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PDB ID Mentions in PubMed Central Article count: 5

Citations in PubMed

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PDB ID Mentions in PubMed Central

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SMAP-WS: a parallel web service for structural proteome-wide ligand-binding site comparison.

(2010) Nucleic Acids Res 38

PubMed: 20484373 | PubMedCentral: PMC2896174 | DOI: 10.1093/nar/gkq400

The estrogen receptor ligand-binding domain (PDB id: 1QKT) is compared with the steroid delta-isomerase (PDB id: 1OHP) without specifying the co-crystallized ligand-binding site (in the web interface,... the option of ‘search only co-crystal ligand sites’ for both structures was set to false).

Two superposed structures of steroid delta-isomerase (PDB id: 1OHP, blue backbone) and estrogen receptor ligand-binding domain (PDB id 1QKT, red backbone) from an SMAP alignment.

The co-crystalized estradiol in 1QKT is shown as a light blue stick model.

Publication Year: 2010


CSAR benchmark exercise of 2010: selection of the protein-ligand complexes.

(2011) J Chem Inf Model 51

PubMed: 21728306 | PubMedCentral: PMC3180202 | DOI: 10.1021/ci200082t

Table 2 Congeneric Series Present in the Data Set protein count ligand series type pdb id pdb id pdb id pdb id pdb id pdb id pdb id pdb id pdb id pdb id pdb id HIV-1 protease (L63P) 11 hydroxyethylami... e 2cem 2cen 2qnq 1g2k 1d4i 1d4j 1ebz 1ec0 1ec1 1ec2 1xl5 HIV-1 protease (WT) 11 hydroxyethylamine 2psv 2q54 2qhy 2qhz 2qi1 2qi3 2qi4 2qi5 2qi6 2i0a 2i0d tyrosine-protein phosphatase 8 thiophene-dicarboxylic acid 2hb1 2qbq 2qbr 2qbs 2zmm 2zn7 2azr 2b07       coagulation factor X 6 pyrrolidin-2-one 2uwl 2uwp 2cji 2j2u 2j34 2j4i           carbonic anhydrase 2 6 sulfamide analogues 2h15 2pov 2pow 3bl0 2hd6 2pou           tRNA guanine transglycosylase 5 quinazolin-4-one 2bbf 1r5y 1s38 1s39 1q4w             HMGCoA reductase 5 atorvastatin analogues 3ccw 3ccz 3cd7 3cd0 3cda             acetylcholinesterase 4 huperzine/hupyridone 1vot 1gpk 1h22 1h23               estrogen receptor alpha 4 phenol 2pog 2r6w 2ayr 1qkt               urokinase 4 benzamidine analogues 1gja 1gj8 1gjd 1gi9               β-1,4-xylanase 3 aza-sugar analogues 1fh8 1fh9 1fhd                 glutamate [NMDA] receptor ζ1 3 small ring amino carboxylic acid 1y1m 1y1z 1y20                 lectin 3 saccharides 1ax1 1ax0 1ax2                 membrane lipoprotein tmpC 3 purine neucloside analogues 2fqw 2fqx 2fqy                 retropepsin 3 macrocyclic peptidomimetic 1b6j 1b6l 1b6m                 transporter (LeuT) 3 small amino acid 3f3d 3f48 3f4j                 The range of affinities in the CSAR-NRC set is quite large, 14 orders of magnitude in p K d .

Publication Year: 2011


Pharmacophore-based virtual screening versus docking-based virtual screening: a benchmark comparison against eight targets.

(2009) Acta Pharmacol Sin 30

PubMed: 19935678 | PubMedCentral: PMC4007494 | DOI: 10.1038/aps.2009.159

Target PDB entries a Number of Actives b ACE 1UZF, 1O86, 1UZE * 14 AChE 1ACJ, 1ACL, 1AMN, 1AX9, 1DX6, 1E3Q, 1E66, 1EVE, 1GPK, 1GPN, 1GQR, 1GQS, 1H22, 1H23, 1HBJ, 1JJB, 1OCE, 1ODC, 1U65, 1UT6, ... VOT, 1W4L, 1W6R, 1W76, 1ZGC, 2ACE, 2ACK * , 2BAG, 2C4H, 2C5F, 2C5G, 2C58, 2CEK, 2CKM, 2CMF, 2J3Q, 2VB4 22 AR 1E3G * , 1GS4, 1T5Z, 1T63, 1T65, 1XJ7, 1XOW, 1XQ3, 1Z95, 2AM9, 2AMA, 2AMB, 2AO6, 2AX6, 2AX7, 2AX8, 2AX9, 2AXA, 2HVC, 2OZ7, 2PIO, 2PIP, 2PIQ, 2PIR, 2PIT, 2PIU, 2PIV, 2PIW, 2PIX, 2PKL, 2PNU, 2Q7I, 2Q7J, 2Q7K, 2Q7L, 2Z4J 16 DacA 1CEF, 1CEG * , 1HVB, 1IKG, 1IKI, 1MPL, 1PW1, 1PW8, 1PWC, 1PWD, 1PWG, 1SCW, 1SDE, 1YQS 3 DHFR 1BOZ * , 1KMS, 1KMV, 1S3U, 1S3V, 1S3W, 2DHF, 1DLS, 1U72, 1MVS, 1MVT, 1DLR, 1U71, 1HFP, 1HFQ, 1HFR, 1OHJ, 1OHK, 1DHF, 1DRF, 1PD8, 1PD9 8 ERα 1A52, 1AKF, 1ERE, 1ERR, 1G50, 1GWQ, 1GWR, 1L2I, 1PCG * , 1QKT, 1R5K, 1UOM, 1X7E, 1X7R, 1XP1, 1XP6, 1XP9, 1XPC, 1YIM, 1ZKY, 2AYR, 2B1V, 2B1Z, 2BJ4, 2FAI, 2G44, 2G5O, 2I0J, 2IOG, 2JF9, 2JFA, 2OUZ, 2P15, 2POG, 2Q6J, 2Q70, 2QE4, 3ERD, 3ERT 32 HIV-pr 1AID, 1HVH, 1HVR, 1HWR, 1IZH, 1IZI, 1JLD, 1KZK, 1NPV, 1NPW, 1T3R, 1T7K, 1TCX, 1XL2, 1XL5, 1YT9, 2A4F * , 2AID, 2F3K, 2FDD, 2FDE, 2FGU, 2FGV, 2HC0, 2NXD, 2NXM, 2P3A, 2P3B, 2P3C, 2P3D, 3AID, 4PHV 9 TK 1E2I, 1E2J, 1E2K * , 1E2L, 1E2M, 1E2N, 1E2P, 1KI2, 1KI3, 1KI4, 1KI6, 1KI7, 1KI8, 1KIM, 1OF1, 1P7C, 1QHI, 1VTK, 2KI5, 2VTK, 3VTK 8 a All the X-ray crystal structures of the complexes of each target in complex with ligands were used in the construction of pharmacophore models.

Publication Year: 2009


Versatility or promiscuity: the estrogen receptors, control of ligand selectivity and an update on subtype selective ligands.

(2014) Int J Environ Res Public Health 11

PubMed: 25162709 | PubMedCentral: PMC4198987 | DOI: 10.3390/ijerph110908709

(Å) Ref 1A52 Dimer Estradiol 2.8 [ 29 ] 1ERE Hexamer Estradiol 3.1 [ 30 ] 1ERR Dimer Raloxifene 2.6 [ 30 ] 3ERD Dimer Diethylstilbestrol 2.03 [ 31 ] 3ERT Monomer 4-Hydroxytamoxifen 1.9 [ 31 ] ... QKT Monomer Estradiol 2.2 [ 32 ] 1QKU Trimer Estradiol 3.2 [ 32 ] 1G50 Trimer Estradiol 2.9 [ 33 ] 1GWQ Dimer Raloxifene core 2.45 [ 34 ] 1GWR Dimer Estradiol 2.4 [ 34 ] 1L2I Dimer ( R,R )-5,11- cis -Diethyl-5,6,11,12-tetrahydrochrysene- 2,8-diol 1.95 [ 35 ] 1PCG Dimer Estradiol 2.7 [ 36 ] 1UOM Monomer 2-Phenyl-1-[4-(2-piperidin-1-yl-ethoxy)-phenyl]-1,2,3, 4-tetrahydroisoquinolin-6-ol 2.28 [ 37 ] 1R5K Trimer (2 E )-3-{4-[(1 E )-1,2-Diphenylbut-1-enyl]phenyl}acrylic acid 2.7 [ 38 ] 1SJ0 Monomer (2 S ,3 R )-2-(4-(2-(Piperidin-1-yl)ethoxy)phenyl)-2,3-dihydro-3-(4-hydroxyphenyl)benzo[b][1,4]oxathiin-6-ol 1.9 [ 39 ] 1XP1 Monomer (2 S ,3 R )-2-(4-{2-[(3 R ,4 R )-3,4-Dimethylpyrrolidin-1-yl]ethoxy}phenyl)-3-(4-hydroxyphenyl)-2,3-dihydro-1,4-benzoxathiin-6-ol 1.8 [ 40 ] 1XP6 Monomer (2 S ,3 R )-2-(4-{2-[(3 S ,4 S )-3,4-Dimethylpyrrolidin-1-yl]ethoxy}phenyl)-3-(4-hydroxyphenyl)-2,3-dihydro-1,4-benzoxathiin-6-ol 1.7 [ 40 ] 1XP9 Monomer (2 S ,3 R )-3-(4-Hydroxyphenyl)-2-(4-{[(2 S )-2-pyrrolidin-1-ylpropyl]oxy}phenyl)-2,3-dihydro-1,4-benzoxathiin-6-ol 1.8 [ 40 ] 1XPC Monomer (2 S ,3 R )-3-(4-Hydroxyphenyl)-2-(4-{[(2 R )-2-pyrrolidin-1-ylpropyl]oxy}phenyl)-2,3-dihydro-1,4-benzoxathiin-6-ol 1.6 [ 40 ] 1X7E Dimer [5-Hydroxy-2-(4-hydroxyphenyl)-1-benzofuran-7-yl]acetonitrile 2.8 [ 41 ] 1X7R Monomer Genistein 2 [ 42 ] 1XQC Tetramer (1 S )-1-{4-[(9a R )-Octahydro-2 H -pyrido[1,2-a]pyrazin-2-yl]phenyl}-2-phenyl-1,2,3,4-tetrahydroisoquinolin-6-ol 2.05 [ 43 ] 1YIM Monomer (2 R ,3 R ,4 S )-3-(4-Hydroxyphenyl)-4-methyl-2-[4-(2-pyrrolidin-1-ylethoxy)phenyl]chroman-6-ol 1.9 [ 44 ] 1YIN Monomer (2 R ,3 R ,4 S )-5-Fluoro-3-(4-hydroxyphenyl)-4-methyl-2-[4-(2-piperidin-1-ylethoxy)phenyl]chroman-6-ol 2.2 [ 44 ] 2AYR Monomer 6-(4-Methylsulfonyl-phenyl)-5-[4-(2-piperidin-1-ylethoxy)phenoxy]naphthalen-2-ol 1.9 [ 45 ] 2B23 Dimer 2.1 [ 46 ] 2BJ4 Dimer 4-Hydroxytamoxifen 2 [ 47 ] 1ZKY Dimer 4-[(1 S ,2 S ,5 S )-5-(Hydroxymethyl)-6,8,9-trimethyl-3-oxabicyclo[3.3.1]non-7-en-2-yl]phenol 2.25 [ 48 ] 2B1V Dimer 4-[(1 S ,2 S ,5 S )-5-(Hydroxymethyl)-8-methyl-3-oxabicyclo[3.3.1]non-7-en-2-yl]phenol 1.8 [ 48 ] 2B1Z Dimer 17-Methyl-17-α-dihydroequilenin 1.78 [ 49 ] 2FAI Dimer 4-[(1 S ,2 S ,5 S ,9 R )-5-(Hydroxymethyl)-8,9-dimethyl-3-oxabicyclo[3.3.1]non-7-en-2-yl]phenol 2.1 [ 48 ] 2I0J Tetramer (3a S ,4 R ,9b R )-4-(4-Hydroxyphenyl)-1,2,3,3a,4,9b-hexahydrocyclopenta[c]chromen-8-ol 2.9 [ 50 ] 2G44 Dimer 4-[(1 S ,2 R ,5 S )-4,4,8-Trimethyl-3-oxabicyclo[3.3.1]non-7-en-2-yl]phenol 2.65 - 2G5O Dimer (9α,13β,17β)-2-[(1 Z )-But-1-en-1-yl]estra-1,3,5(10)-triene-3,17-diol 2.3 - 2IOG Monomer N-[(1 R )-3-(4-Hydroxyphenyl)-1-methylpropyl]-2-[2-phenyl-6-(2-piperidin-1-ylethoxy)-1h-indol-3-yl]acetamide 1.6 [ 51 ] 2IOK Dimer N-[(1 R )-3-(4-Hydroxyphenyl)-1-methylpropyl]-2-(2-phenyl-1 H -indol-3-yl)acetamide 2.4 [ 51 ] 2JF9 Trimer 4-Hydroxytamoxifen 2.1 [ 52 ] 2JFA Dimer Raloxifene 2.55 [ 52 ] 2OCF Monomer Estradiol 2.95 [ 53 ] 2OUZ Monomer (5 R ,6 S )-6-Phenyl-5-[4-(2-pyrrolidin-1-ylethoxy)phenyl]-5,6,7,8-tetrahydronaphthalen-2-ol 2 [ 54 ] 2P15 Dimer (17β)-17-{( E )-2-[2-(Trifluoromethyl)phenyl]vinyl}estra-1(10),2,4-triene-3,17-diol 1.94 [ 55 ] 2POG Dimer (3a S ,4 R ,9b R )-4-(4-Hydroxyphenyl)-1,2,3,3a,4,9b-hexahydrocyclopenta[c]chromen-9-ol 1.84 [ 56 ] 2Q6J Dimer 4-[(Dimesitylboryl)(2,2,2-trifluoroethyl)amino]phenol 2.7 [ 57 ] 2Q70 Dimer (3a S ,4 R ,9b R )-2,2-Difluoro-4-(4-hydroxyphenyl)-1,2,3,3a,4,9b-hexahydrocyclopenta[c]chromen-8-ol 1.95 [ 58 ] 2QE4 Dimer (3a S ,4 R ,9b R )-4-(4-Hydroxyphenyl)-6-(methoxymethyl)-1,2,3,3a,4,9b-hexahydrocyclopenta[c]chromen-8-ol 2.4 [ 50 ] 2QA6 Dimer 4-(6-Hydroxy-1 H -indazol-3-yl)benzene-1,3-diol 2.6 [ 46 ] 2QA8 Dimer Genistein 1.85 [ 46 ] 2QAB Dimer 3-Ethyl-2-(4-hydroxyphenyl)-2 H -indazol-5- ol 1.89 [ 46 ] 2QGT Dimer (9β,11α,13α,14β,17α)-11-(methoxymethyl)estra-1(10),2,4-triene-3,17-diol 2.15 [ 46 ] 2QGW Dimer 3-Chloro-2-(4-hydroxyphenyl)-2 H -indazol-5-ol 2.39 [ 46 ] 2QH6 Dimer Diethyl (1 R ,2 S ,3 R ,4 S )-5,6-bis(4-hydroxyphenyl)-7-oxabicyclo[2.2.1]hept-5-ene-2,3-dicarboxylate 2.7 [ 46 ] 2QR9 Dimer Dimethyl (1 R ,4 S )-5,6-bis(4-hydroxyphenyl)-7-oxabicyclo[2.2.1]hepta-2,5-diene-2,3-dicarboxylate 2 [ 46 ] 2QSE Dimer 4-(2-Amino-1-methyl-1 H -imidazo[4,5-b]pyridin-6-yl)phenol 1.85 [ 46 ] 2QXM Dimer 2-Amino-1-methyl-6-phenylimidazo[4,5-b]pyrid 2.3 [ 46 ] 2QXS Dimer Raloxifene 1.7 [ 59 ] 2QZO Dimer 4-[1-Allyl-7-(trifluoromethyl)-1h-indazol- 3-yl]bezene-1,3-diol 1.72 [ 59 ] 2R6W Dimer [6-Hydroxy-2-(4-hydroxyphenyl)-1-benzothien-3-yl]{4-[2-(4-methylpiperidin-1-yl)ethoxy]phenyl}methanone 2 [ 60 ] 2R6Y Dimer [6-Hydroxy-2-(4-hydroxyphenyl)-1-benzothien-3-yl][4-(2-pyrrolidin-1-ylethoxy)phenyl]methanone 2 [ 60 ] 3DT3 Dimer 5-(4-Hydroxyphenoxy)-6-(3-hydroxyphenyl)- 7-methylnapthalen-2-ol 2.4 [ 61 ] 3HLV Dimer (9β,13α,16β)-3,16-Dihydroxyestra- 1,3,5(10)-trien-17-one 3 - 3HM1 Dimer (9β,13α)-3-Hydroxyestra-1,3,5(10)-trien-17-one 2.33 - 3L03 Dimer (14β,15α,16α,17α)-Estra-1,3,5(10)-triene-3,15,16,17-tetrol 1.9 - 3OS8 Tetramer 4-[1-Benzyl-7-(trifluoromethyl)-1 H -indazol-3-yl]benzene-1, 3-diol 2.03 [ 59 ] 3OS9 Tetramer 4-[1-Allyl-7-(trifluoromethyl)-1 H -indazol-3-yl]benzene-1,3-diol 2.3 [ 59 ] 3OSA Tetramer 4-[1-(3-Methylbut-2-en-1-yl)-7-(trifluoromethyl)-1 H -indazol-3-yl]benzene-1,3-diol 2.3 [ 59 ] 2YAT Monomer Estradiol-pyridinium tetraacetic acid 2.6 [ 62 ] 2YJA Monomer Estradiol 1.82 [ 63 ] 3Q95 Dimer Estriol 2.05 - 3Q97 Dimer 4,4’-[(1 Z )-1-(4-Ethoxyphenyl)but-1-ene-1,2-diyl]diphenol; 4,4’-[2-(4-Ethoxyphenyl)but-1-ene-1,1-diyl]diphenol 2.1 - 3UU7 Dimer 4,4’-Propane-2,2-diyldiphenol 2.2 [ 64 ] 3UUA Dimer 4,4’-(1,1,1,3,3,3-Hexafluoropropane-2,2-diyl)diphenol 2.05 [ 64 ] 3UUC Tetramer 4,4’-(2,2-Dichloroethene-1,1-diyl)diphenol 2.1 [ 64 ] 3UUD Dimer Estradiol 1.6 [ 64 ] 4DMA Dimer 2’-Bromo-6’-(furan-3-yl)-4’-(hydroxymethyl)biphenyl-4-ol 2.3 [ 65 ] 4IU7 Dimer 4-[2-Ethyl-7-(trifluoromethyl)-2 H -indazol-3-yl]benzene-1, 3-diol 2.29 [ 66 ] 4IUI Dimer 4-[1-Butyl-7-(trifluoromethyl)-1 H -indazol-3-yl]benzene-1, 3-diol 2.3 [ 66 ] 4IV2 Dimer 4-[1-(2-Methylpropyl)-7-(trifluoromethyl)-1 H -indazol-3-yl]benzene-1,3-diol 2.14 [ 66 ] 4IV4 Dimer 4-[2-(2-Methylpropyl)-7-(trifluoromethyl)- 2h-indazol-3-yl]benzene-1,3-diol 2.3 [ 66 ] 4IVW Dimer 4-[2-Benzyl-7-(trifluoromethyl)-2 H -indazol-3-yl]benzene-1,3-diol 2.06 [ 66 ] 4IVY Dimer 4-[1-(But-3-en-1-yl)-7-(trifluoromethyl)-1 H -indazol-3-yl]benzene-1,3-diol 1.95 [ 66 ] 4IW6 Dimer 4-[2-(But-3-en-1-yl)-7-(trifluoromethyl)-2 H -indazol-3-yl]benzene-1,3-diol 1.98 [ 66 ] 4IW8 Dimer 4-[1-(3-Methylbut-2-en-1-yl)-7-(trifluoromethyl)-1 H -indazol-3-yl]benzene-1,3-diol 2.04 [ 66 ] 4IWC Dimer 4,4’-Thiene-2,5-diylbis(3-methylphenol) 2.24 [ 66 ] 4IWF Dimer 2-Chloro-3’-fluoro-3-[( E )-(hydroxyimino)methyl]biphenyl- 4,4’-diol 1.93 [ 66 ] ijerph-11-08709-t002_Table 2 Table 2 Crystal structures of ERβ ligand binding domain bound with ligands in PDB.

Publication Year: 2014


Competitive molecular docking approach for predicting estrogen receptor subtype ? agonists and antagonists.

(2014) BMC Bioinformatics 15 Suppl 11

PubMed: 25349983 | PubMedCentral: PMC4251048 | DOI: 10.1186/1471-2105-15-S11-S4

Color codes: 1QKT (orange), 2QA8 (blue), 2QGT (pink), 2Q6J (orange red), 3DT3 (green) and 1XP1 (light green).

Publication Year: 2014