SMTL ID : 8aty.1

Crystal structure of PPAR gamma (PPARG) in complex with JP85 (compound 1).

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

monomer

Ligands

2 x O7O: 2-[4-chloranyl-6-(5,6,7,8-tetrahydronaphthalen-1-ylamino)pyrimidin-2-yl]sulfanylethanoic acid(Non-covalent)

O7O.1: 18 residues within 4Å: Chain A: F.82, C.85, Q.86, R.88, S.89, I.126, Y.127, L.130, L.133, V.139, L.140, F.163, M.164, K.167, H.249, L.253, Y.273 Ligands: O7O.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:R.88, A:I.126, A:L.130, A:L.133, A:V.139 Hydrogen bonds: A:C.85, A:Q.86, A:S.89 Water bridges: A:Y.273 Salt bridges: A:H.249 O7O.2: 14 residues within 4Å: Chain A: I.49, L.55, E.59, I.62, F.64, Q.73, R.80, G.84, C.85, R.88, I.141, S.142, M.148 Ligands: O7O.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:E.59, A:I.62, A:F.64, A:R.80 Hydrogen bonds: A:E.59, A:S.142 Water bridges: A:E.143 Salt bridges: A:R.88

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 3 residues within 4Å: Chain A: R.34, N.135, K.136 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.34, A:K.136 Water bridges: A:R.34 GOL.4: 3 residues within 4Å: Chain A: K.136, D.137, E.151 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.137 Water bridges: A:R.150 GOL.5: 5 residues within 4Å: Chain A: K.65, H.66, V.90, E.91, Q.94 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.94, A:H.266 GOL.6: 4 residues within 4Å: Chain A: V.93, L.118, K.119, I.272 No protein-ligand interaction detected (PLIP) GOL.7: 4 residues within 4Å: Chain A: K.173, L.177, K.234, K.238 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.173, A:K.234, A:K.238

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Arifi, S. et al., Targeting the Alternative Vitamin E Metabolite Binding Site Enables Noncanonical PPAR gamma Modulation. J.Am.Chem.Soc. (2023)

Release Date

2023-07-12

Peptides

Peroxisome proliferator-activated receptor gamma: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Peroxisome proliferator-activated receptor gamma

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