SMTL ID : 4oxk.1

Multiple binding modes of inhibitor PT155 to the Mycobacterium tuberculosis enoyl-ACP reductase InhA within a tetramer

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.84 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 20 PLIP interactions: 20 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:G.116, A:K.185, A:I.214, A:I.214, A:T.216, A:T.216 Water bridges: A:G.34, A:A.42, A:F.61, A:F.61, A:I.115 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, M.181, K.185, A.211, G.212, P.213, I.214, T.216, A.218 Ligands: 1S5.4 22 PLIP interactions: 22 interactions with chain B Hydrophobic interactions: B:I.41, B:F.169, 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, B:T.216, B:A.218 Water bridges: B:G.34, B:A.42, B:F.61, B:I.115, B:L.217 pi-Stacking: B:F.61 NAD.7: 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: 1S5.8 22 PLIP interactions: 22 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, C:A.218 Water bridges: C:G.34, C:A.42, C:F.61, C:I.115, C:L.217 pi-Stacking: C:F.61 NAD.9: 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, A.218 Ligands: 1S5.10 22 PLIP interactions: 22 interactions with chain D Hydrophobic interactions: D:I.41, D:F.169, 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:G.116, D:K.185, D:I.214, D:I.214, D:T.216, D:A.218 Water bridges: D:G.34, D:A.42, D:F.61, D:I.115, D:L.217 pi-Stacking: D:F.61

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

1S5.2: 15 residues within 4Å: Chain A: G.116, F.117, M.118, M.123, F.169, P.176, A.177, Y.178, M.181, K.185, I.214, A.218, M.219, L.238 Ligands: NAD.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.169, A:A.177, A:Y.178, A:Y.178, A:A.218, A:L.238 Hydrogen bonds: A:M.118, A:M.118 1S5.4: 14 residues within 4Å: Chain B: G.116, F.117, M.118, F.169, M.175, P.176, Y.178, M.181, K.185, A.218, M.219, A.221, I.222 Ligands: NAD.3 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:F.169, B:Y.178, B:A.218, B:A.221, B:I.222 Hydrogen bonds: B:M.118, B:M.118 1S5.8: 15 residues within 4Å: Chain C: G.116, F.117, M.118, F.169, M.175, P.176, Y.178, M.181, K.185, I.214, A.218, M.219, I.235, L.238 Ligands: NAD.7 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:F.169, C:F.169, C:Y.178, C:A.218, C:I.235, C:L.238, C:L.238 Hydrogen bonds: C:M.118, C:M.118, C:Y.178 1S5.10: 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, I.214, A.218, M.219, I.235, L.238 Ligands: NAD.9 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:F.169, D:Y.178, D:Y.178, D:A.218, D:L.238 Hydrogen bonds: D:M.118, D:M.118, D:Y.178

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

2NV.5: 5 residues within 4Å: Chain B: L.237, G.241, W.242, R.245 Ligands: 2NV.6 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.242 2NV.6: 2 residues within 4Å: Chain B: Q.234 Ligands: 2NV.5 No protein-ligand interaction detected (PLIP)

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
C

D
D

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

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