SMTL ID : 9ms2.1 (1 other biounit)

Crystal structure of human CYP3A5 in complex with SJYHJ-111

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

monomer

Ligands

1 x HEM: PROTOPORPHYRIN IX CONTAINING FE(Non-covalent)

HEM.1: 26 residues within 4Å: Chain A: R.84, I.97, S.98, W.105, R.109, F.116, F.281, A.284, G.285, T.288, V.348, A.349, L.352, R.354, P.412, F.413, G.414, T.415, R.418, N.419, C.420, I.421, G.422, A.426, M.430 Ligands: 01.2 18 PLIP interactions: 18 interactions with chain A, Hydrophobic interactions: A:I.97, A:F.116, A:V.348, A:A.349, A:L.352, A:F.413, A:F.413, A:I.421, A:A.426 Hydrogen bonds: A:T.415 Water bridges: A:R.84, A:E.353 Salt bridges: A:R.84, A:R.84, A:R.109, A:R.354, A:R.418 Metal complexes: A:C.420

1 x 01: N'-(2-chlorophenyl)-N-[(3-hydroxyphenyl)methyl]-N-[(2P)-2-(1H-imidazol-1-yl)-5-(trifluoromethyl)phenyl]urea

01.2: 13 residues within 4Å: Chain A: R.84, S.98, L.99, F.192, G.193, F.220, I.280, F.283, A.284, T.288, G.459, L.460 Ligands: HEM.1 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.280, A:A.284, A:L.460, A:L.460 Hydrogen bonds: A:S.98 pi-Stacking: A:F.283

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

EDO.3: 6 residues within 4Å: Chain A: Y.386, W.387, S.404, I.405, D.406, I.409 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.386, A:D.406 EDO.4: 4 residues within 4Å: Chain A: Y.386, W.387, T.388, R.397 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.388, A:R.397 EDO.5: 6 residues within 4Å: Chain A: R.109, N.419, C.420, I.421, R.424 Ligands: EDO.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.109, A:N.419, A:I.421 Water bridges: A:R.424 EDO.7: 2 residues within 4Å: Chain A: R.424 Ligands: EDO.5 1 PLIP interactions: 1 interactions with chain A Water bridges: A:N.419

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 4 residues within 4Å: Chain A: W.37, L.453, K.454, L.455 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.378, A:Y.378, A:L.455 Water bridges: A:L.455, A:E.464

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.8: 2 residues within 4Å: Chain A: S.118, R.424 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.118, A:S.118 Water bridges: A:R.424, A:R.424 Salt bridges: A:R.424

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wang, J. et al., Crystal structure of human CYP3A4 in complex with SJ000362065. Nat Commun (2025)

Release Date

2025-04-16

Peptides

Cytochrome P450 3A5: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cytochrome P450 3A5

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