SMTL ID : 8hf8.1

Human PPAR delta ligand binding domain in complex with a synthetic agonist V1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.11 Å

Oligo State

homo-dimer

Ligands

2 x LOO: 2-[4-[[2,5-bis(oxidanylidene)-3-[4-(trifluoromethyl)phenyl]imidazolidin-1-yl]methyl]-2,6-dimethyl-phenoxy]-2-methyl-propanoic acid(Non-covalent)

LOO.1: 23 residues within 4Å: Chain A: I.54, L.60, W.69, V.86, F.87, R.89, C.90, Q.91, T.93, T.94, H.128, F.132, L.135, L.144, V.146, V.153, F.157, L.158, I.169, H.254, M.258, L.274, Y.278 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.86, A:F.87, A:F.87, A:R.89, A:F.132, A:V.146, A:V.153, A:V.153, A:L.158, A:I.169 Hydrogen bonds: A:Y.278 Salt bridges: A:H.128, A:H.254 LOO.3: 23 residues within 4Å: Chain B: I.54, L.60, W.69, V.86, F.87, R.89, C.90, Q.91, T.93, T.94, H.128, F.132, L.135, L.144, V.146, V.153, L.158, I.168, I.169, H.254, M.258, L.274, Y.278 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:V.86, B:R.89, B:F.132, B:V.146, B:V.153, B:L.158, B:I.168, B:I.169 Hydrogen bonds: B:T.94 Salt bridges: B:H.128, B:H.254

2 x BOG: octyl beta-D-glucopyranoside(Non-covalent)

BOG.2: 18 residues within 4Å: Chain A: S.112, S.113, L.114, F.115, L.116, N.117, Q.119 Chain B: V.98, R.99, T.102, E.103, K.106, V.120, L.123, K.124, L.273, E.276, I.277 10 PLIP interactions: 5 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:N.117, B:T.102, B:L.123, B:K.124, B:I.277 Hydrogen bonds: A:S.112, A:L.116, A:Q.119, B:E.103 Water bridges: A:R.210 BOG.4: 17 residues within 4Å: Chain A: V.98, R.99, T.102, E.103, V.120, L.123, K.124, L.273, E.276, I.277 Chain B: S.112, S.113, L.114, F.115, L.116, N.117, Q.119 13 PLIP interactions: 6 interactions with chain B, 7 interactions with chain A Hydrophobic interactions: B:F.115, B:N.117, A:V.98, A:V.120, A:L.273, A:E.276, A:I.277 Hydrogen bonds: B:S.112, B:S.113, B:L.116, B:Q.119 Water bridges: A:K.106, A:K.106

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Feng, Z. et al., Discovery of the First Subnanomolar PPAR alpha / delta Dual Agonist for the Treatment of Cholestatic Liver Diseases. J.Med.Chem. (2023)

Release Date

2023-09-06

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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