SMTL ID : 8otm.1

structure of InhA from mycobacterium tuberculosis in complex with N-((1-(3-hydroxy-4-phenoxybenzyl)-1H-1,2,3-triazol-4-yl)methyl)-2-oxo-2H-chromene-3-carboxamide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 27 residues within 4Å: Chain A: G.16, I.17, I.18, S.22, I.23, F.43, L.65, D.66, V.67, S.96, I.97, G.98, I.124, M.149, D.150, F.151, M.163, K.167, A.193, G.194, P.195, I.196, T.198, L.199, A.200, M.201 Ligands: VZI.2 23 PLIP interactions: 23 interactions with chain A Hydrophobic interactions: A:I.23, A:F.151, A:A.193 Hydrogen bonds: A:G.16, A:S.22, A:I.23, A:D.66, A:V.67, A:I.97, A:G.98, A:K.167, A:I.196, A:I.196, A:T.198, A:A.200 Water bridges: A:A.24, A:F.43, A:F.43, A:F.43, A:F.43, A:I.97, A:L.199 pi-Stacking: A:F.43 NAD.6: 26 residues within 4Å: Chain B: G.16, I.17, I.18, S.22, I.23, F.43, L.65, D.66, V.67, S.96, I.97, G.98, I.124, M.149, D.150, F.151, M.163, K.167, A.193, G.194, P.195, I.196, T.198, L.199, A.200 Ligands: VZI.7 24 PLIP interactions: 24 interactions with chain B Hydrophobic interactions: B:I.23, B:F.151, B:A.193 Hydrogen bonds: B:G.16, B:S.22, B:I.23, B:D.66, B:D.66, B:V.67, B:I.97, B:G.98, B:Y.160, B:K.167, B:I.196, B:I.196, B:A.200 Water bridges: B:A.24, B:F.43, B:F.43, B:F.43, B:I.97, B:L.199, B:L.199 pi-Stacking: B:F.43 NAD.10: 28 residues within 4Å: Chain C: G.16, I.17, I.18, S.22, I.23, F.43, L.65, D.66, V.67, S.96, I.97, G.98, I.124, M.149, D.150, F.151, Y.160, M.163, K.167, A.193, G.194, P.195, I.196, T.198, L.199, A.200, M.201 Ligands: VZI.11 21 PLIP interactions: 21 interactions with chain C Hydrophobic interactions: C:I.23, C:F.151, C:A.193 Hydrogen bonds: C:G.16, C:S.22, C:I.23, C:D.66, C:V.67, C:I.97, C:G.98, C:K.167, C:I.196, C:I.196, C:T.198, C:A.200 Water bridges: C:A.24, C:F.43, C:F.43, C:F.43, C:I.97 pi-Stacking: C:F.43 NAD.14: 27 residues within 4Å: Chain D: G.16, I.17, I.18, S.22, I.23, F.43, L.65, D.66, V.67, S.96, I.97, G.98, I.124, M.149, D.150, F.151, M.163, K.167, A.193, G.194, P.195, I.196, T.198, L.199, A.200, M.201 Ligands: VZI.15 24 PLIP interactions: 24 interactions with chain D Hydrophobic interactions: D:I.23, D:F.151, D:A.193 Hydrogen bonds: D:G.16, D:S.22, D:I.23, D:D.66, D:D.66, D:V.67, D:I.97, D:G.98, D:Y.160, D:K.167, D:I.196, D:I.196, D:A.200 Water bridges: D:A.24, D:F.43, D:F.43, D:F.43, D:I.97, D:L.199, D:L.199 pi-Stacking: D:F.43

4 x VZI: 2-oxidanylidene-~{N}-[[1-[(3-oxidanyl-4-phenoxy-phenyl)methyl]-1,2,3-triazol-4-yl]methyl]chromene-3-carboxamide(Non-covalent)

VZI.2: 21 residues within 4Å: Chain A: G.98, F.99, M.100, F.151, M.157, P.158, A.159, Y.160, M.163, K.167, A.200, M.201, I.204, V.205, Q.216, I.217, L.220, R.227 Chain C: L.270, L.271 Ligands: NAD.1 12 PLIP interactions: 1 interactions with chain C, 11 interactions with chain A Hydrophobic interactions: C:L.270, A:F.151, A:M.157, A:Y.160, A:A.200, A:M.201, A:I.204, A:I.204, A:L.220 Hydrogen bonds: A:Y.160, A:Y.160, A:Q.216 VZI.7: 18 residues within 4Å: Chain B: G.98, F.99, M.100, F.151, M.157, P.158, A.159, Y.160, M.163, K.167, A.200, M.201, I.204, V.205, L.220, R.227 Chain D: L.270 Ligands: NAD.6 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: B:M.157, B:Y.160, B:A.200, B:M.201, B:I.204, B:I.204, B:L.220, D:L.270, D:L.270 Hydrogen bonds: B:Y.160, B:Y.160 pi-Stacking: B:F.151 VZI.11: 19 residues within 4Å: Chain A: L.271 Chain C: G.98, F.99, M.100, M.105, F.151, M.157, P.158, A.159, Y.160, M.163, A.200, M.201, I.204, V.205, Q.216, L.219, L.220 Ligands: NAD.10 11 PLIP interactions: 10 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:F.151, C:A.200, C:M.201, C:I.204, C:I.204, C:V.205, C:L.219, C:L.220, C:L.220, A:L.271 Hydrogen bonds: C:Y.160 VZI.15: 20 residues within 4Å: Chain B: L.270, L.271 Chain D: G.98, F.99, M.100, M.105, F.151, M.157, P.158, A.159, Y.160, M.163, K.167, A.200, M.201, I.204, V.205, L.220, R.227 Ligands: NAD.14 12 PLIP interactions: 10 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:F.151, D:M.157, D:Y.160, D:A.200, D:M.201, D:I.204, D:I.204, D:L.220, B:L.270, B:L.270 Hydrogen bonds: D:Y.160, D:Y.160

3 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 4 residues within 4Å: Chain A: P.109, F.111, D.112 Chain B: K.134 2 PLIP interactions: 2 interactions with chain B Water bridges: B:E.180, B:E.180 EDO.4: 6 residues within 4Å: Chain A: Q.226, R.227, P.229, Q.269, L.271 Chain D: R.179 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:R.227, D:R.179 EDO.8: 5 residues within 4Å: Chain B: Q.226, R.227, P.229, Q.269 Chain C: R.179 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.227 Water bridges: B:P.229, B:P.229

5 x NA: SODIUM ION(Non-functional Binders)

NA.5: 3 residues within 4Å: Chain A: D.225, Q.226, A.228 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.228 NA.9: 3 residues within 4Å: Chain B: D.225, Q.226, A.228 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.226 NA.13: 3 residues within 4Å: Chain C: D.225, Q.226, A.228 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:D.225 NA.16: 3 residues within 4Å: Chain D: D.225, Q.226, A.228 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.225 NA.17: 6 residues within 4Å: Chain D: K.10, G.143, R.187, L.248, S.249, D.250 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:R.187, D:D.250, D:D.250

1 x ACT: ACETATE ION(Non-functional Binders)

ACT.12: 3 residues within 4Å: Chain C: L.63, E.64, R.79 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.64 Water bridges: C:L.62 Salt bridges: C:R.79

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]