SMTL ID : 6sq9.1

Crystal structure of M. tuberculosis InhA in complex with NAD+ and 3-hydroxynaphthalene-2-carboxylic acid

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.75 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 24 residues within 4Å: Chain A: G.15, I.16, I.17, S.21, I.22, F.42, L.64, D.65, V.66, S.95, I.96, G.97, I.123, M.148, D.149, F.150, K.166, A.192, G.193, P.194, I.195, T.197, M.200 Ligands: BZJ.2 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:I.22, A:F.150, A:A.192 Hydrogen bonds: A:G.15, A:S.21, A:I.22, A:D.65, A:V.66, A:I.96, A:G.97, A:K.166, A:I.195, A:I.195 Water bridges: A:A.23, A:F.42, A:F.42, A:F.42, A:I.96, A:G.97, A:T.197, A:T.197, A:L.198 pi-Stacking: A:F.42 NAD.4: 24 residues within 4Å: Chain B: G.15, I.16, I.17, S.21, I.22, F.42, L.64, D.65, V.66, S.95, I.96, G.97, I.123, M.148, D.149, F.150, K.166, A.192, G.193, P.194, I.195, T.197, M.200 Ligands: BZJ.5 23 PLIP interactions: 23 interactions with chain B Hydrophobic interactions: B:I.22, B:F.150, B:A.192 Hydrogen bonds: B:G.15, B:S.21, B:I.22, B:D.65, B:V.66, B:I.96, B:G.97, B:K.166, B:I.195, B:I.195 Water bridges: B:A.23, B:F.42, B:F.42, B:F.42, B:I.96, B:G.97, B:T.197, B:T.197, B:L.198 pi-Stacking: B:F.42 NAD.7: 24 residues within 4Å: Chain C: G.15, I.16, I.17, S.21, I.22, F.42, L.64, D.65, V.66, S.95, I.96, G.97, I.123, M.148, D.149, F.150, K.166, A.192, G.193, P.194, I.195, T.197, M.200 Ligands: BZJ.8 23 PLIP interactions: 23 interactions with chain C Hydrophobic interactions: C:I.22, C:F.150, C:A.192 Hydrogen bonds: C:G.15, C:S.21, C:I.22, C:D.65, C:D.65, C:V.66, C:I.96, C:G.97, C:K.166, C:I.195, C:I.195 Water bridges: C:A.23, C:F.42, C:F.42, C:F.42, C:I.96, C:G.97, C:T.197, C:T.197 pi-Stacking: C:F.42 NAD.10: 24 residues within 4Å: Chain D: G.15, I.16, I.17, S.21, I.22, F.42, L.64, D.65, V.66, S.95, I.96, G.97, I.123, M.148, D.149, F.150, K.166, A.192, G.193, P.194, I.195, T.197, M.200 Ligands: BZJ.11 23 PLIP interactions: 23 interactions with chain D Hydrophobic interactions: D:I.22, D:F.150, D:A.192 Hydrogen bonds: D:G.15, D:S.21, D:I.22, D:D.65, D:D.65, D:V.66, D:I.96, D:G.97, D:K.166, D:I.195, D:I.195 Water bridges: D:A.23, D:F.42, D:F.42, D:F.42, D:I.96, D:G.97, D:T.197, D:T.197 pi-Stacking: D:F.42

4 x BZJ: 3-hydroxynaphthalene-2-carboxylic acid(Non-covalent)

BZJ.2: 8 residues within 4Å: Chain A: F.150, Y.159, M.162, T.163, K.166, M.200, L.219 Ligands: NAD.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:F.150, A:Y.159, A:L.219 Salt bridges: A:K.166 pi-Stacking: A:F.150, A:F.150, A:Y.159, A:Y.159 BZJ.5: 8 residues within 4Å: Chain B: F.150, Y.159, M.162, T.163, K.166, M.200, L.219 Ligands: NAD.4 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.150, B:Y.159, B:L.219 Salt bridges: B:K.166 pi-Stacking: B:F.150, B:F.150, B:Y.159, B:Y.159 BZJ.8: 8 residues within 4Å: Chain C: F.150, Y.159, M.162, T.163, K.166, M.200, L.219 Ligands: NAD.7 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:F.150, C:Y.159, C:L.219 Salt bridges: C:K.166 pi-Stacking: C:F.150, C:F.150, C:Y.159, C:Y.159 BZJ.11: 8 residues within 4Å: Chain D: F.150, Y.159, M.162, T.163, K.166, M.200, L.219 Ligands: NAD.10 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:F.150, D:Y.159, D:L.219 Salt bridges: D:K.166 pi-Stacking: D:F.150, D:F.150, D:Y.159, D:Y.159

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

EPE.3: 6 residues within 4Å: Chain A: D.43, R.44, L.45, R.46, E.63, H.71 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.45, A:R.46 Water bridges: A:L.47 Salt bridges: A:E.63, A:E.63 EPE.6: 6 residues within 4Å: Chain B: D.43, R.44, L.45, R.46, E.63, H.71 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.45, B:R.46 Water bridges: B:L.47 Salt bridges: B:E.63, B:E.63 EPE.9: 6 residues within 4Å: Chain C: D.43, R.44, L.45, R.46, E.63, H.71 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:L.45, C:R.46 Water bridges: C:L.47 Salt bridges: C:E.63, C:E.63 EPE.12: 6 residues within 4Å: Chain D: D.43, R.44, L.45, R.46, E.63, H.71 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:L.45, D:R.46 Water bridges: D:L.47 Salt bridges: D:E.63, D:E.63

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sabbah, M. et al., Fragment-Based Design ofMycobacterium tuberculosisInhA Inhibitors. J.Med.Chem. (2020)

Release Date

2020-04-22

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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