SMTL ID : 9knc.1

Crystal structure of human ERRg LBD in complex with 6-nitroindole

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.90 Å

Oligo State

hetero-2-2-mer

Ligands

2 x 01: 6-nitro-1~{H}-indole

01.1: 13 residues within 4Å: Chain A: L.61, L.64, A.65, E.68, M.99, L.102, I.103, V.106, Y.119, L.138, I.142, A.224, F.228 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:L.64, A:A.65, A:L.102, A:V.106 Water bridges: A:V.106 pi-Stacking: A:Y.119, A:Y.119 01.8: 13 residues within 4Å: Chain C: L.61, L.64, A.65, E.68, M.99, L.102, I.103, V.106, Y.119, L.138, I.142, A.224, F.228 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:L.64, C:A.65, C:L.102, C:V.106 Water bridges: C:V.106 pi-Stacking: C:Y.119, C:Y.119

12 x PGR: R-1,2-PROPANEDIOL(Non-covalent)

PGR.2: 4 residues within 4Å: Chain A: I.42, Y.43, M.45, R.67 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.43, A:R.67 PGR.3: 8 residues within 4Å: Chain A: E.40, K.41, I.42, L.64, E.68, R.109, Y.119, A.120 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:K.41 Hydrogen bonds: A:E.40, A:I.42, A:E.68 PGR.4: 5 residues within 4Å: Chain A: K.232, V.237, P.238, M.239, L.244 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.237, A:M.239 Water bridges: A:G.235 PGR.5: 7 residues within 4Å: Chain A: G.81, T.84, L.85, A.180, K.183, L.184, V.187 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:K.183 Hydrogen bonds: A:G.81 PGR.6: 4 residues within 4Å: Chain A: S.83, T.84, L.85, S.86 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.83 Water bridges: A:L.87 PGR.7: 3 residues within 4Å: Chain A: K.41, Y.108, K.156 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:Y.108 PGR.9: 4 residues within 4Å: Chain C: I.42, Y.43, M.45, R.67 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:Y.43, C:R.67 PGR.10: 8 residues within 4Å: Chain C: E.40, K.41, I.42, L.64, E.68, R.109, Y.119, A.120 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:K.41 Hydrogen bonds: C:E.40, C:I.42, C:E.68 PGR.11: 5 residues within 4Å: Chain C: K.232, V.237, P.238, M.239, L.244 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:V.237, C:M.239 Water bridges: C:G.235 PGR.12: 7 residues within 4Å: Chain C: G.81, T.84, L.85, A.180, K.183, L.184, V.187 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:K.183 Hydrogen bonds: C:G.81 PGR.13: 4 residues within 4Å: Chain C: S.83, T.84, L.85, S.86 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:S.83 Water bridges: C:L.87 PGR.14: 3 residues within 4Å: Chain C: K.41, Y.108, K.156 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:Y.108

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shuai, Y.Y. et al., Identification of indoles as potential endogenous ligands of ERR gamma and their modulation on drug binding. Acta Pharmacol.Sin. (2025)

Release Date

2025-04-16

Peptides

Estrogen-related receptor gamma: AC
Nuclear receptor-interacting protein 1: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
C

D
C

Estrogen-related receptor gamma

Nuclear receptor-interacting protein 1

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