Citations in PubMed

Primary Citation PubMed: 19172745 Citations in PubMed

PDB ID Mentions in PubMed Central Article count: 5

Citations in PubMed

This linkout lists citations, indexed by PubMed, to the Primary Citation for this PDB ID.

PDB ID Mentions in PubMed Central

Data mentions are occurrences of PDB IDs in the full text articles from the PubMedCentral Open Access Subset of currently about 1 million articles. For each article, the sentences containing the PDB ID are listed. Article titles can be filtered by keywords and sorted by year.

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Dietary ?-eleostearic acid ameliorates experimental inflammatory bowel disease in mice by activating peroxisome proliferator-activated receptor-?.

(2011) PLoS One 6

PubMed: 21904603 | PubMedCentral: PMC3164124 | DOI: 10.1371/journal.pone.0024031

PDB Ligand ID PDB ID Reference Ligand Name 1 243 2VST [46] 13-hydroxyoctadecadienoic acid(13-HODE) 570 1FM9 [37] GI262570(Farglitazar) 4HD 2VV1 [46] (4S,5E,7Z,10Z,13Z,16Z,19Z)-4-hydroxydocosa-5,7,10,1... ,16,19-hexaenoic acid(4-HDHA) 9HO 2VSR [46] 9-hydroxyoctadecadienoic acid(9-HODE) DRH 2I4P [45] (2S)-2-[4-[2-(1,3-benzoxazol-2-yl-heptyl-amino)ethyl]phenoxy]-2-methyl-butanoic acid((2S)-ureidofibrate-like derivative) DRJ 2I4J [45] (2R)-2-[4-[2-(1,3-benzoxazol-2-yl-heptyl-amino)ethyl]phenoxy]-2-methyl-butanoic acid((2R)-ureidofibrate-like derivative) DRY 2HWQ [44] [(1-{3-[(6-benzoyl-1-propyl-2-naphthyl)oxy]propyl}-1H-indol-5-yl)oxy]acetic acid(5-substituted indoleoxyacetic acid analogue) EHA 2F4B [43] (5-{3-[(6-benzoyl-1-propyl-2-naphthyl)oxy]propoxy}-1H-indol-1-yl)acetic acid(Indol-1-yl acetic acid) ET1 3ET3 [47] 3-[5-methoxy-1-(4-methoxyphenyl)sulfonyl-indol-3-yl] propanoic acid(indeglitazar) HXA 2VV0 [46] Docosa-4,7,10,13,16,19-hexaenoic acid PTG 2ZK12ZK2 [48] 15-deoxy-delta(12,14)-prostaglandin J2 (PTG) Ligand IDs from respective PDB files were used.

Publication Year: 2011


Network pharmacology-based prediction of the multi-target capabilities of the compounds in Taohong Siwu decoction, and their application in osteoarthritis.

(2013) Exp Ther Med 6

PubMed: 23935733 | PubMedCentral: PMC3735841 | DOI: 10.3892/etm.2013.1106

Protein PDB code ADAMTS-4 2RJP TNF-α 2AZ5 iNOS 2Y37 COX-1 3NT1 COX-2 3N8X MMP-1 966C MMP-3 1C3I MMP-8 1ZS0 MMP-9 1GKC MMP-12 3RTS MMP-13 3I7I VDR 1DB1 PPARγ 2VSR CDK2 3PXY HO-1 3TGM PD... , Protein Data Bank; ADAMTS-4, aggrecanase-1; TNF-α, tumor necrosis factor-α; iNOS, inducible nitric oxide synthase; COX, cyclooxygenase; MMP, matrix metalloproteinase; VDR, vitamin D nuclear receptor; PPARγ, peroxisome proliferator activated receptor-γ, CDK2, cyclin-dependent kinase-2; HO-1, heme oxygenase.

Publication Year: 2013


Honokiol: a non-adipogenic PPAR? agonist from nature.

(2013) Biochim Biophys Acta 1830

PubMed: 23811337 | PubMedCentral: PMC3790966 | DOI: 10.1016/j.bbagen.2013.06.021

2.9 Molecular docking Docking experiments of honokiol into the hPPARγ ligand binding domain (Protein Data Bank, www.pdb.org , PDB ID: 2VSR [24] ) were performed using the CDOCKER module of Dis... overy Studio 2.5 ( www.accelrys.com ) with default settings.

Publication Year: 2013


An alternate binding site for PPAR? ligands.

(2014) Nat Commun 5

PubMed: 24705063 | PubMedCentral: PMC4070320 | DOI: 10.1038/ncomms4571

(e) Co-crystal structure of the PPARγ LBD bound to two molecules of 9-(S)-HODE (PDB: 2VSR).

Publication Year: 2014


Natural product agonists of peroxisome proliferator-activated receptor gamma (PPAR?): a review.

(2014) Biochem Pharmacol 92

PubMed: 25083916 | PubMedCentral: PMC4212005 | DOI: 10.1016/j.bcp.2014.07.018

Depicted in Fig. 2 are the binding modes of a selection of ligands co-crystallized with the PPARγ LBD: the full thiazolidinedione agonist rosiglitazone (protein data bank (PDB) [200] entry PDB... 4ema [199] , Fig. 2 B); (9 S ,10 E ,12 Z )-9-hydroxyoctadeca-10,12-dienoic acid (9-( S )-HODE) as a representative endogenous ligand that binds as a homodimer (PDB: 2vsr [43] , Fig. 2 C); the natural product amorfrutin B (PDB: 4a4w [197] , Fig. 2 D); the neolignan magnolol that binds as a homodimer (PDB: 3r5n [193] , Fig. 2 E); and the flavonoid luteolin binding concomitantly with myristic acid (PDB: 3sz1 [195] , Fig. 2 F).

Observed protein-ligand interactions are presented between the human PPARγ LBD and (B) the synthetic agonist rosiglitazone (PDB: 4ema), (C) the endogenous agonist 9-( S )-HODE binding as a homodimer (PDB: 2vsr), the natural ligands (D) amorfrutin B (PDB: 4a4w), (E) magnolol binding as homodimer (PDB: 3r5n), and (F) luteolin binding as a mixed dimer with myristic acid (PDB: 3sz1).

Whereas just one molecule of the thiazolidinedione agonists such as rosiglitazone is binding to the LBD (PDB: 4ema [199] , Fig. 2 B), some endogenous ligands such as 9-( S )-HODE were demonstrated to activate the receptor as homodimers (PDB: 2vsr [43] , Fig. 2 C).

Publication Year: 2014