational 3D models were built from scratch, and minimized employing the MMFF94x force field and default parameters in MOE.

Publication Year: 2010


Predicting inactive conformations of protein kinases using active structures: conformational selection of type-II inhibitors.

(2011) PLoS One 6

PubMed: 21818358 | PubMedCentral: PMC3144914 | DOI: 10.1371/journal.pone.0022644

>GIN(2HZ0), KIN(2HZN), PRC(1FPU), STI(1IEP, 1OPJ, 2HYY) BRAF1 2FB8(A,B) BAX(1UWH, 1UWJ) EPHA3 2QOQ(A) IFC(3DZQ) KIT 1PKG(A,B) STI(1T46) LCK 3LCK(A) 1N8(2OG8), 242(2OFV), 9NH(3B2W), STI(2PL0) M... 14 1M7Q(A) 1PP(2BAJ), AQZ(2BAK), B96(1KV2), BMU(1KV1), L09(1WBN), L10(1W82), L11(1W83), LI2(1WBS), LI3(1WBV), WBT(1WBT) SRC 1Y57(A) STI(2OIQ) Results and Discussion Outward movements of N-lobes in DFG-out structures We searched the Protein Dada Bank (PDB) at the beginning of this study and found seven kinases with both the DFG-in and DFG-out structures, as listed in Table 1 .

Publication Year: 2011


Applying ligands profiling using multiple extended electron distribution based field templates and feature trees similarity searching in the discovery of new generation of urea-based antineoplastic kinase inhibitors.

(2012) PLoS One 7

PubMed: 23185312 | PubMedCentral: PMC3502486 | DOI: 10.1371/journal.pone.0049284

g005 Figure 5 P38 MAP Kinase in Complex with urea-based inhibitor (1KV1): (A) The color codes represent the different regions of the binding site: G-loop, Hyd1, alphaC, Hinge, HRD and DFG regions.

Publication Year: 2012


Structure-based druggability assessment of the mammalian structural proteome with inclusion of light protein flexibility.

(2014) PLoS Comput Biol 10

PubMed: 25079060 | PubMedCentral: PMC4117425 | DOI: 10.1371/journal.pcbi.1003741

Target Structural data Docking-based druggability Protein flexibility Variation PDB ID RMSD ave (Å) [A] dock hit rate [B] DScore+ [A] [B] CDK2 1aq1 1.32 1.7 21% 11% 1buh 1.8 1.44 1.7 1dm2 1.8 ... .62 1.9 ER 1l2i 1.69 2.9 9% 7% 3ert 2.6 1.55 2.7 1err 2.0 1.61 2.8 HIV RT 1vrt 1.66 2.5 8% 13% 1rt1 1.5 1.75 2.3 1c1c 1.9 1.61 2.2 1rth 1.6 1.61 2.3 p38α 1a9u 1.00 1.8 49% 15% kinase 1kv1 3.8 1.16 2.1 1kv2 3.5 1.61 2.1 PPARγ 1fm6 1.46 2.9 13% 34% 1fm9 1.5 1.62 3.0 2prg 0.7 1.43 2.1 TK 1kim 1.58 2.7 12% 4% 1ki4 1.8 1.40 2.6 IL-2 1z92 0.13 * 107% 13% 1py2 2.6 0.62 * 1m48 2.5 0.62 * Bcl-XL 2bzw 1.04 2.4 21% 4% 2yxj 2.5 0.84 2.5 TNF 1tnf 0.95 2.4 1% 18% 2az5 2.9 0.96 2.0 MDM2 1ycr 0.45 2.5 69% 18% 1rv1 1.8 0.92 2.2 1t4e 1.6 0.66 2.1 HPV E2 1tue -0.24 * 323% 31% 1r6n 2.8 1.02 * Targets are from Huang and Jacobson [17] , and include all targets where at least two structures have an RMSD ave greater than 1.5 Å.

Publication Year: 2014


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