SMTL ID : 5edt.1

Crystal structure of Mycobacterium tuberculosis CYP121 in complex with LIG9

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.45 Å

Oligo State

monomer

Ligands

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

HEM.1: 23 residues within 4Å: Chain A: M.61, M.85, H.145, F.229, A.232, G.233, S.236, T.237, F.240, F.279, L.283, R.285, L.308, A.336, F.337, G.338, H.342, C.344, P.345, G.346, L.349, G.350 Ligands: SO4.3 16 PLIP interactions: 15 interactions with chain A, 1 Ligand-Water interactions, Hydrophobic interactions: A:F.229, A:F.229, A:A.232, A:F.240, A:F.279, A:F.279, A:L.283, A:L.308, A:F.337, A:P.345, A:L.349 Salt bridges: A:R.285, A:H.342 pi-Stacking: A:F.337 Metal complexes: A:C.344, H2O.1

1 x 5MK: 2-azanyl-5-chloranyl-benzamide(Non-covalent)

5MK.2: 13 residues within 4Å: Chain A: T.76, V.77, S.162, A.166, F.167, A.177, N.180, W.181, D.184, V.227, T.228, G.231, A.232 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.77, A:A.166, A:A.166, A:V.227 Hydrogen bonds: A:T.76, A:S.162, A:D.184, A:D.184 pi-Stacking: A:W.181

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

SO4.3: 5 residues within 4Å: Chain A: F.167, A.232, F.279, R.385 Ligands: HEM.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.236 Water bridges: A:R.385, A:R.385 Salt bridges: A:R.385 SO4.4: 6 residues within 4Å: Chain A: R.57, S.60, M.61, K.62, Q.341, H.342 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:M.61, A:K.62 Salt bridges: A:R.57, A:H.342 SO4.5: 5 residues within 4Å: Chain A: R.133, N.134, F.160, S.164, R.380 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:S.164, A:E.389 Water bridges: A:R.133, A:N.134, A:R.380, A:R.380, A:R.380 Salt bridges: A:R.133, A:R.380 SO4.6: 1 residues within 4Å: Chain A: K.210 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:K.210 SO4.7: 3 residues within 4Å: Chain A: I.151, P.152, Q.153 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.153, A:E.154 SO4.8: 3 residues within 4Å: Chain A: R.251, S.323, I.324 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.324, A:I.324 Salt bridges: A:R.251 SO4.9: 7 residues within 4Å: Chain A: D.15, R.16, I.17, R.251, I.275, L.277, F.313 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.17 Water bridges: A:L.277 Salt bridges: A:R.251 SO4.10: 2 residues within 4Å: Chain A: S.11, R.13 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.11, A:S.11 Water bridges: A:R.16 Salt bridges: A:R.16 SO4.11: 3 residues within 4Å: Chain A: P.18, D.19, A.20 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.19, A:A.20 Water bridges: A:R.16 SO4.12: 3 residues within 4Å: Chain A: E.154, P.157, R.161 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.161

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kavanagh, M.E. et al., Fragment-Based Approaches to the Development of Mycobacterium tuberculosis CYP121 Inhibitors. J.Med.Chem. (2016)

Release Date

2016-04-06

Peptides

Cytochrome P450 121: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Cytochrome P450 121

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