SMTL ID : 3peq.3 (2 other biounits)

PPARd complexed with a phenoxyacetic acid partial agonist

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x 3EQ: [(4-{butyl[2-methyl-4'-(methylsulfanyl)biphenyl-3-yl]sulfamoyl}naphthalen-1-yl)oxy]acetic acid(Non-covalent)

3EQ.1: 22 residues within 4Å: Chain A: L.49, W.58, V.75, F.76, R.78, C.79, T.83, H.117, F.121, L.124, V.128, L.133, V.135, V.142, I.157, I.158, K.161, F.162, H.243, M.247, L.263, Y.267 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:V.75, A:F.76, A:R.78, A:L.124, A:L.124, A:V.128, A:L.133, A:V.135, A:V.142, A:I.157, A:I.158, A:I.158, A:K.161, A:F.162, A:F.162 Hydrogen bonds: A:Y.267 Salt bridges: A:H.117, A:H.243 pi-Stacking: A:H.243 3EQ.8: 21 residues within 4Å: Chain B: L.49, V.75, F.76, R.78, C.79, T.83, H.117, F.121, L.124, V.128, L.133, V.142, L.147, I.157, I.158, K.161, F.162, H.243, M.247, L.263, Y.267 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:V.75, B:F.76, B:R.78, B:F.121, B:L.124, B:V.128, B:L.133, B:V.142, B:L.147, B:I.157, B:I.158, B:I.158, B:I.158, B:K.161, B:F.162, B:F.162 Hydrogen bonds: B:T.83, B:K.161 Salt bridges: B:H.117, B:H.243 pi-Stacking: B:H.243

3 x JZR: hexyl beta-D-glucopyranoside(Non-covalent)

JZR.2: 11 residues within 4Å: Chain A: T.91, V.109, L.112, K.113, E.265, I.266, K.268 Chain B: L.105, N.106, T.110 Ligands: JZR.9 9 PLIP interactions: 4 interactions with chain B, 5 interactions with chain A Hydrophobic interactions: B:L.105, B:N.106, A:L.112, A:I.266 Hydrogen bonds: B:T.110, A:E.265, A:E.265 Water bridges: B:T.110 Salt bridges: A:K.113 JZR.3: 10 residues within 4Å: Chain A: Q.80, A.244, M.247, Q.248, K.251, L.259, L.263, Y.267, K.268, D.269 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:M.247, A:K.251, A:L.259, A:L.263, A:Y.267 Hydrogen bonds: A:K.251, A:K.251, A:D.269 Salt bridges: A:K.251 JZR.9: 12 residues within 4Å: Chain A: L.105, N.106, V.109, T.110 Chain B: T.91, V.109, L.112, K.113, E.265, I.266, K.268 Ligands: JZR.2 12 PLIP interactions: 6 interactions with chain B, 6 interactions with chain A Hydrophobic interactions: B:L.112, B:L.112, B:E.265, B:I.266, A:L.105, A:N.106 Hydrogen bonds: B:E.265, B:K.268, A:N.106, A:T.110 Water bridges: A:N.106, A:N.106

6 x IOD: IODIDE ION(Non-functional Binders)

IOD.4: 2 residues within 4Å: Chain A: N.129, N.169 Ligand excluded by PLIP IOD.5: 1 residues within 4Å: Chain B: M.195 Ligand excluded by PLIP IOD.6: 2 residues within 4Å: Chain A: P.153, M.246 Ligand excluded by PLIP IOD.7: 1 residues within 4Å: Chain A: K.24 Ligand excluded by PLIP IOD.10: 2 residues within 4Å: Chain B: N.129, N.169 Ligand excluded by PLIP IOD.11: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Evans, K.A. et al., Phenoxyacetic acid PPARd partial agonists for the treatment of type 2 diabetes: synthesis, optimization, and in vivo efficacy. Bioorg.Med.Chem.Lett. (2011)

Release Date

2011-10-12

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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