SMTL ID : 4oxn.1

Substrate-like binding mode of inhibitor PT155 to the Mycobacterium tuberculosis enoyl-ACP reductase InhA

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.29 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 25 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, A.218 Ligands: 1S5.2 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:I.41, A:F.169, A:F.169, A:A.211 Hydrogen bonds: A:G.34, 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:T.216 Water bridges: A:A.42, A:F.61, A:F.61, A:F.61, A:I.115, A:A.218, A:A.218 pi-Stacking: A:F.61 NAD.8: 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, M.181, K.185, A.211, G.212, P.213, I.214, T.216 Ligands: 1S5.9, 2NV.12 19 PLIP interactions: 19 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:V.85, B:I.115, B:G.116, B:K.185, B:I.214, B:I.214, B:T.216 Water bridges: B:A.42, B:F.61, B:F.61, B:F.61, B:I.115 pi-Stacking: B:F.61 NAD.16: 25 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, A.218 Ligands: 1S5.17 23 PLIP interactions: 23 interactions with chain C Hydrophobic interactions: C:I.41, C:F.169, C:F.169, C:A.211 Hydrogen bonds: C:G.34, C:I.41, C:D.84, C:D.84, C:V.85, C:I.115, C:G.116, C:K.185, C:I.214, C:I.214, C:T.216 Water bridges: C:A.42, C:F.61, C:F.61, C:F.61, C:I.115, C:A.218, C:A.218 pi-Stacking: C:F.61 NAD.23: 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, M.181, K.185, A.211, G.212, P.213, I.214, T.216 Ligands: 1S5.24, 2NV.27 19 PLIP interactions: 19 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:V.85, D:I.115, D:G.116, D:K.185, D:I.214, D:I.214, D:T.216 Water bridges: D:A.42, D:F.61, D:F.61, D:F.61, D:I.115 pi-Stacking: D:F.61

4 x 1S5: 5-(4-amino-2-methylphenoxy)-2-hexyl-4-hydroxy-1-methylpyridinium(Non-covalent)

1S5.2: 12 residues within 4Å: Chain A: G.116, F.117, M.118, M.123, F.169, M.175, Y.178, K.185, A.218, M.219, L.238 Ligands: NAD.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.169, A:Y.178, A:Y.178, A:A.218, A:L.238 Hydrogen bonds: A:M.118, A:M.118, A:Y.178 1S5.9: 14 residues within 4Å: Chain B: G.116, F.117, M.118, M.123, F.169, A.177, Y.178, M.181, K.185, M.219, I.222, I.235 Ligands: NAD.8, 2NV.12 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.169, B:F.169, B:F.169, B:A.177, B:Y.178, B:Y.178, B:I.222, B:I.235 Hydrogen bonds: B:M.118, B:M.118 1S5.17: 12 residues within 4Å: Chain C: G.116, F.117, M.118, M.123, F.169, M.175, Y.178, K.185, A.218, M.219, L.238 Ligands: NAD.16 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.169, C:Y.178, C:Y.178, C:A.218, C:L.238 Hydrogen bonds: C:M.118, C:M.118, C:Y.178 1S5.24: 14 residues within 4Å: Chain D: G.116, F.117, M.118, M.123, F.169, A.177, Y.178, M.181, K.185, M.219, I.222, I.235 Ligands: NAD.23, 2NV.27 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:F.169, D:F.169, D:F.169, D:A.177, D:Y.178, D:Y.178, D:I.222, D:I.235 Hydrogen bonds: D:M.118, D:M.118

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

CL.3: 2 residues within 4Å: Chain A: E.82, R.97 Ligand excluded by PLIP CL.11: 3 residues within 4Å: Chain B: L.81, E.82, R.97 Ligand excluded by PLIP CL.18: 2 residues within 4Å: Chain C: E.82, R.97 Ligand excluded by PLIP CL.26: 3 residues within 4Å: Chain D: L.81, E.82, R.97 Ligand excluded by PLIP

16 x 2NV: 3,6,9,12,15-pentaoxaoctadecan-17-amine(Non-covalent)

2NV.4: 6 residues within 4Å: Chain A: S.39, H.44, R.215, K.253, D.254, A.255 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.254, A:A.255 2NV.5: 5 residues within 4Å: Chain A: L.237, G.241, W.242, Q.244, R.245 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.245 2NV.6: 3 residues within 4Å: Chain A: Q.234, L.237 Chain C: L.289 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.237 2NV.7: 8 residues within 4Å: Chain A: T.22, L.24, W.269 Chain B: T.22, G.23, L.24, D.268, W.269 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.269 2NV.12: 7 residues within 4Å: Chain B: F.61, F.117, M.118, K.138, L.227 Ligands: NAD.8, 1S5.9 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.138, B:K.138 Water bridges: B:R.63 2NV.13: 2 residues within 4Å: Chain B: R.63, L.217 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.63 2NV.14: 6 residues within 4Å: Chain B: E.88, A.92, Y.145, K.152 Chain C: F.129, D.130 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.152 2NV.15: 7 residues within 4Å: Chain B: F.129, D.130, A.131 Chain C: L.91, Y.145, K.152, A.153 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:K.152, C:A.153 Hydrogen bonds: C:K.152 2NV.19: 6 residues within 4Å: Chain C: S.39, H.44, R.215, K.253, D.254, A.255 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:D.254, C:A.255 2NV.20: 5 residues within 4Å: Chain C: L.237, G.241, W.242, Q.244, R.245 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.245 2NV.21: 3 residues within 4Å: Chain A: L.289 Chain C: Q.234, L.237 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:L.237 2NV.22: 8 residues within 4Å: Chain C: T.22, L.24, W.269 Chain D: T.22, G.23, L.24, D.268, W.269 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:W.269 2NV.27: 7 residues within 4Å: Chain D: F.61, F.117, M.118, K.138, L.227 Ligands: NAD.23, 1S5.24 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.138, D:K.138 Water bridges: D:R.63 2NV.28: 2 residues within 4Å: Chain D: R.63, L.217 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.63 2NV.29: 6 residues within 4Å: Chain A: F.129, D.130 Chain D: E.88, A.92, Y.145, K.152 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:K.152 2NV.30: 7 residues within 4Å: Chain A: L.91, Y.145, K.152, A.153 Chain D: F.129, D.130, A.131 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.152, A:A.153 Hydrogen bonds: A:K.152

2 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.10: 6 residues within 4Å: Chain B: D.62, R.63, L.64, R.65, E.82, H.90 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:L.64, B:R.65, B:H.90 Salt bridges: B:R.65, B:E.82, B:E.82 EPE.25: 6 residues within 4Å: Chain D: D.62, R.63, L.64, R.65, E.82, H.90 6 PLIP interactions: 6 interactions with chain D Hydrogen bonds: D:L.64, D:R.65, D:H.90 Salt bridges: D:R.65, D:E.82, D:E.82

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, H.J. et al., A Structural and Energetic Model for the Slow-Onset Inhibition of the Mycobacterium tuberculosis Enoyl-ACP Reductase InhA. Acs Chem.Biol. (2014)

Release Date

2014-04-30

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

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

Related Entries With Identical Sequence