SMTL ID : 7vwe.1

Human peroxisome proliferator-activated receptor (PPAR) delta ligand binding domain in complex with a synthetic partial agonist JK122

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-dimer

Ligands

2 x B7G: heptyl beta-D-glucopyranoside(Non-covalent)

B7G.1: 12 residues within 4Å: Chain A: V.92, V.114, K.118, L.267, E.270, I.271, K.273, D.274 Chain B: L.110, N.111, T.115 Ligands: B7G.3 13 PLIP interactions: 8 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:V.92, A:L.267, A:E.270, A:I.271, B:L.110, B:N.111 Hydrogen bonds: A:E.270, A:K.273, A:D.274, B:N.111, B:T.115, B:T.115 Salt bridges: A:K.118 B7G.3: 13 residues within 4Å: Chain A: L.110, N.111, T.115 Chain B: V.92, T.96, V.114, L.117, K.118, L.267, E.270, I.271, K.273 Ligands: B7G.1 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:V.92, B:L.117, B:L.117, B:K.118, B:L.267, B:I.271, A:L.110, A:N.111 Hydrogen bonds: B:E.270, B:E.270, B:K.273, A:T.115

2 x 81O: 5-[4-butoxy-3-[[[2-fluoranyl-4-(trifluoromethyl)phenyl]carbonylamino]methyl]phenyl]-4,6-dimethyl-pyridine-3-carboxylic acid(Non-covalent)

81O.2: 24 residues within 4Å: Chain A: I.48, L.54, V.80, F.81, R.83, C.84, T.87, T.88, H.122, F.126, L.129, V.133, L.138, V.140, V.147, I.162, I.163, K.166, F.167, A.170, H.248, M.252, L.268, Y.272 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:V.80, A:R.83, A:F.126, A:L.129, A:L.129, A:V.133, A:V.140, A:I.162, A:I.163, A:K.166, A:K.166, A:F.167, A:A.170 Hydrogen bonds: A:T.87, A:T.88, A:T.88 Salt bridges: A:H.122, A:H.248 pi-Stacking: A:H.248 81O.4: 25 residues within 4Å: Chain B: I.48, L.54, W.63, V.80, F.81, R.83, C.84, T.87, T.88, H.122, F.126, L.129, V.133, L.138, V.140, V.147, I.162, I.163, K.166, F.167, A.170, H.248, M.252, L.268, Y.272 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:V.80, B:R.83, B:F.126, B:V.133, B:V.140, B:I.162, B:I.163, B:F.167, B:A.170 Hydrogen bonds: B:T.88, B:Y.272 Salt bridges: B:H.122, B:H.248 pi-Stacking: B:H.248

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Oyama, T. et al., Crystal structures of the ligand-binding domain of human peroxisome proliferator-activated receptor delta in complexes with phenylpropanoic acid derivatives and a pyridine carboxylic acid derivative. Acta Crystallogr.,Sect.F (2022)

Release Date

2022-02-09

Peptides

Peroxisome proliferator-activated receptor delta: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Peroxisome proliferator-activated receptor delta

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