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Improved docking, screening and selectivity prediction for small molecule nuclear receptor modulators using conformational ensembles.
(2010) J Comput Aided Mol Des 24
PubMed: 20455005 | PubMedCentral: PMC2881208 | DOI: 10.1007/s10822-010-9362-4
Table 1 Composition of the nuclear receptor library Ensemble ID Description PDB IDs and co-crystallized ligand Het IDs 1 ERα− Estrogen receptor α, inactive conformation... 1xp6 (AIU), 1xqc_a (AEJ), 1sj0 (E4D), 2ouz (C3D) 2 ERα+ Estrogen receptor α, active conformation 2b1v_a (458), 2b1z_a (17M), 2fai_a (459), 1l2i_a (ETC.) 3 ERβ− Estrogen receptor β, inactive conformation 1hj1 (AOE), 1qkm (GEN), 1qkn (RAL) 4 ERβ+ Estrogen receptor β, active conformation 1u3r_a (338), 1yy4_a (4NA), 1zaf_b (789) 5 GR+ Glucocorticoid receptor, agonist—bound 1m2z_a (DEX), 1p93_a (DEX), 3bqd (DAY) 6 wtMR+ Mineralocorticoid receptor, agonist—bound 2aa7 (1CA), 2a3i (C0R), 2aa2 (AS4), 7 S810L MR+ Mineralocorticoid receptor, agonist—bound 1y9r_a (1CA), 2aa6_a (STR), 1ya3_a (STR), 2aax_a (STR) 8 PR+ Progesterone receptor, agonist—bound 1e3k _a(R18), 1zuc_b (T98), 2ovh (AS0) 9 RARγ+ Retinoic acid receptor γ, agonist—bound 1exa (394), 1fcx (184), 2lbd (REA) 10 RXRα+ Retinoic acid receptor α, agonist—bound 1fm9 (REA), 1mzn_a (BM6), 1rdt (L79), 1xvp_a (CID), 2p1u (4TN) 11 VDR+ Vitamin D3 receptor, a agonist—bound 1db1 (VDX), 1s19 (MC9), 1txi (TX5), 2har (OCC), 2has (C3O), 2hb7 (O1C) 12 wtAR+ Androgen receptor, agonist—bound 1e3g (R18), 2am9 (TES), 1t7t (DHT), 2hvc (LGD) 13 T877A AR+ Androgen receptor, agonist—bound 1gs4 (ZK5), 2ax7 (FHM), 2oz7 (CA4) 14 PPARα+ Peroxisome proliferator-activated receptor α, agonist—bound 2npa_c (MMB), 2rew (REW), 2p54 (735), 1k7l_a (544), 15 PPARδ+ Peroxisome proliferator-activated receptor δ, agonist—bound 1gwx_a (433), 1y0s_a (331), 2j14_b (GN1) 16 PPARγ+ Peroxisome proliferator-activated receptor γ, agonist—bound 1rdt (L79),1k74 (544), 1knu (YPA), 1nyx (DRF), 2f4b (EHA), 2gtk (208) 17 TRβ+ Thyroid hormone receptor β, agonist—bound 1n46_b (PFA), 1nax (IH5), 1q4x (G24), 2h6w (T3) (+): agonist-bound or active state, (−): antagonist-bound or inactive state Prediction of ligand binding geometry by single receptor cross-docking We first studied the ability of the collected pocket structures to correctly reproduce the binding geometry of their cognate ligands and other ligands in their ensembles.
Table 3 Accuracy of VLS in single receptor mode measured by their ROC AUC values Receptor PDB ID ROC % Receptor PDB ID ROC % Receptor PDB ID ROC % ERα− 1xp6 71 PR+ 1zuc_b 60 PPARα+ 2npa_c 88 1xqc_c 82 1e3k_a 75 2p54 78 1sj0 73 2ovh 88 2rew 83 2ouz 89 RARγ+ 1exa 97 1k7l_a 92 ERα+ 2b1v_a 85 1fcx 96 PPARδ+ 1y0s_a 95 2fai_a 80 2lbd 95 1gwx_a 97 1l2i_a 81 RXRα+ 2p1u 90 2j14_b 99 2b1z_a 80 1rdt 92 PPARγ+ 1rdt 89 ERβ- 1hj1 90 1mzn 88 1nyx 86 1qkn 75 1fm9 86 1k74 89 1qkm 61 1xvp 92 1knu 90 ERβ+ 1u3r_a 96 VDR+ 1db1 96 2f4b 87 1yy4_a 98 1txi 78 2gtk 91 1zaf_b 97 2has 97 TRβ+ 2h6w 93 GR+ 1m2z_a 80 1s19 76 1n46_b 93 1p93_a 75 2har 76 1q4x 93 3bdq 65 2hb7 92 1nax 91 wtMR+ 2aa7 98 wtAR+ 2hvc 81 2a3i 96 1e3g 81 2aa2 99 1t7t 87 S810LMR+ 1y9r_a 80 2am9 83 1ya3_a 95 T877AAR+ 1gs4 89 2aa6_a 91 2oz7 87 2aax_a 93 2ax7 87 The crystal structure 1rdt is a heterodimer of PPARγ and RXRα and was used separately for both receptors When used in the ensemble mode, the ligand hit lists from different structures in the ensemble were combined and each ligand was represented by its best score in the ensemble.
Publication Year: 2010
Identification of PPARgamma partial agonists of natural origin (I): development of a virtual screening procedure and in vitro validation.
(2012) PLoS One 7
PubMed: 23226391 | PubMedCentral: PMC3511273 | DOI: 10.1371/journal.pone.0050816
Full agonists Partial agonists cluster 1 cluster 2 cluster 3 cluster 4 cluster 5 1FM9 1I7I 1FM6 2GTK 2G0G 4PRG 2Q6R 2FVJ 2Q6S 1RDT 1KNU 1ZGY 3B3K 2G0H 2Q61 2WM0 1K74 2F4B 2PRG 2ATH 2Q5S 3BC5 2HWQ 2FVJ... 1NYX 2Q5P 2Q8S 2HWR 1ZEO 2HFP 2P4Y Generation of Structure-Based Pharmacophores LigandScout v2.03 (Inte:ligand, Vienna, Austria, http://www.inteligand.com/ligandscout/ )  ,  was used for the analysis of the 31 PPARγ structures from Table 5 and the analysis of the possible interactions between the crystallized ligands and the ligand-binding pocket of PPARγ.
Publication Year: 2012
The human orphan nuclear receptor tailless (TLX, NR2E1) is druggable.
(2014) PLoS One 9
PubMed: 24936658 | PubMedCentral: PMC4060991 | DOI: 10.1371/journal.pone.0099440
At the time of that study, in both cases, the known X-ray structures of two human NRs: COUP-TFII (COUP Transcription Factor II, pdb 3CJW  ) and RXRα (Retinoid X Receptor α, pdb 1RD...  ) were selected since they possess the highest consensus scores and share reasonable homologous sequence identity of 38% and 35%, respectively.
Publication Year: 2014
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