1K74

The 2.3 Angstrom resolution crystal structure of the heterodimer of the human PPARgamma and RXRalpha ligand binding domains respectively bound with GW409544 and 9-cis retinoic acid and co-activator peptides.


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PDB ID Mentions in PubMed Central Article count: 13

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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


Benchmarking and analysis of protein docking performance in Rosetta v3.2.

(2011) PLoS One 6

PubMed: 21829626 | PubMedCentral: PMC3149062 | DOI: 10.1371/journal.pone.0022477

PDB Difficulty | type N 5 µ (N 5 ) [σ(N 5 )] P success Irmsd Classification PDB Difficulty | type N 5 µ (N 5 ) [σ(N 5 )] P success Irmsd Classification 1K74 rigid-body ... O 2 2.5 [1.1] 0.20 1.63 RB sampling 1EER difficult | O 1 0.9 [1.0] 0.02 2.23 BB sampling 1Z5Y rigid-body | O 2 2.4 [1.1] 0.16 1.14 BB sampling 1FAK difficult | O 1 0.9 [0.9] 0.01 3.30 discrimination 1WEJ rigid-body | A 2 2.2 [1.1] 0.14 2.60 discrimination 1TMQ rigid-body | E 1 0.8 [0.9] 0.01 1.47 RB sampling 1HE8 medium | O 2 2.2 [1.1] 0.13 3.19 BB sampling 1I4D rigid-body | O 1 0.8 [0.9] 0.01 3.13 RB sampling 1ATN difficult | O 2 2.1 [1.2] 0.12 1.53 RB sampling 1RLB rigid-body | O 1 0.8 [0.9] 0.01 3.88 RB sampling 2HQS rigid-body | O 2 2.1 [1.2] 0.13 2.69 BB sampling 1Z0K rigid-body | O 1 0.7 [0.8] 0.00 3.56 BB sampling 1JMO difficult | O 2 2.1 [1.2] 0.11 2.82 BB sampling 1EFN rigid-body | O 1 0.7 [0.8] 0.00 3.58 BB sampling 2O8V rigid-body | E 2 2.1 [1.2] 0.12 3.62 BB sampling 1I9R rigid-body | AB 1 0.6 [0.8] 0.00 0.52 RB sampling 1J2J rigid-body | O 2 2.0 [1.4] 0.14 1.10 BB sampling 1AZS rigid-body | O 0 0.5 [0.9] 0.01 5.41 RB sampling 1NSN rigid-body | AB 2 2.0 [1.2] 0.10 1.15 discrimination 2B42 rigid-body | E 0 0.4 [0.6] 0.00 5.85 RB sampling 1K5D medium | O 2 2.0 [1.1] 0.09 2.87 BB sampling 2BTF rigid-body | O 0 0.3 [0.6] 0.00 4.44 BB sampling 1FQ1 difficult | E 2 1.7 [1.3] 0.08 2.18 RB sampling 1KKL medium | E 0 0.2 [0.5] 0.00 4.60 RB sampling 2AJF rigid-body | O 2 1.7 [1.1] 0.06 1.23 RB sampling 1F51 rigid-body | O 0 0.2 [0.5] 0.00 12.35 BB sampling 1E96 rigid-body | O 1 1.6 [1.1] 0.05 3.38 BB sampling 1KAC rigid-body | O 0 0.1 [0.5] 0.00 4.01 BB sampling 1I2M medium | O 1 1.5 [1.0] 0.03 2.68 BB sampling 1MLC rigid-body | A 0 0.1 [0.4] 0.00 4.31 BB sampling 1QFW rigid-body | AB 1 1.5 [1.1] 0.03 1.93 RB sampling 1S1Q rigid-body | O 0 0.1 [0.3] 0.00 4.37 BB sampling 1GLA rigid-body | O 2 1.5 [1.1] 0.05 2.98 BB sampling 1M10 medium | E 0 0.0 [0.0] 0.00 4.46 BB sampling 1AKJ rigid-body | O 1 1.2 [1.0] 0.02 1.48 BB sampling 1A2K rigid-body | O 0 0.0 [0.0] 0.00 5.20 BB sampling 1EZU rigid-body | E 1 1.2 [1.0] 0.02 2.82 RB sampling 1R8S difficult | O 0 0.0 [0.0] 0.00 5.21 BB sampling 1F34 rigid-body | E 1 1.2 [1.0] 0.02 4.00 RB sampling 1GP2 medium | O 0 0.0 [0.0] 0.00 5.23 BB sampling 1GRN medium | O 1 1.1 [1.0] 0.02 1.24 BB sampling 1IBR difficult | O 0 0.0 [0.0] 0.00 5.46 RB sampling 1NW9 medium | E 1 1.1 [1.0] 0.02 2.33 BB sampling 1BKD difficult | O 0 0.0 [0.0] 0.00 5.62 BB sampling 2H7V medium | O 1 1.1 [1.0] 0.02 3.65 BB sampling 2OT3 difficult | O 0 0.0 [0.0] 0.00 6.00 BB sampling 1GHQ rigid-body | O 1 1.0 [1.0] 0.01 2.69 BB sampling 1FQJ rigid-body | O 0 0.0 [0.0] 0.00 6.48 RB sampling 2NZ8 medium | O 1 1.0 [1.0] 0.02 3.91 BB sampling 1PXV difficult | E 0 0.0 [0.0] 0.00 9.49 BB sampling 1IB1 medium | O 1 1.0 [1.0] 0.01 3.95 discrimination 1H1V difficult | O 0 0.0 [0.0] 0.00 9.96 BB sampling 1K4C rigid-body | AB 1 1.0 [1.1] 0.02 2.15 BB sampling 1Y64 difficult | O 0 0.0 [0.0] 0.00 13.70 discrimination 1EWY rigid-body | E 1 1.0 [1.1] 0.02 3.01 BB sampling 1DQJ rigid-body | A 0 0.0 [0.2] 0.00 6.15 BB sampling 2PCC rigid-body | E 1 1.0 [0.9] 0.01 3.38 discrimination 1ACB medium | E 0 0.0 [0.1] 0.00 4.56 RB sampling 1KLU rigid-body | O 0 0.0 [0.1] 0.00 8.16 BB sampling Unsuccessful docking predictions are classified as cases for which the five lowest-energy decoys did not contain at least three near-native structures.

Publication Year: 2011


Design novel dual agonists for treating type-2 diabetes by targeting peroxisome proliferator-activated receptors with core hopping approach.

(2012) PLoS One 7

PubMed: 22685582 | PubMedCentral: PMC3369836 | DOI: 10.1371/journal.pone.0038546

g001 Figure 1 Illustration to show the conformation obtained by docking GW409544 and Comp#1, respectively, to (A) PPARα (1k7l) and (B) PPARγ (1k74).

Shown in Fig. 1 is the docked conformation of Comp#1 when aligned with GW409544 extracted from ( A ) the crystal complex in PPARα (1k7l) and ( B ) the crystal complex in PPARγ (1k74), respectively.

For a comparison study, the 10 ns molecular dynamics simulations were performed, respectively, for the crystal structures of PPARα (1k7l), PPARγ (1k74), as well as their complexes with GW409544 and Comp#1, i.e., PPARα-GW409544, PPARγ-GW409544, PPARα-Comp#1, and PPARγ-Comp#1.

The binding-site encompassed the ligand GW409544, which was observed in the crystal structures of both PPARα (1k71) and PPARγ (1k74) as a ligand.

The representative complex crystal structures of PPARα (PDB ID 1k7l) and PPARγ (PDB ID 1k74) with the same ligand GW409544 [37] were download from the PDB Bank [38] , and were to be used for the molecular modelling studies.

Preparation of Receptor Structures and Databases The proteins with PDB codes 1k71 and 1k74 were chosen for modeling.

Publication Year: 2012


Scaffold-based pan-agonist design for the PPAR?, PPAR? and PPAR? receptors.

(2012) PLoS One 7

PubMed: 23119024 | PubMedCentral: PMC3485212 | DOI: 10.1371/journal.pone.0048453

pdb [6] and 1k74.

pdb) and PPARγ receptors (1k74.

Publication Year: 2012


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/ ) [33] , [34] 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


Find novel dual-agonist drugs for treating type 2 diabetes by means of cheminformatics.

(2013) Drug Des Devel Ther 7

PubMed: 23630413 | PubMedCentral: PMC3623550 | DOI: 10.2147/DDDT.S42113

Modeling of PPAR agonist complex The best ten potential lead compounds or candidates obtained via the above step were redocked into the two receptors, PPARα (1k71) and PPARγ (1k74), re... pectively.

pdb) having 2.50 Å and the other (1k74.

45 – 47 The binding site encompassed the ligand GW409544, which was observed in the crystal structures of both PPARα (1k7l) and PPARγ (1k74).

As shown in the panels A and B of Figure 1 , the best docked poses of the ten compounds are superposed together in the active pockets of the two receptors, PPARα (1k71) and PPARγ (1k74), respectively.

pdb) and PPARγ (1k74.

41 , 42 Materials and methods The representative complex crystal structures of PPARα (Protein Data Bank [PDB] ID 1k7l) and PPARγ (PDB ID 1k74) were downloaded from the PDB, 43 , 44 and were to be used for the molecular modeling studies.

Publication Year: 2013


A tandem regression-outlier analysis of a ligand cellular system for key structural modifications around ligand binding.

(2013) J Cheminform 5

PubMed: 23627990 | PubMedCentral: PMC3648400 | DOI: 10.1186/1758-2946-5-21

Figure  3 shows that, around the bound structure of the 1K47 ligand, a important ES symbol, ssO, can detect the key interaction between 1K74 ligand ether oxygen and Cys285 side-chain sulfur (3... 63 Å) or Met364 sulfur (4.87 Å).

We then look at the crystallographic image of the 1K74 ligand-PPARγ complex (PDB code: 1K47) [ 36 ].

Around a bound structure of 1K47 ligand (PDB: 1k47), the important ES symbol ssO can detect the key interaction between 1K74 ligand ether oxygen and Cys285 side-chain sulfur (3.63 Å) or Met364 sulfur (4.87 Å).

Publication Year: 2013


The crystal structure of the orphan nuclear receptor NR2E3/PNR ligand binding domain reveals a dimeric auto-repressed conformation.

(2013) PLoS One 8

PubMed: 24069298 | PubMedCentral: PMC3771917 | DOI: 10.1371/journal.pone.0074359

Overlay of the NR2E3 LBD structure with the SRC1 LXXLL motif (in green) from the RXR structure (1K74).

Publication Year: 2013


A network pharmacology approach to understanding the mechanisms of action of traditional medicine: Bushenhuoxue formula for treatment of chronic kidney disease.

(2014) PLoS One 9

PubMed: 24598793 | PubMedCentral: PMC3943740 | DOI: 10.1371/journal.pone.0089123

Protein Targets Name Gene Symbol PDB-ID Positive Drugs Cutoff Value No a Known target proteins Carbonic anhydrase II CA2 1BN3 Topiramate −8.4 10 Raf kinase RAF1 1C1Y Sorafenib −9.6 12 ... acrophage migration inhibitory factor MIF 1GCZ ethyl 7-hydroxy-2-oxochromene-3-carboxylate −8.9 10 Hepatocyte growth factor HGF 1GMO N,O6-Disulfo-Glucosamine −7 79 Hypoxia-inducible factor 1α HIF1A 1H2K Everolimus −6.3 66 Soluble epoxide hydrolase EPHX2 1ZD3 4-{[(cyclohexylamino)carbonyl]amino} butanoic acid −7.4 15 Carbonic anhydrase XII CA12 1JD0 Hydrochlorothiazide −6.9 26 Peroxisome proliferator-activated receptor PPARG 1K74 Fenofibrate −9.4 39 Angiotensin converting enzyme ACE 1O86 Candoxatril −9 74 Monoamine oxidase B MAOB 1OJ9 Pargyline −9.2 39 Mitogen-activated protein kinase 1 MAPK1 1PME 4-[4-(4-fluorophenyl)-2-[4-[(S)-methylsulfinyl]phenyl]-1H-imidazol-5-yl] pyridine −9.4 27 Mast stem cell growth factor receptor KIT 1T46 Sorafenib −10.1 34 Thymidine phosphorylase TYMP 1UOU Chloro-6-[(2-Iminopyrrolidin-1-Yl)Methyl]Pyrimidine-2,4(1 h,3 h)-Dione −7.7 76 Macrophage metalloelastase MMP12 1UTT (6R)-4-benzyl-6-(1-methyl-2,2-dioxido-1,3-dihydro-2,1-benzisothiazol-5-yl)morpholin-3-one −10.6 6 β2 adrenergic receptor ADRB2 3D4S Carvedilol −9.3 45 Adenosine A2α receptor ADORA2A 3EML Mefloquine −9.8 71 C-C chemokine receptor type 1 CCR1 1Y5D Maraviroc −8.2 35 Mitogen-activated protein kinase 14 MAPK14 1ZZ2 N-[(3z)-5-Tert-Butyl-2-Phenyl-1,2-Dihydro-3h-Pyrazol-3-Ylidene]-N ′ -(4-Chlorophenyl)Urea −8.4 14 Lymphocyte function-associated antigen ITGAL 1CQP Lovastatin −7.2 0 Vasopressin V1α receptor AVPR1A 1YTV Conivaptan −10.5 20 Placeta growth factor PGF 1FZV Suplatast tosylate −5 25 Transforming growth factor beta 1 TGFB1 1KLD NO ligand Tumor necrosis factor ligand superfamily member 5 TNFSF5 1I9R NO ligand Nuclear factor NF-κB NFKB1 1NFI NO ligand Carbonic anhydrase IV CA4 1ZNC NO ligand C-C motif chemokine-2 CCL2/MCP1 2BDN NO ligand DNA-directed RNA polymerase II 19 kDa polypeptide POLR2D 2C35 NO ligand Carbonic anhydrase IX CA9 2HKF NO ligand Known target proteins Plasminogen activator inhibitor-1 SERPINE1 1OC0 NO ligand RAC-α serine/threonine kinase No symbol 1AO2 NO ligand Protein-glutamine γ-glutamyltransferase TGM2 2Q3Z NO ligand Putative targets Tyrosine-protein kinase BTK BTK 3OCS Staurosporine −9.6 53 Small inducible cytokine A5 CCL5 1U4M Heparin_Disaccharide_I-S −6 15 Epidermal growth factor receptor EGFR 2GS7 Flavopiridol −9 19 Estrogen receptor ESR1 3Q97 Estradiol −10 1 Heat shock cognate 71 kDa protein HSPA8 3FZK (2R,3R,4S,5R)-2-[6-amino-8-[(3,4-dichlorophenyl)methylamino]purin-9-yl]-5-(hydroxymethyl)oxolane-3,4-diol −8.2 34 Insulin receptor INSR 2HR7 Hydrochloride) −9.5 21 Proto-oncogene tyrosine-protein kinase LCK LCK 3AC1 N-(2-chloro-6-methylphenyl)-8-[(3S)-3-methylpiperazin-1-yl]imidazo[1,5-a]quinoxalin-4-amine −8.2 60 Hepatocyte nuclear factor 4-alpha HNF4A 1PZL 1_methyl_2-nitro_benzo[e]benzofuran −7.4 79 Glucocorticoid receptor NR3C1 3K22 Flunisolide −10 26 Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha isoform PIK3CA 3HHM Wortmannin −9.1 20 Plasminogen activator, tissue PLAT 1A5H Iloprost −8.5 87 Acyl-CoA dehydrogenase family member 8, mitochondrial ACTN1 1RX0 Methacrylyl-Coenzyme_A −9 16 Protein tyrosine phosphatase PTPN1 1BZH (Oxalyl-Amino)-Naphthalene-2-Carboxylic_Acid −8 19 Protein kinase C, beta PRKCB 2I0E Vitamin_E −9.7 13 E3 ubiquitin protein ligase VHL 3ZRC 4-((naphthalen-2-ylamino)methyl)benzene-1,2-diol −7.7 21 FYN oncogene related to SRC, FGR, YES FYN 1AOT 2,5,8,11-Tetraoxadodecane −6.6 29 9-mer from C-C chemokine receptor type 5 CCR5 2RLL NO ligand Fc fragment of IgG, low affinity IIb, receptor (CD32) FCGR2B 2FCB NO ligand Fibronectin 1 FN1 3MQL NO ligand Myeloma immunoglobulin D lambda IGHG1 1ZVO NO ligand Solute carrier family 4 SLC4A1 1BTT NO ligand Signal transducer and activator of transcription STAT1 1BF5 NO ligand Jun proto-oncogene JUN 1FOS NO ligand KIAA0101 KIAA0101 No PDB data Catechol-O-methyltransferase COMT No PDB data Protein Targets Name Gene Symbol PDB-ID Positive Drugs Cutoff Value No Putative targets Decorin DCN No PDB data Clusterin CLU No PDB data Transforming growth factor, beta receptor 1 TGFBR1 No PDB data Interleukin 8 IL8 No PDB data Apolipoprotein A–I APOA1 No PDB data Signal transducer and activator of transcription 5B STAT5B No PDB data No a : The number of effective molecular docking.

Publication Year: 2014


Encounter complexes and dimensionality reduction in protein-protein association.

(2014) Elife 3

PubMed: 24714491 | PubMedCentral: PMC3978769 | DOI: 10.7554/eLife.01370

The PDB entry of the complex is 1K74, but we docked the unbound (separately crystallized) RXRα and PPARγ structures rather than the components from the complex.

Shape of the energy landscape along the five PCA eigenvectors for the complex of PPAR-γ and RXR-α (PDB code 1K74).

Publication Year: 2014


Molecular modelling study of the PPAR? receptor in relation to the mode of action/adverse outcome pathway framework for liver steatosis.

(2014) Int J Mol Sci 15

PubMed: 24857909 | PubMedCentral: PMC4057697 | DOI: 10.3390/ijms15057651

Figure 6 illustrates the ligand-protein interactions of rosiglitazone in the PPARγ complex 1FM6 and GW409544 (PDB ligand ID 544) in complex 1K74 [ 25 ].

Publication Year: 2014


Protein-protein docking with dynamic residue protonation states.

(2014) PLoS Comput Biol 10

PubMed: 25501663 | PubMedCentral: PMC4263365 | DOI: 10.1371/journal.pcbi.1004018

Docking plots generated using RosettaDock and pHDock for (A) tumor susceptibility gene 101 protein–Ubiquitin complex (1S1Q; pH 4.6), (B) PPARgamma+RXRalpha–GW409544+co-activator peptid... complex (1K74; pH 7.5), and (C) CDK2 kinase–cell cycle-regulatory protein CksHs1 complex (1BUH; pH 7.5).

Publication Year: 2014


PubMed ID is not available.

Published in 2015

PubMedCentral: PMC4372819

For instance, GW409544 that binds into both the LBP1 and LBP2 (PDB: 1K74) 30 has very good overlap with APOLAR FragMaps A1, A2, and A3 (Figure 2 C), leading to a favorable LGFE that correlates with it... high binding affinity compared to the partial agonist decanoic acid or the thiazolidinediones such as the rosiglitazone.

Similarly, simulations with the decanoic acid-bound conformation of the LBP of PPARγ identify favorable water affinities close to S342, which align well with the crystal water that mediates interactions between S342 and GW409544 in PDB 1K74.

Figure 2 PPARγ FragMaps overlaid on the LBP of PPARγ (PDB 3U9Q) with ligands A) decanoic acid, B) Rosiglitazone (PDB: 2PRG,) C) GW409544 (PDB: 1K74), and D) Cerco-A (PDB: 3B1M) in their crystallographic orientations; receptor atoms occluding the view of the binding pocket were removed to facilitate visualization.

Publication Year: 2015