SMTL ID : 9fzg.1

Crystal structure of the hPXR-LBD in complex with compound JMV7035

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x 01: 2-(1-adamantyl)-~{N}-[2-[2-[2-oxidanylidene-2-[7-[1-(phenylmethyl)-5-[(2,4,6-trimethylphenyl)sulfonylamino]benzimidazol-2-yl]heptylamino]ethoxy]ethoxy]ethyl]ethanamide

01.1: 21 residues within 4Å: Chain A: S.90, L.91, I.118, L.121, M.125, S.129, F.133, F.163, Q.167, F.170, W.181, Y.188, E.203, M.205, L.206, H.289, R.292, L.293, I.296, F.302, M.307 24 PLIP interactions: 24 interactions with chain A Hydrophobic interactions: A:M.125, A:F.163, A:F.170, A:W.181, A:W.181, A:W.181, A:Y.188, A:Y.188, A:E.203, A:M.205, A:L.206, A:L.293, A:L.293, A:I.296, A:F.302, A:F.302 Hydrogen bonds: A:L.91, A:S.129, A:S.129, A:Q.167, A:R.292 Water bridges: A:L.91 pi-Stacking: A:F.170, A:W.181

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 4 residues within 4Å: Chain A: H.218, E.219, E.220, Y.258 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.219, A:Y.258, A:Y.258 Water bridges: A:L.217, A:E.219 GOL.3: 6 residues within 4Å: Chain A: T.172, V.173, F.174, N.175, E.182, K.213 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:V.173, A:K.213 Water bridges: A:T.172, A:T.172, A:A.176, A:K.213

2 x IPA: ISOPROPYL ALCOHOL(Non-functional Binders)

IPA.4: 4 residues within 4Å: Chain A: L.56, P.57, G.58, V.59 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.56, A:V.59 Water bridges: A:L.56 IPA.5: 3 residues within 4Å: Chain A: I.155, L.158, L.310 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.155, A:L.158, A:L.310

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Carivenc, C. et al., A two-in-one expression construct for biophysical and structural studies of the human pregnane X receptor ligand-binding domain, a pharmaceutical and environmental target. Acta Crystallogr.,Sect.F (2025)

Release Date

2025-02-19

Peptides

Nuclear receptor subfamily 1 group I member 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Nuclear receptor subfamily 1 group I member 2

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