SMTL ID : 4oim.1

Crystal structure of Mycobacterium tuberculosis InhA in complex with inhibitor PT119 in 2.4 M acetate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.85 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 Ligands: JUS.2, ACT.3 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:I.41, A:F.169, A:A.211 Hydrogen bonds: A:G.34, A:I.41, 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:T.216, A:T.216, A:A.218 Water bridges: A:A.42, A:A.42, A:F.61, A:L.217 pi-Stacking: A:F.61 NAD.14: 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 Ligands: JUS.15, ACT.16 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:I.41, B:F.169, B:A.211 Hydrogen bonds: B:G.34, B:I.41, 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:A.218 Water bridges: B:A.42, B:A.42, B:F.61, B:L.217 pi-Stacking: B:F.61 NAD.27: 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 Ligands: JUS.28, ACT.29 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:I.41, C:F.169, C:A.211 Hydrogen bonds: C:G.34, 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:T.216, C:T.216, C:A.218 Water bridges: C:A.42, C:A.42, C:F.61, C:L.217 pi-Stacking: C:F.61 NAD.40: 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 Ligands: JUS.41, ACT.42 21 PLIP interactions: 21 interactions with chain D Hydrophobic interactions: D:I.41, D:F.169, D:A.211 Hydrogen bonds: D:G.34, D:I.41, D:D.84, 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:A.42, D:F.61, D:L.217 pi-Stacking: D:F.61

4 x JUS: 2-(2-CYANOPHENOXY)-5-HEXYLPHENOL(Non-covalent)

JUS.2: 15 residues within 4Å: Chain A: G.116, F.117, M.118, M.123, F.169, P.176, Y.178, M.181, K.185, A.218, M.219, I.222, L.238 Ligands: NAD.1, ACT.4 7 PLIP interactions: 7 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 JUS.15: 15 residues within 4Å: Chain B: G.116, F.117, M.118, M.123, F.169, P.176, Y.178, M.181, K.185, A.218, M.219, I.222, L.238 Ligands: NAD.14, ACT.17 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.169, B:Y.178, B:A.218, B:M.219, B:I.222, B:L.238 Hydrogen bonds: B:Y.178, B:Y.178 JUS.28: 15 residues within 4Å: Chain C: G.116, F.117, M.118, M.123, F.169, P.176, Y.178, M.181, K.185, A.218, M.219, I.222, L.238 Ligands: NAD.27, ACT.30 7 PLIP interactions: 7 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 JUS.41: 15 residues within 4Å: Chain D: G.116, F.117, M.118, M.123, F.169, P.176, Y.178, M.181, K.185, A.218, M.219, I.222, L.238 Ligands: NAD.40, ACT.43 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:F.169, D:Y.178, D:A.218, D:M.219, D:I.222, D:L.238 Hydrogen bonds: D:Y.178, D:Y.178

44 x ACT: ACETATE ION(Non-functional Binders)

ACT.3: 5 residues within 4Å: Chain A: F.61, Q.86, F.117, I.142 Ligands: NAD.1 Ligand excluded by PLIP ACT.4: 5 residues within 4Å: Chain A: F.117, M.118, M.123, A.221 Ligands: JUS.2 Ligand excluded by PLIP ACT.5: 4 residues within 4Å: Chain A: L.227, G.228, G.232, A.233 Ligand excluded by PLIP ACT.6: 7 residues within 4Å: Chain A: D.38, S.39, H.44, I.214, K.253, D.254, A.255 Ligand excluded by PLIP ACT.7: 5 residues within 4Å: Chain A: R.29, G.105, N.106, K.107, N.159 Ligand excluded by PLIP ACT.8: 2 residues within 4Å: Chain A: K.201, Y.202 Ligand excluded by PLIP ACT.9: 4 residues within 4Å: Chain A: E.82, S.93, R.97 Ligands: ACT.10 Ligand excluded by PLIP ACT.10: 5 residues within 4Å: Chain A: L.80, L.81, E.82, R.97 Ligands: ACT.9 Ligand excluded by PLIP ACT.11: 5 residues within 4Å: Chain A: P.160, G.200, K.201, Y.202, G.203 Ligand excluded by PLIP ACT.12: 5 residues within 4Å: Chain A: I.248, G.249, W.250, N.251 Ligands: ACT.13 Ligand excluded by PLIP ACT.13: 3 residues within 4Å: Chain A: D.243, W.250 Ligands: ACT.12 Ligand excluded by PLIP ACT.16: 5 residues within 4Å: Chain B: F.61, Q.86, F.117, I.142 Ligands: NAD.14 Ligand excluded by PLIP ACT.17: 5 residues within 4Å: Chain B: F.117, M.118, M.123, A.221 Ligands: JUS.15 Ligand excluded by PLIP ACT.18: 4 residues within 4Å: Chain B: L.227, G.228, G.232, A.233 Ligand excluded by PLIP ACT.19: 7 residues within 4Å: Chain B: D.38, S.39, H.44, I.214, K.253, D.254, A.255 Ligand excluded by PLIP ACT.20: 5 residues within 4Å: Chain B: R.29, G.105, N.106, K.107, N.159 Ligand excluded by PLIP ACT.21: 2 residues within 4Å: Chain B: K.201, Y.202 Ligand excluded by PLIP ACT.22: 4 residues within 4Å: Chain B: E.82, S.93, R.97 Ligands: ACT.23 Ligand excluded by PLIP ACT.23: 5 residues within 4Å: Chain B: L.80, L.81, E.82, R.97 Ligands: ACT.22 Ligand excluded by PLIP ACT.24: 5 residues within 4Å: Chain B: P.160, G.200, K.201, Y.202, G.203 Ligand excluded by PLIP ACT.25: 5 residues within 4Å: Chain B: I.248, G.249, W.250, N.251 Ligands: ACT.26 Ligand excluded by PLIP ACT.26: 3 residues within 4Å: Chain B: D.243, W.250 Ligands: ACT.25 Ligand excluded by PLIP ACT.29: 5 residues within 4Å: Chain C: F.61, Q.86, F.117, I.142 Ligands: NAD.27 Ligand excluded by PLIP ACT.30: 5 residues within 4Å: Chain C: F.117, M.118, M.123, A.221 Ligands: JUS.28 Ligand excluded by PLIP ACT.31: 4 residues within 4Å: Chain C: L.227, G.228, G.232, A.233 Ligand excluded by PLIP ACT.32: 7 residues within 4Å: Chain C: D.38, S.39, H.44, I.214, K.253, D.254, A.255 Ligand excluded by PLIP ACT.33: 5 residues within 4Å: Chain C: R.29, G.105, N.106, K.107, N.159 Ligand excluded by PLIP ACT.34: 2 residues within 4Å: Chain C: K.201, Y.202 Ligand excluded by PLIP ACT.35: 4 residues within 4Å: Chain C: E.82, S.93, R.97 Ligands: ACT.36 Ligand excluded by PLIP ACT.36: 5 residues within 4Å: Chain C: L.80, L.81, E.82, R.97 Ligands: ACT.35 Ligand excluded by PLIP ACT.37: 5 residues within 4Å: Chain C: P.160, G.200, K.201, Y.202, G.203 Ligand excluded by PLIP ACT.38: 5 residues within 4Å: Chain C: I.248, G.249, W.250, N.251 Ligands: ACT.39 Ligand excluded by PLIP ACT.39: 3 residues within 4Å: Chain C: D.243, W.250 Ligands: ACT.38 Ligand excluded by PLIP ACT.42: 5 residues within 4Å: Chain D: F.61, Q.86, F.117, I.142 Ligands: NAD.40 Ligand excluded by PLIP ACT.43: 5 residues within 4Å: Chain D: F.117, M.118, M.123, A.221 Ligands: JUS.41 Ligand excluded by PLIP ACT.44: 4 residues within 4Å: Chain D: L.227, G.228, G.232, A.233 Ligand excluded by PLIP ACT.45: 7 residues within 4Å: Chain D: D.38, S.39, H.44, I.214, K.253, D.254, A.255 Ligand excluded by PLIP ACT.46: 5 residues within 4Å: Chain D: R.29, G.105, N.106, K.107, N.159 Ligand excluded by PLIP ACT.47: 2 residues within 4Å: Chain D: K.201, Y.202 Ligand excluded by PLIP ACT.48: 4 residues within 4Å: Chain D: E.82, S.93, R.97 Ligands: ACT.49 Ligand excluded by PLIP ACT.49: 5 residues within 4Å: Chain D: L.80, L.81, E.82, R.97 Ligands: ACT.48 Ligand excluded by PLIP ACT.50: 5 residues within 4Å: Chain D: P.160, G.200, K.201, Y.202, G.203 Ligand excluded by PLIP ACT.51: 5 residues within 4Å: Chain D: I.248, G.249, W.250, N.251 Ligands: ACT.52 Ligand excluded by PLIP ACT.52: 3 residues within 4Å: Chain D: D.243, W.250 Ligands: ACT.51 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pan, P. et al., Time-Dependent Diaryl Ether Inhibitors of InhA: Structure-Activity Relationship Studies of Enzyme Inhibition, Antibacterial Activity, and in vivo Efficacy. Chemmedchem (2014)

Release Date

2014-04-23

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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