SMTL ID : 5y7x.1

Human Peroxisome proliferator-activated receptor (PPAR) delta in complexed with a potent and selective agonist

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x 8RR: 2-[2-methyl-4-[[4-methyl-2-[4-(trifluoromethyl)phenyl]-1,3-selenazol-5-yl]methylsulfanyl]phenoxy]ethanoic acid(Non-covalent)

8RR.1: 17 residues within 4Å: Chain A: W.79, V.96, F.97, R.99, C.100, T.103, T.104, H.138, F.142, L.145, V.156, V.163, K.182, H.264, M.268, L.284, Y.288 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:V.96, A:F.97, A:R.99, A:F.142, A:V.156 Hydrogen bonds: A:T.104, A:T.104 Salt bridges: A:H.138, A:H.264 pi-Stacking: A:H.264 8RR.6: 19 residues within 4Å: Chain B: W.79, V.96, F.97, R.99, C.100, Q.101, T.103, T.104, H.138, F.142, L.145, L.154, V.156, V.163, K.182, H.264, M.268, L.284, Y.288 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:V.96, B:F.97, B:R.99, B:T.104, B:F.142, B:V.156 Hydrogen bonds: B:T.104, B:Y.288 Salt bridges: B:H.138, B:H.264 pi-Stacking: B:H.264

1 x K: POTASSIUM ION(Non-covalent)

K.2: 4 residues within 4Å: Chain A: R.49, V.149, N.150, N.190 No protein-ligand interaction detected (PLIP)

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain B: N.150, N.190 Ligand excluded by PLIP

1 x PGO: S-1,2-PROPANEDIOL(Non-covalent)

PGO.4: 6 residues within 4Å: Chain A: I.51, L.52, P.61, V.63, N.150, F.162 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.52, A:N.150

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

JZR.5: 14 residues within 4Å: Chain A: V.108, T.112, V.130, L.133, K.134, L.283, E.286, I.287, K.289 Chain B: L.126, N.127, V.130, T.131 Ligands: JZR.8 13 PLIP interactions: 8 interactions with chain A, 5 interactions with chain B Hydrophobic interactions: A:L.133, A:L.133, A:E.286, A:I.287, B:L.126, B:N.127 Hydrogen bonds: A:K.134, A:K.289, B:N.127 Salt bridges: A:K.134, A:K.289 Water bridges: B:N.127, B:N.127 JZR.8: 14 residues within 4Å: Chain A: L.126, N.127, V.130, T.131 Chain B: V.108, T.112, V.130, L.133, K.134, L.283, E.286, I.287, K.289 Ligands: JZR.5 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:V.108, B:L.133, B:E.286, B:I.287, A:L.126 Hydrogen bonds: B:E.286, B:K.289, A:N.127 Water bridges: B:E.286, A:N.127 Salt bridges: B:K.134, B:K.289

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kim, H.J. et al., Highly potent and selective PPAR delta agonist reverses memory deficits in mouse models of Alzheimer's disease. Theranostics (2024)

Release Date

2018-08-01

Peptides

Peroxisome proliferator-activated receptor delta: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Peroxisome proliferator-activated receptor delta