SMTL ID : 6sql.1

Crystal structure of M. tuberculosis InhA in complex with NAD+ and N-(3-(aminomethyl)phenyl)-5-chloro-3-methylbenzo[b]thiophene-2-sulfonamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.35 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: LTK.2 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:I.22, A:F.150, A:A.192 Hydrogen bonds: A:G.15, A:I.22, A:D.65, 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:L.198 pi-Stacking: A:F.42 NAD.3: 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: LTK.4 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:I.22, B:F.150, B:A.192 Hydrogen bonds: B:G.15, B:I.22, B:D.65, 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:L.198 pi-Stacking: B:F.42 NAD.5: 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: LTK.6 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:I.22, C:F.150, C:A.192 Hydrogen bonds: C:G.15, C:I.22, 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:T.197, C:T.197, C:L.198 pi-Stacking: C:F.42 NAD.7: 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: LTK.8 21 PLIP interactions: 21 interactions with chain D Hydrophobic interactions: D:I.22, D:F.150, D:A.192 Hydrogen bonds: D:G.15, D:I.22, 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:T.197, D:T.197, D:L.198 pi-Stacking: D:F.42

4 x LTK: ~{N}-[3-(aminomethyl)phenyl]-5-chloranyl-3-methyl-1-benzothiophene-2-sulfonamide(Non-covalent)

LTK.2: 11 residues within 4Å: Chain A: G.97, F.98, M.104, F.150, A.158, Y.159, M.162, A.199, M.200, I.216 Ligands: NAD.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.159, A:Y.159, A:Y.159, A:I.216, A:I.216 Hydrogen bonds: A:Y.159, A:Y.159 pi-Stacking: A:F.150 LTK.4: 11 residues within 4Å: Chain B: G.97, F.98, M.104, F.150, A.158, Y.159, M.162, A.199, M.200, I.216 Ligands: NAD.3 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:Y.159, B:Y.159, B:Y.159, B:I.216, B:I.216 Hydrogen bonds: B:Y.159, B:Y.159 pi-Stacking: B:F.150 LTK.6: 11 residues within 4Å: Chain C: G.97, F.98, M.104, F.150, A.158, Y.159, M.162, A.199, M.200, I.216 Ligands: NAD.5 8 PLIP interactions: 8 interactions with chain C Hydrophobic interactions: C:Y.159, C:Y.159, C:Y.159, C:I.216, C:I.216 Hydrogen bonds: C:Y.159 Water bridges: C:T.197 pi-Stacking: C:F.150 LTK.8: 11 residues within 4Å: Chain D: G.97, F.98, M.104, F.150, A.158, Y.159, M.162, A.199, M.200, I.216 Ligands: NAD.7 8 PLIP interactions: 8 interactions with chain D Hydrophobic interactions: D:Y.159, D:Y.159, D:Y.159, D:I.216, D:I.216 Hydrogen bonds: D:Y.159 Water bridges: D:T.197 pi-Stacking: D:F.150

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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