SMTL ID : 7nqn.1

Mycobacterium tuberculosis Cytochrome P450 CYP121 in complex with lead compound 14

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

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

HEM.1: 30 residues within 4Å: Chain A: M.62, N.85, M.86, R.95, I.102, H.146, F.230, A.233, G.234, S.237, T.238, F.241, L.274, N.277, F.280, L.284, R.286, L.309, A.337, F.338, G.339, H.343, F.344, C.345, P.346, G.347, L.350, G.351 Ligands: UMT.2, SO4.6 20 PLIP interactions: 19 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:F.230, A:F.230, A:A.233, A:F.241, A:F.280, A:F.280, A:L.284, A:F.338, A:P.346, A:L.350 Water bridges: A:M.86, A:R.95, A:R.95, A:P.285, A:R.286, A:Q.342 Salt bridges: A:R.286, A:H.343 Metal complexes: A:C.345, H2O.1

1 x UMT: 4-[4-[2-(1~{H}-indol-3-yl)ethyl]pyrimidin-2-yl]morpholine(Non-covalent)

UMT.2: 21 residues within 4Å: Chain A: T.77, V.78, V.82, V.83, N.85, S.163, L.164, A.167, F.168, A.178, N.181, W.182, D.185, V.228, T.229, F.230, G.232, A.233, Q.385 Ligands: HEM.1, SO4.6 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:V.78, A:A.167, A:F.168, A:F.168, A:N.181, A:W.182, A:W.182, A:W.182 Hydrogen bonds: A:N.85 Water bridges: A:S.163, A:S.163

2 x MES: 2-(N-MORPHOLINO)-ETHANESULFONIC ACID(Non-covalent)

MES.3: 8 residues within 4Å: Chain A: D.91, A.92, G.93, A.214, Y.215, H.217, V.218 Ligands: CL.15 2 PLIP interactions: 2 interactions with chain A Water bridges: A:H.217, A:S.219 MES.4: 6 residues within 4Å: Chain A: R.134, N.135, F.161, R.162, S.165, R.381 9 PLIP interactions: 9 interactions with chain A Water bridges: A:S.165, A:S.165, A:S.165, A:R.381, A:R.381, A:E.390, A:E.390 Salt bridges: A:R.134, A:R.381

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

SO4.5: 6 residues within 4Å: Chain A: R.58, S.61, M.62, K.63, Q.342, H.343 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:S.61, A:M.62, A:K.63 Water bridges: A:R.58, A:R.58, A:R.58, A:S.61, A:H.343, A:H.343 Salt bridges: A:R.58, A:H.343 SO4.6: 7 residues within 4Å: Chain A: F.168, A.233, S.237, F.280, R.386 Ligands: HEM.1, UMT.2 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.386, A:R.386, A:R.386 Salt bridges: A:R.386 SO4.7: 5 residues within 4Å: Chain A: P.330, N.331, P.332, T.333, S.334 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.333, A:T.333, A:T.333, A:S.334, A:S.334 SO4.8: 3 residues within 4Å: Chain A: R.252, S.324, I.325 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.324, A:I.325 Water bridges: A:R.252, A:R.252, A:S.324, A:I.325 Salt bridges: A:R.252 SO4.9: 2 residues within 4Å: Chain A: R.58, Q.342 2 PLIP interactions: 2 interactions with chain A Water bridges: A:Q.342 Salt bridges: A:R.58 SO4.10: 3 residues within 4Å: Chain A: P.158, K.159, R.162 5 PLIP interactions: 5 interactions with chain A Water bridges: A:E.155, A:K.159, A:R.162, A:R.162 Salt bridges: A:R.162 SO4.11: 3 residues within 4Å: Chain A: S.12, R.14, R.17 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.12, A:R.14 Water bridges: A:S.12, A:A.13, A:R.17 Salt bridges: A:R.17 SO4.12: 3 residues within 4Å: Chain A: A.3, T.4, V.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.4, A:V.5 SO4.13: 5 residues within 4Å: Chain A: G.108, L.109, E.110, Q.111, R.114 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.108, A:E.110, A:Q.111, A:R.114 Water bridges: A:L.109, A:L.109

6 x CL: CHLORIDE ION(Non-functional Binders)

CL.14: 2 residues within 4Å: Chain A: A.67, A.68 Ligand excluded by PLIP CL.15: 1 residues within 4Å: Ligands: MES.3 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain A: S.165, M.169 Ligand excluded by PLIP CL.17: 4 residues within 4Å: Chain A: Y.48, A.49, E.317, H.318 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain A: R.59, I.292, Q.293 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain A: P.19, D.20 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Frederickson, M. et al., A new strategy for hit generation: Novel in cellulo active inhibitors of CYP121A1 from Mycobacterium tuberculosis via a combined X-ray crystallographic and phenotypic screening approach (XP screen). Eur.J.Med.Chem. (2022)

Release Date

2022-02-02

Peptides

Mycocyclosin synthase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Mycocyclosin synthase

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