SMTL ID : 9vnx.1

Crystal Structure of the mutant ROR gamma LBD With Compound 28

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 Å

Oligo State

hetero-1-1-mer

Ligands

1 x 01: (2~{R})-~{N}-[5-(5-cyano-6-propan-2-yloxy-pyridin-3-yl)-1-(trifluoromethyl)pyrazol-3-yl]-1-ethanoyl-4-propan-2-ylsulfonyl-piperazine-2-carboxamide

01.1: 23 residues within 4Å: Chain A: Q.26, L.27, W.57, C.60, H.63, L.64, A.67, M.98, V.101, R.104, M.105, A.108, V.116, F.117, F.118, E.119, F.128, C.133, L.136, I.137, I.140, F.141, H.219 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:W.57, A:W.57, A:L.64, A:A.67, A:V.101, A:R.104, A:I.140 Hydrogen bonds: A:F.117, A:E.119 pi-Stacking: A:F.118

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.2: 6 residues within 4Å: Chain A: M.53, W.57, L.131, G.132, R.222, I.225 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.132, A:R.222, A:R.222 EDO.3: 5 residues within 4Å: Chain A: Q.235, A.236, F.238, P.240, K.243 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.236, A:K.243 EDO.4: 5 residues within 4Å: Chain A: L.29, C.106, R.107, S.148, F.152 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.148

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.5: 4 residues within 4Å: Chain A: H.198, R.199, Q.200, S.201 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:H.198 Hydrogen bonds: A:Q.200, A:S.201

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fukuda, S. et al., A Concise and Modular Approach to Generate Novel ROR gamma Agonists. J.Med.Chem. (2025)

Release Date

2025-07-30

Peptides

Nuclear receptor ROR-gamma: A
Nuclear receptor coactivator 1: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Nuclear receptor ROR-gamma

Nuclear receptor coactivator 1

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