SMTL ID : 6ma8.1

Human CYP3A4 bound to PMSF

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.83 Å

Oligo State

homo-dimer

Ligands

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

HEM.1: 26 residues within 4Å: Chain A: R.85, I.98, S.99, W.106, R.110, F.117, A.285, G.286, T.289, V.293, I.349, A.350, L.353, R.355, P.414, F.415, G.416, S.417, R.420, N.421, C.422, I.423, G.424, A.428, M.432 Ligands: PMF.4 18 PLIP interactions: 17 interactions with chain A, 1 Ligand-Water interactions Hydrophobic interactions: A:I.98, A:F.117, A:V.293, A:I.349, A:A.350, A:L.353, A:F.415, A:F.415, A:I.423 Hydrogen bonds: A:S.417 Water bridges: A:R.355 Salt bridges: A:R.85, A:R.85, A:R.110, A:R.355, A:R.420 Metal complexes: A:C.422, H2O.5 HEM.13: 26 residues within 4Å: Chain B: R.85, I.98, S.99, W.106, R.110, F.117, A.285, G.286, T.289, V.293, I.349, A.350, L.353, R.355, P.414, F.415, G.416, S.417, R.420, N.421, C.422, I.423, G.424, A.428, M.432 Ligands: PMF.16 18 PLIP interactions: 17 interactions with chain B, 1 Ligand-Water interactions Hydrophobic interactions: B:I.98, B:F.117, B:V.293, B:I.349, B:A.350, B:L.353, B:F.415, B:F.415, B:I.423 Hydrogen bonds: B:S.417 Water bridges: B:R.355 Salt bridges: B:R.85, B:R.85, B:R.110, B:R.355, B:R.420 Metal complexes: B:C.422, H2O.14

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 11 residues within 4Å: Chain A: K.35, G.36, F.37, C.38, M.39, M.351, S.458, G.460, G.461, L.462, L.463 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.35, A:F.37, A:C.38, A:M.39, A:G.461 GOL.3: 7 residues within 4Å: Chain A: P.21, S.32, F.40, E.43, C.44, K.47, Y.48 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.32, A:E.43, A:K.47, A:Y.48 Water bridges: A:S.32, A:E.43 GOL.14: 11 residues within 4Å: Chain B: K.35, G.36, F.37, C.38, M.39, M.351, S.458, G.460, G.461, L.462, L.463 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.35, B:F.37, B:C.38, B:M.39, B:G.461 GOL.15: 7 residues within 4Å: Chain B: P.21, S.32, F.40, E.43, C.44, K.47, Y.48 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.32, B:K.47, B:Y.48, B:Y.48 Water bridges: B:S.32, B:E.43

2 x PMF: PHENYLMETHYLSULFONYL FLUORIDE(Non-covalent)

PMF.4: 7 residues within 4Å: Chain A: R.85, S.99, R.192, I.281, F.284, A.285 Ligands: HEM.1 No protein-ligand interaction detected (PLIP) PMF.16: 7 residues within 4Å: Chain B: R.85, S.99, R.192, I.281, F.284, A.285 Ligands: HEM.13 No protein-ligand interaction detected (PLIP)

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

EDO.5: 5 residues within 4Å: Chain A: K.189, L.191, F.193, P.222 Ligands: EDO.6 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.191, A:L.191 EDO.6: 7 residues within 4Å: Chain A: F.193, D.197, F.199, F.200, V.220 Ligands: EDO.5, DMS.12 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.197, A:V.220 Water bridges: A:F.199 EDO.7: 1 residues within 4Å: Chain A: K.14 No protein-ligand interaction detected (PLIP) EDO.8: 4 residues within 4Å: Chain A: E.288, S.292, I.349, L.463 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.288, A:S.292, A:I.349 EDO.9: 5 residues within 4Å: Chain A: K.153, G.157, Y.287, E.288, S.291 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:K.153, A:K.153, A:D.154, A:S.291, A:S.291 EDO.10: 3 residues within 4Å: Chain A: V.135, R.138, D.174 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.138, A:R.138, A:D.174 EDO.11: 3 residues within 4Å: Chain A: K.310, M.338, E.397 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.397 Water bridges: A:K.401 EDO.17: 5 residues within 4Å: Chain B: K.189, L.191, F.193, P.222 Ligands: EDO.18 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.191, B:L.191 EDO.18: 7 residues within 4Å: Chain B: F.193, D.197, F.199, F.200, V.220 Ligands: EDO.17, DMS.24 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.197, B:V.220 Water bridges: B:F.199 EDO.19: 1 residues within 4Å: Chain B: K.14 No protein-ligand interaction detected (PLIP) EDO.20: 4 residues within 4Å: Chain B: E.288, S.292, I.349, L.463 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.288, B:S.292, B:I.349 EDO.21: 5 residues within 4Å: Chain B: K.153, G.157, Y.287, E.288, S.291 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.153, B:K.153, B:S.291, B:S.291 EDO.22: 3 residues within 4Å: Chain B: V.135, R.138, D.174 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.138, B:R.138 EDO.23: 3 residues within 4Å: Chain B: K.310, M.338, E.397 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.397 Water bridges: B:E.334, B:K.401

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.12: 4 residues within 4Å: Chain A: F.199, C.219, V.220 Ligands: EDO.6 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:F.199 DMS.24: 4 residues within 4Å: Chain B: F.199, C.219, V.220 Ligands: EDO.18 1 PLIP interactions: 1 interactions with chain B pi-Cation interactions: B:F.199

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sevrioukova, I., Interaction of Human Drug-Metabolizing CYP3A4 with Small Inhibitory Molecules. Biochemistry (2019)

Release Date

2019-01-16

Peptides

Cytochrome P450 3A4: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Cytochrome P450 3A4

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