SMTL ID : 7nqm.1

Mycobacterium tuberculosis Cytochrome P450 CYP121 in complex with lead compound 10

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x HEC: HEME C(Non-covalent)

HEC.1: 29 residues within 4Å: Chain A: M.62, M.86, I.102, H.146, F.230, A.233, G.234, S.237, T.238, F.241, L.274, N.277, S.279, F.280, L.284, R.286, L.309, A.337, F.338, G.339, Q.342, H.343, F.344, C.345, P.346, G.347, L.350, G.351 Ligands: SO4.8 18 PLIP interactions: 17 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.309, A:F.338, A:P.346 Hydrogen bonds: A:Q.342, A:H.343 Water bridges: A:M.86, A:R.286 Salt bridges: A:R.286, A:H.343 pi-Stacking: A:F.338 Metal complexes: A:C.345, H2O.4

1 x UMZ: 3-(2-pyrimidin-4-ylethyl)-1~{H}-indole(Non-covalent)

UMZ.2: 16 residues within 4Å: Chain A: M.62, T.77, V.78, V.82, V.83, N.85, A.167, F.168, W.182, V.228, T.229, G.232, A.233, P.285, Q.385 Ligands: SO4.8 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.168 Hydrogen bonds: A:T.77, A:V.83 pi-Stacking: A:F.168

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

MES.3: 4 residues within 4Å: Chain A: Y.48, A.49, E.317, H.318 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.317 Water bridges: A:Y.48, A:A.49 Salt bridges: A:E.317, A:H.318 MES.4: 7 residues within 4Å: Chain A: D.91, A.92, G.93, A.214, Y.215, H.217, V.218 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.92 Water bridges: A:Y.215, A:H.217 MES.5: 6 residues within 4Å: Chain A: R.134, N.135, F.161, R.162, S.165, R.381 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.135 Water bridges: A:R.381, A:R.381, A:E.390, A:E.390 Salt bridges: A:R.134, A:R.381 MES.6: 5 residues within 4Å: Chain A: R.59, D.291, I.292, Q.293, L.298 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Q.293 Water bridges: A:R.59, A:R.59, A:Q.293 Salt bridges: A:R.59

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

SO4.7: 6 residues within 4Å: Chain A: R.58, S.61, M.62, K.63, Q.342, H.343 Ligand excluded by PLIP SO4.8: 7 residues within 4Å: Chain A: F.168, A.233, S.237, F.280, R.386 Ligands: HEC.1, UMZ.2 Ligand excluded by PLIP SO4.9: 4 residues within 4Å: Chain A: S.12, A.13, R.14, R.17 Ligand excluded by PLIP SO4.10: 4 residues within 4Å: Chain A: Q.251, L.371, P.374, I.375 Ligand excluded by PLIP SO4.11: 4 residues within 4Å: Chain A: T.199, T.200, G.201, R.208 Ligand excluded by PLIP SO4.12: 1 residues within 4Å: Chain A: R.58 Ligand excluded by PLIP SO4.13: 3 residues within 4Å: Chain A: R.252, S.324, I.325 Ligand excluded by PLIP SO4.14: 1 residues within 4Å: Chain A: R.58 Ligand excluded by PLIP SO4.15: 5 residues within 4Å: Chain A: P.330, N.331, P.332, T.333, S.334 Ligand excluded by PLIP SO4.16: 1 residues within 4Å: Chain A: K.301 Ligand excluded by PLIP SO4.17: 4 residues within 4Å: Chain A: R.17, P.19, D.20, A.21 Ligand excluded by PLIP SO4.18: 3 residues within 4Å: Chain A: P.158, K.159, R.162 Ligand excluded by PLIP SO4.19: 8 residues within 4Å: Chain A: G.15, D.16, R.17, I.18, R.252, I.276, L.278, F.314 Ligand excluded by PLIP SO4.20: 4 residues within 4Å: Chain A: Q.111, R.114, D.115, N.118 Ligand excluded by PLIP SO4.21: 4 residues within 4Å: Chain A: R.95, G.341, Q.342, F.344 Ligand excluded by PLIP SO4.22: 6 residues within 4Å: Chain A: P.107, G.108, L.109, E.110, Q.111, R.114 Ligand excluded by PLIP

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

CL.23: 2 residues within 4Å: Chain A: P.153, Q.154 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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