SMTL ID : 5ugt.1

Crystal structure of M. tuberculosis InhA inhibited by PT504

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 26 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 Ligands: XTW.2 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:I.41, A:F.169, A:A.211 Hydrogen bonds: A:G.34, A:I.35, A:S.40, A:I.41, A:D.84, A:D.84, A:V.85, A:I.115, A:G.116, A:K.185, A:I.214, A:I.214, A:A.218 pi-Stacking: A:F.61 NAD.3: 25 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, K.185, A.211, G.212, P.213, I.214, T.216, L.217, A.218 Ligands: XTW.4 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:I.41, B:F.169 Hydrogen bonds: B:I.35, B:I.41, B:F.61, B:D.84, 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:L.217, B:A.218 pi-Stacking: B:F.61 NAD.5: 26 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 Ligands: XTW.6 20 PLIP interactions: 20 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: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:G.34, C:F.61, C:L.217 pi-Stacking: C:F.61, C:F.61 NAD.7: 25 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, K.185, A.211, G.212, P.213, I.214, T.216, L.217, A.218 Ligands: XTW.8 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:I.41, D:F.169 Hydrogen bonds: D:G.34, D:S.40, D:I.41, D:D.84, D:V.85, D:I.115, D:G.116, D:K.185, D:I.214, D:I.214, D:T.216, D:A.218 pi-Stacking: D:F.61

4 x XTW: 2-(2-chloranylphenoxy)-5-[(4-cyclopropyl-1,2,3-triazol-1-yl)methyl]phenol(Non-covalent)

XTW.2: 16 residues within 4Å: Chain A: G.116, F.117, M.118, M.123, F.169, P.176, A.177, Y.178, M.181, P.213, A.218, M.219, V.223, L.238, E.239 Ligands: NAD.1 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.169, A:A.177, A:Y.178, A:Y.178, A:V.223, A:L.238 Hydrogen bonds: A:Y.178 XTW.4: 16 residues within 4Å: Chain B: G.116, F.117, M.118, M.123, F.169, P.176, A.177, Y.178, M.181, K.185, A.218, M.219, I.222, L.238, E.239 Ligands: NAD.3 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:A.177, B:Y.178, B:Y.178, B:I.222, B:L.238 Hydrogen bonds: B:Y.178 pi-Stacking: B:F.169 XTW.6: 15 residues within 4Å: Chain C: G.116, F.117, M.118, M.123, F.169, P.176, A.177, Y.178, M.181, A.218, M.219, V.223, L.238, E.239 Ligands: NAD.5 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:A.177, C:Y.178, C:M.219, C:V.223, C:L.238 Hydrogen bonds: C:Y.178 pi-Stacking: C:F.169 XTW.8: 16 residues within 4Å: Chain D: G.116, F.117, M.118, M.123, F.169, M.175, P.176, Y.178, M.181, K.185, A.218, M.219, I.222, L.238, E.239 Ligands: NAD.7 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:Y.178, D:L.238 pi-Stacking: D:F.169

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
B

C
E

D
G

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

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