SMTL ID : 8zfn.1

Crystal Structure of Human PPARgamma Ligand Binding Domain in Complex with GW9662 and BVT.13

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.54 Å

Oligo State

homo-dimer

Ligands

2 x GW9: 2-chloro-5-nitro-N-phenylbenzamide(Non-covalent)(Covalent)

GW9.1: 15 residues within 4Å: Chain A: F.80, C.83, Q.84, R.86, S.87, I.124, Y.125, L.128, F.161, M.162, H.247, L.251, L.267, Y.271 Ligands: PLB.2 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.80, A:F.80, A:R.86, A:I.124, A:L.128, A:L.128, A:F.161 Hydrogen bonds: A:C.83 GW9.3: 14 residues within 4Å: Chain B: F.80, C.83, Q.84, R.86, S.87, H.121, I.124, Y.125, L.128, F.161, H.247, L.251, D.273 Ligands: PLB.4 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:F.80, B:Q.84, B:R.86, B:I.124, B:L.128, B:F.161 Hydrogen bonds: B:C.83, B:S.87, B:H.247

2 x PLB: 2-[(2,4-DICHLOROBENZOYL)AMINO]-5-(PYRIMIDIN-2-YLOXY)BENZOIC ACID(Non-covalent)

PLB.2: 16 residues within 4Å: Chain A: L.53, F.62, R.78, I.79, G.82, C.83, R.86, L.128, M.132, V.137, I.139, S.140, M.146, L.151, M.162 Ligands: GW9.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:L.53, A:I.79, A:L.128, A:V.137, A:I.139, A:I.139, A:L.151, A:M.162 Hydrogen bonds: A:S.140 pi-Stacking: A:F.62 PLB.4: 19 residues within 4Å: Chain B: L.53, E.57, F.62, H.64, R.78, I.79, G.82, C.83, R.86, L.128, M.132, V.137, I.139, S.140, M.146, L.151, M.162, K.165 Ligands: GW9.3 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:L.53, B:I.79, B:L.128, B:V.137, B:I.139 Hydrogen bonds: B:S.140

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shang, J. et al., Unanticipated mechanisms of covalent inhibitor and synthetic ligand cobinding to PPAR gamma. Elife (2024)

Release Date

2024-08-07

Peptides

Peroxisome proliferator-activated receptor gamma: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Peroxisome proliferator-activated receptor gamma

Related Entries With Identical Sequence