SMTL ID : 7nqo.1

Mycobacterium tuberculosis Cytochrome P450 CYP121 in complex with lead compound 21

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

1 x HEC: HEME C(Non-covalent)

HEC.1: 33 residues within 4Å: Chain A: L.55, 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, S.279, F.280, L.284, R.286, L.309, L.336, A.337, F.338, G.339, Q.342, H.343, F.344, C.345, P.346, G.347, L.350, G.351 Ligands: ULZ.2 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.309, A:F.338, A:P.346 Water bridges: A:M.86, A:R.95, A:P.285, A:R.286, A:Q.342, A:H.343 Salt bridges: A:R.286, A:H.343 pi-Stacking: A:F.338 Metal complexes: A:C.345, H2O.8

1 x ULZ: 4-[4-[2-(5-bromanyl-1~{H}-indol-3-yl)ethyl]pyrimidin-2-yl]morpholine(Non-covalent)

ULZ.2: 14 residues within 4Å: Chain A: M.62, T.77, V.78, V.82, V.83, N.85, F.168, T.229, G.232, A.233, F.280, Q.385, R.386 Ligands: HEC.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:V.78, A:F.168, A:A.233 Hydrogen bonds: A:R.386 Water bridges: A:T.77, A:Q.385, A:R.386

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

MES.3: 7 residues within 4Å: Chain A: D.91, A.92, G.93, A.214, Y.215, H.217, V.218 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 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.135 Water bridges: A:D.139, A:S.165, A:S.165, A:R.381, A:R.381 Salt bridges: A:R.134, A:R.381

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

DMS.5: 7 residues within 4Å: Chain A: A.106, P.107, G.108, L.109, E.110, Q.111, R.114 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.108, A:E.110, A:Q.111 Water bridges: A:L.109

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

SO4.6: 6 residues within 4Å: Chain A: R.58, S.61, M.62, K.63, Q.342, H.343 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:S.61, A:M.62, A:K.63, A:N.84 Water bridges: A:R.58 Salt bridges: A:R.58, A:H.343 SO4.7: 3 residues within 4Å: Chain A: R.252, S.324, I.325 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:S.324, A:I.325 Water bridges: A:R.252, A:R.252, A:S.324 Salt bridges: A:R.252 SO4.8: 3 residues within 4Å: Chain A: S.12, R.14, R.17 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.12, A:S.12 Water bridges: A:A.13 Salt bridges: A:R.17 SO4.9: 4 residues within 4Å: Chain A: R.17, P.19, D.20, A.21 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.17, A:D.20, A:A.21 Water bridges: A:I.18 SO4.10: 2 residues within 4Å: Chain A: T.4, V.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:V.5 SO4.11: 3 residues within 4Å: Chain A: P.158, K.159, R.162 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.159 Water bridges: A:E.155 Salt bridges: A:R.162 SO4.12: 4 residues within 4Å: Chain A: Y.48, A.49, E.317, H.318 3 PLIP interactions: 3 interactions with chain A Water bridges: A:A.49, A:A.49 Salt bridges: A:H.318 SO4.13: 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 SO4.14: 1 residues within 4Å: Chain A: R.58 4 PLIP interactions: 4 interactions with chain A Water bridges: A:D.91, A:Q.342, A:Q.342 Salt bridges: A:R.58

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

CL.15: 2 residues within 4Å: Chain A: P.153, Q.154 Ligand excluded by PLIP CL.16: 2 residues within 4Å: Chain A: A.67, A.68 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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