SMTL ID : 5ugu.1

Crystal structure of M. tuberculosis InhA inhibited by PT506

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

homo-tetramer

Ligands

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 27 residues within 4Å: Chain A: G.34, I.35, I.36, S.40, I.41, F.61, L.83, D.84, V.85, S.114, I.115, G.116, I.142, M.167, D.168, F.169, M.181, K.185, A.211, G.212, P.213, I.214, T.216, L.217, A.218, M.219 Ligands: XTV.2 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:I.41, A:F.169, A:A.211 Hydrogen bonds: A:G.34, A:S.40, A:I.41, A:D.84, A:D.84, A:V.85, A:I.115, A:I.115, A:G.116, A:K.185, A:I.214, A:I.214, A:A.218 Water bridges: A:A.42, A:F.61, A:F.61, A:F.61, A:L.217 pi-Stacking: A:F.61 NAD.3: 27 residues within 4Å: Chain B: G.34, I.35, I.36, S.40, I.41, F.61, L.83, D.84, V.85, S.114, I.115, G.116, I.142, M.167, D.168, F.169, M.181, K.185, A.211, G.212, P.213, I.214, T.216, L.217, A.218, M.219 Ligands: XTV.4 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:I.41, B:F.169, B:A.211 Hydrogen bonds: B:G.34, B:S.40, B:I.41, B:D.84, B:V.85, B:I.115, B:I.115, B:G.116, B:K.185, B:I.214, B:I.214, B:T.216, B:A.218 Water bridges: B:A.42, B:F.61, B:F.61, B:F.61, B:L.217 pi-Stacking: B:F.61 NAD.5: 27 residues within 4Å: Chain C: G.34, I.35, I.36, S.40, I.41, F.61, L.83, D.84, V.85, S.114, I.115, G.116, I.142, M.167, D.168, F.169, M.181, K.185, A.211, G.212, P.213, I.214, T.216, L.217, A.218, M.219 Ligands: XTV.6 22 PLIP interactions: 22 interactions with chain C Hydrophobic interactions: C:I.41, C:F.169, C:A.211 Hydrogen bonds: C:G.34, C:S.40, C:I.41, C:D.84, C:D.84, C:V.85, C:I.115, C:I.115, C:G.116, C:K.185, C:I.214, C:I.214, C:A.218 Water bridges: C:A.42, C:F.61, C:F.61, C:F.61, C:L.217 pi-Stacking: C:F.61 NAD.7: 27 residues within 4Å: Chain D: G.34, I.35, I.36, S.40, I.41, F.61, L.83, D.84, V.85, S.114, I.115, G.116, I.142, M.167, D.168, F.169, M.181, K.185, A.211, G.212, P.213, I.214, T.216, L.217, A.218, M.219 Ligands: XTV.8 22 PLIP interactions: 22 interactions with chain D Hydrophobic interactions: D:I.41, D:F.169, D:A.211 Hydrogen bonds: D:G.34, D:S.40, D:I.41, D:D.84, D:V.85, D:I.115, D:I.115, D:G.116, D:K.185, D:I.214, D:I.214, D:T.216, D:A.218 Water bridges: D:A.42, D:F.61, D:F.61, D:F.61, D:L.217 pi-Stacking: D:F.61

4 x XTV: 2-[4-[(4-cyclopropyl-1,2,3-triazol-1-yl)methyl]-2-oxidanyl-phenoxy]benzenecarbonitrile(Non-covalent)

XTV.2: 16 residues within 4Å: Chain A: G.116, F.117, M.118, M.123, F.169, P.176, Y.178, M.181, K.185, P.213, A.218, M.219, I.222, L.238, E.239 Ligands: NAD.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.169, A:Y.178, A:A.218, A:M.219, A:I.222, A:L.238 Hydrogen bonds: A:Y.178, A:E.239 XTV.4: 16 residues within 4Å: Chain B: G.116, F.117, M.118, M.123, F.169, P.176, Y.178, M.181, K.185, P.213, A.218, M.219, I.222, L.238, E.239 Ligands: NAD.3 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:F.169, B:Y.178, B:A.218, B:M.219, B:I.222, B:L.238 XTV.6: 16 residues within 4Å: Chain C: G.116, F.117, M.118, M.123, F.169, P.176, Y.178, M.181, K.185, P.213, A.218, M.219, I.222, L.238, E.239 Ligands: NAD.5 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.169, C:Y.178, C:A.218, C:M.219, C:I.222, C:L.238 Hydrogen bonds: C:Y.178, C:E.239 XTV.8: 16 residues within 4Å: Chain D: G.116, F.117, M.118, M.123, F.169, P.176, Y.178, M.181, K.185, P.213, A.218, M.219, I.222, L.238, E.239 Ligands: NAD.7 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:F.169, D:Y.178, D:A.218, D:M.219, D:I.222, D:L.238

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Spagnuolo, L.A. et al., Evaluating the Contribution of Transition-State Destabilization to Changes in the Residence Time of Triazole-Based InhA Inhibitors. J. Am. Chem. Soc. (2017)

Release Date

2017-02-15

Peptides

Enoyl-[acyl-carrier-protein] reductase [NADH]: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

Enoyl-[acyl-carrier-protein] reductase [NADH]

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