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PDB ID Mentions in PubMed Central Article count: 15

Citations in PubMed

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PDB ID Mentions in PubMed Central

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Using least median of squares for structural superposition of flexible proteins.

(2009) BMC Bioinformatics 10

PubMed: 19159484 | PubMedCentral: PMC2639377 | DOI: 10.1186/1471-2105-10-29

Table 1 Superposition results of protein systems with conformational changes using the LMS fit Protein system PDB1 PDB2 RMSD #Res 1 #Subset Core% 2 Time(s) ER α 3erd 3ert 4.9 244 203 83.2% 0.2... RAN 1byu 1rrp 14.4 200 141 70.5% 0.19 Myosin 1b7t 1dfk 13.0 720 403 56.0% 0.58 Calmodulin 1cll 1ctr 14.7 138 72 52.2% 0.09 Topo II 1bgw 1bjt 18.4 665 389 58.5% 0.55 Pneumolysin 2bk1 2bk2 21.8 435 139 32.0% 0.39 1 "#Res" is the number of atom pairs used for superposition by removing any inappropriate residues.

Figure 3 Superposition comparison for the ER α structures: 3erd (light gray) and 3ert (dark gray) .

Publication Year: 2009


Robust probabilistic superposition and comparison of protein structures.

(2010) BMC Bioinformatics 11

PubMed: 20594332 | PubMedCentral: PMC2912885 | DOI: 10.1186/1471-2105-11-363

Table 1 Marginal likelihood of different models Protein PDB IDs Student t K Laplace Gauss GroEL 1AON - 1OEL -4328.57 -4307.22 -5132.84 -5722.35 DNA Pol 1IH7 - 1IG9 -5574.80 -5750.12 -6340.01 -8011.05 ... AN 1RRP - 1BYU -1124.86 -1176.53 -1795.92 -2286.10 Topo II 1BGW - 1BJT -4496.17 -4553.50 -7210.74 -8042.00 Pneumolysin 2BK2 - 2BK1 -2692.73 -2465.09 -5195.85 -5491.90 ER 3ERD - 3ERT -538.11 -622.69 -1290.81 -1980.96 RNA Pol 1QLN - 1MSW -5296.61 -5455.79 -8471.69 -10168.07 Adenylate Kinase 1AKE - 4AKE -1499.73 -1502.75 -1685.11 -2000.35 Myosin 1B7T - 1DFK -4819.91 -5046.02 -6380.11 -7701.83 Synthetic data Student t -9179.46 -9253.48 -12465.97 -13951.94 Synthetic data Gauss -5108.73 -5112.43 -5077.97 -5115.98 Logarithm of the marginal likelihood P ( M | D ) of the different displacement models obtained for nine structure pairs undergoing domain movements.

Publication Year: 2010


Training a scoring function for the alignment of small molecules.

(2010) J Chem Inf Model 50

PubMed: 20831240 | PubMedCentral: PMC2946173 | DOI: 10.1021/ci100227h

The 6 smaller ligands ( 1A52 , 1GWQ , 1L2I , 1X7E , 1X7R , and 3ERD ) are in cyan.

Publication Year: 2010


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


Consistent two-dimensional visualization of protein-ligand complex series.

(2011) J Cheminform 3

PubMed: 21702959 | PubMedCentral: PMC3224603 | DOI: 10.1186/1758-2946-3-21

The data set is an representative collection of crystal structures from the PDB (PDB codes, ordered according to the complex scoring of PoseView: 1ERR , 2JFA , 1G50 , 1PCG , 1YIN , 1QKU , 1X7E , 1X7R ... 1YIM , 2B1V , 3ERD , 3ERT ).

The diagrams show complexes of proteins with co-crystallized ligands with the following PDB accession codes: 1ERR (a), 2JFA (b), 1G50 (c), 1PCG (d), 1YIN (e), 1QKU (f), 1X7E (g), 1X7R (h), 1YIM (i), 2B1V (j), 3ERD (k), 3ERT (l).

Publication Year: 2011


Ligand-binding dynamics rewire cellular signaling via estrogen receptor-?.

(2013) Nat Chem Biol 9

PubMed: 23524984 | PubMedCentral: PMC3631275 | DOI: 10.1038/nchembio.1214

Division on Earth and Life Studies A new biology for the 21st century 2009 Washington, D.C. National Academies Press 47 Adams PD PHENIX: a comprehensive Python-based system for macromolecular structur... solution Acta Crystallogr D Biol Crystallogr 2010 66 213 221 20124702 48 Schuttelkopf AW van Aalten DM PRODRG: a tool for high-throughput crystallography of protein-ligand complexes Acta Crystallogr D Biol Crystallogr 2004 60 1355 1363 15272157 49 Emsley P Cowtan K Coot: model-building tools for molecular graphics Acta Crystallogr D Biol Crystallogr 2004 60 2126 2132 15572765 50 McNicholas S Potterton E Wilson KS Noble ME Presenting your structures: the CCP4mg molecular-graphics software Acta Crystallogr D Biol Crystallogr 2011 67 386 394 21460457 Figure 1 ERα structure and ligand sets a) The LBD is shown as ribbon, with h12 bound to either full-agonist diethylstilbesterol (PDB ID: 3ERD) or tamoxifen (PDB ID: 3ERT), demonstrating how tamoxifen positioning of h12 blocks binding of SRC2.

Publication Year: 2013


Structural characterization of the binding interactions of various endogenous estrogen metabolites with human estrogen receptor ? and ? subtypes: a molecular modeling study.

(2013) PLoS One 8

PubMed: 24098659 | PubMedCentral: PMC3786999 | DOI: 10.1371/journal.pone.0074615

The 3-D structure of the ligand binding domain (LBD) of human ERα in complex with DES, a non-steroidal estrogen, has been previously determined (PDB code: 3ERD).

The docking model of the ERα-DES complex was then compared with the known crystal structure of the ERα-DES complex (PDB code: 3ERD) by superimposing these two structures.

The known crystal structure of ERα LBD in complex with DES (PDB code: 3ERD) was colored in yellow with DES colored in green.

Similarly, we used the known crystal structure of ERα LBD that was complexed with DES (PDB code: 3ERD) as a template and then docked E 2 into the LBD.

We compared the ERα structures in complex with three ERα agonists, namely, E 2 (PDB codes 1ERE and 1A52), DES (PDB code 3ERD), and genistein (GEN) (PDB code 1X7R) by superimposing these structures on each other.

Publication Year: 2013


BioSuper: a web tool for the superimposition of biomolecules and assemblies with rotational symmetry.

(2013) BMC Struct Biol 13

PubMed: 24330655 | PubMedCentral: PMC3924234 | DOI: 10.1186/1472-6807-13-32

Figure 2 Examples of the three superimposition types available in the BioSuper web server ( http://ablab.ucsd.edu/BioSuper ): a) standard superimposition of the angiogenin protein; PDB IDs: 1agi, chai... A (green) and 1gio, chain A from first NMR model (lilac), b) weighted superimposition of the estrogen receptor alpha in different conformations; PDB IDs: 3ert, chain A (green) and 3erd, chain A (lilac), c) structural superimposition of the β 2 adrenergic receptor and the adenosine A 2A receptor; PDB IDs: 2rh1, chain A (green), and 3EML, chain A (lilac).

Publication Year: 2013


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


Structural insights into Resveratrol's antagonist and partial agonist actions on estrogen receptor alpha.

(2013) BMC Struct Biol 13

PubMed: 24160181 | PubMedCentral: PMC4015837 | DOI: 10.1186/1472-6807-13-27

Methods Modeling of the receptor-resveratrol complex The crystal structure of ERα LBD homo-dimer (PDB ID: 3ERD) where each monomer is bound with an agonist ligand DES was considered as ER�... b1; LBD agonist conformation.

The lowest energy docked complexes of each ERα LBD monomer with RES was selected to build the dimer based on the ERα LBD dimer crystal structure (PDB ID: 3ERD) as a template.

Publication Year: 2013


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4059272

For comparison reasons, the other two experimental structures of the agonist conformation of ERα were extracted, PDB entries 1GWR (ERα cocrystallized with E2) 29 and 3ERD (the receptor... cocrystallized with diethylstilbestrol, DES).

Docking runs performed at the agonist conformations of ER (the receptor cocrystallized to E 2 , PDB entry 1GWR (Figure 7 B), and to DES, PDB entry 3ERD) have led to conflicting results; thus, no valid docking pose could be found.

Molecular Modeling To study the binding mode of FR derivatives of endoxifen and 4OHT in the ER binding pocket, flexible docking simulations were carried out against both conformations of ER ligand-binding domain (LBD), agonist (PDB codes 1GWR (ER LBD cocrystallized with E 2 ), 29 3ERD (ER LBD cocrystallized with DES), 30 3Q97 (ER LBD cocrystallized with ethoxytriphenylethylene isomers), 31 and antagonist (PDB codes 3ERT (ER LBD cocrystallized with 4OHT), 30 1UOM (ER LBD cocrystallized with 2-phenyl-1-[4-(2-piperidin-1-ylethoxy)phenyl]-1,2,3,4-tetrahydroisoquinolin-6-ol, PTI), 32 2OUZ (ER LBD cocrystallized with lasofoxifene) 33 ).

Publication Year: 2014


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


PubMed ID is not available.

Published in 2014

PubMedCentral: PMC4207530

Figure 10 ER conformation is dependent upon ligand binding: (A) ER bound in an agonist conformation (gray ribbon; diethylstilbestrol, colored spheres; helix-12 in orange; coactivator peptide in red; P... B code 3ERD); (B) ER bound in an antagonist conformation (gray ribbon; hydroxytamoxifen, colored spheres; helix-12 in orange; PDB code 3ERT).

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

The remaining agonists i.e. genistein, dimethyl(1R,4S)-5,6-bis(4-hydroxyphenyl)-7-oxabicyclo[2.2.1]hepta-2,5-diene-2,3-dicarboxylate, 2-amino-1-methyl-6-phenylimidazole[4,5-B]pyrine, diethylstilbestro... , 2'-bromo-6'-(furan-3-yl)-4'-(hydroxymethyl) biphenyl-4-ol, 4-[1-(but-3-en-1-yl)-7-(trifluoromethyl)-1H-indazol-3-yl]benzene-1,3-diol and 4-[1-(3-methylbut-2-en-1-yl)-7-(trifluoromethyl)-1H-indazol-3-yl]benzene-1,3-diol (PDB ID: 2QA8 [ 51 ], 2QR9 [ 51 ], 2QXM [ 51 ], 3ERD [ 65 ], 4DMA [ 66 ], 4IVY [ 67 ] and 4IW8 [ 67 ]) that were predicted as antagonists docked to both agonist and antagonist ER structures, but scored better as antagonists due to more favorable interactions.

Publication Year: 2014


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4397262

2004b ), and PDB 3ERD (Shiau et al.

Table 1 MolDock docking energies of co-crystallized ligands and root-mean-squared deviations between the co-crystallized ligand and the re-docked poses of the co-crystallized ligand with human estrogen receptors α and β Protein PDB code Co-crystallized ligand E dock (kJ/mol) RMSD (Å) ERα 1X7E [5-hydroxy-2-(4-hydroxyphenyl)-1-benzofuran-7-yx]acetonitrile −100.9 0.46 1X7R genistein −95.3 0.44 3ERD diethylstilbestrol −97.0 0.75 ERβ 1U3Q 4-(6-hydroxybenzo[d]isoxazol-3-yl)benzene-1,3-diol −98.9 1.40 1U3R 2-(5-hydroxynaphthalen-1-yl)-1,3-benzooxazol-6-ol −111.3 0.36 1U3S 3-(6-hydroxynaphthalen-2-yl)-benzo[d]isoxazol-6-ol −107.7 0.35 1U9E 2-(4-hydroxyphenyl)benzofuran-5-ol −90.4 0.62 1X7B 2-(3-fluoro-4-hydroxyphenyl)-7-vinyl-1,3-benzoxazol-5-ol −107.9 0.46 1X7J genistein −99.9 0.66 1X76 5-hydroxy-2-(4-hydroxyphenyl)-1-benzofuran-7-carbonitrile −101.3 0.42 1X78 [5-hydroxy-2-(4-hydroxyphenyl)-1-benzofuran-7-yl]carbonitrile −107.7 0.40 Table 2 MolDock molecular docking energies (kJ/mol) for alkaloids with human estrogen receptors α and β Compound Plant Source ERα ERβ cimitrypazepine Cimicifuga racemosa −87.6 −75.5 cis- clovamide Trifolium pratense −119.8 −124.9 trans- clovamide Trifolium pratense −113.6 −122.0 dihydrodioscorine Dioscorea spp.

Publication Year: 2015