SMTL ID : 8otn.1

structure of InhA from mycobacterium tuberculosis in complex with inhibitor 7-((1-(3-Hydroxy-4-phenoxybenzyl)-1H-1,2,3-triazol-4-yl)methoxy)-4-methyl-2H-chromen-2-one

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.96 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 27 residues within 4Å: Chain A: G.17, I.18, I.19, S.23, I.24, F.44, L.66, D.67, V.68, S.97, I.98, G.99, F.100, I.125, M.150, D.151, F.152, M.164, K.168, A.194, G.195, P.196, I.197, T.199, L.200, A.201 Ligands: VZR.2 22 PLIP interactions: 22 interactions with chain A Hydrophobic interactions: A:I.24, A:F.152, A:F.152, A:A.194 Hydrogen bonds: A:G.17, A:I.24, A:D.67, A:D.67, A:V.68, A:I.98, A:G.99, A:Y.161, A:K.168, A:I.197, A:I.197, A:A.201 Water bridges: A:G.17, A:A.25, A:F.44, A:I.98, A:L.200 pi-Stacking: A:F.44 NAD.3: 28 residues within 4Å: Chain B: G.17, I.18, I.19, S.23, I.24, F.44, L.66, D.67, V.68, S.97, I.98, G.99, F.100, I.125, M.150, D.151, F.152, Y.161, M.164, K.168, A.194, G.195, P.196, I.197, T.199, L.200, A.201 Ligands: VZR.4 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:I.24, B:F.152, B:A.194 Hydrogen bonds: B:G.17, B:I.24, B:D.67, B:V.68, B:I.98, B:G.99, B:Y.161, B:K.168, B:I.197, B:I.197, B:A.201 Water bridges: B:G.17, B:A.25, B:F.44, B:I.98, B:L.200 pi-Stacking: B:F.44 NAD.5: 27 residues within 4Å: Chain C: G.17, I.18, I.19, S.23, I.24, F.44, L.66, D.67, V.68, S.97, I.98, G.99, F.100, I.125, M.150, D.151, F.152, M.164, K.168, A.194, G.195, P.196, I.197, T.199, L.200, A.201 Ligands: VZR.6 22 PLIP interactions: 22 interactions with chain C Hydrophobic interactions: C:I.24, C:F.152, C:A.194 Hydrogen bonds: C:G.17, C:I.24, C:D.67, C:V.68, C:I.98, C:G.99, C:K.168, C:I.197, C:I.197, C:T.199, C:A.201 Water bridges: C:F.44, C:F.44, C:F.44, C:S.97, C:S.97, C:I.98, C:L.200 pi-Stacking: C:F.44 NAD.7: 27 residues within 4Å: Chain D: G.17, I.18, I.19, S.23, I.24, F.44, L.66, D.67, V.68, S.97, I.98, G.99, F.100, I.125, M.150, D.151, F.152, M.164, K.168, A.194, G.195, P.196, I.197, T.199, L.200, A.201 Ligands: VZR.8 23 PLIP interactions: 23 interactions with chain D Hydrophobic interactions: D:I.24, D:F.152, D:A.194 Hydrogen bonds: D:G.17, D:I.24, D:D.67, D:D.67, D:V.68, D:I.98, D:G.99, D:K.168, D:I.197, D:I.197, D:T.199, D:T.199, D:A.201 Water bridges: D:A.25, D:F.44, D:F.44, D:I.98, D:L.200, D:L.200 pi-Stacking: D:F.44

4 x VZR: 4-methyl-7-[[1-[(3-oxidanyl-4-phenoxy-phenyl)methyl]-1,2,3-triazol-4-yl]methoxy]chromen-2-one(Non-covalent)

VZR.2: 21 residues within 4Å: Chain A: G.99, F.100, M.101, M.106, F.152, M.158, P.159, A.160, Y.161, M.164, K.168, A.201, M.202, I.205, V.206, Q.217, I.218, L.220, L.221 Chain B: L.271 Ligands: NAD.1 12 PLIP interactions: 11 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:M.101, A:F.152, A:M.158, A:Y.161, A:A.201, A:I.205, A:I.205, A:L.221, B:L.271 Hydrogen bonds: A:Y.161, A:Y.161, A:Q.217 VZR.4: 21 residues within 4Å: Chain A: L.271, L.272 Chain B: G.99, F.100, M.101, M.106, F.152, M.158, P.159, A.160, Y.161, M.164, A.201, M.202, I.205, V.206, Q.217, L.220, L.221, R.228 Ligands: NAD.3 11 PLIP interactions: 9 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.152, B:Y.161, B:A.201, B:I.205, B:I.205, B:L.221, A:L.271, A:L.272 Hydrogen bonds: B:Y.161, B:Y.161 pi-Stacking: B:F.152 VZR.6: 20 residues within 4Å: Chain C: G.99, F.100, M.101, M.106, F.152, M.158, P.159, A.160, Y.161, M.164, K.168, A.201, M.202, I.205, V.206, Q.217, L.220, L.221 Chain D: L.272 Ligands: NAD.5 10 PLIP interactions: 9 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:P.159, C:Y.161, C:A.201, C:M.202, C:I.205, C:I.205, C:L.221, D:L.272 Hydrogen bonds: C:Y.161 pi-Stacking: C:F.152 VZR.8: 21 residues within 4Å: Chain C: L.271, L.272 Chain D: G.99, F.100, M.101, M.106, F.152, M.158, P.159, A.160, Y.161, M.164, K.168, A.201, M.202, I.205, V.206, Q.217, L.220, L.221 Ligands: NAD.7 10 PLIP interactions: 8 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:Y.161, D:A.201, D:M.202, D:I.205, D:I.205, D:L.221, C:L.271, C:L.272 Hydrogen bonds: D:Y.161 pi-Stacking: D:F.152

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chebaiki, M. et al., Discovery of new diaryl ether inhibitors against Mycobacterium tuberculosis targeting the minor portal of InhA. Eur.J.Med.Chem. (2023)

Release Date

2023-08-16

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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