SMTL ID : 6yuu.1

Crystal structure of M. tuberculosis InhA inhibited by SKTS1

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 26 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, L.217, A.218 Ligands: F9T.2 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:I.41, A:F.169, A:F.169, A:A.211 Hydrogen bonds: A:G.34, A:I.41, A:D.84, A:D.84, A:V.85, A:I.115, A:I.115, A:G.116, A:K.185, A:I.214, A:I.214, A:A.218 Water bridges: A:A.42, A:F.61, A:F.61, A:F.61 NAD.9: 26 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, L.217, A.218 Ligands: F9T.10 20 PLIP interactions: 20 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:D.84, B:V.85, B:I.115, B:I.115, B:G.116, B:K.185, B:I.214, B:I.214, B:A.218 Water bridges: B:A.42, B:F.61, B:F.61, B:F.61 NAD.17: 26 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, L.217, A.218 Ligands: F9T.18 20 PLIP interactions: 20 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:V.85, C:I.115, C:I.115, C:G.116, C:K.185, C:I.214, C:I.214, C:T.216, C:A.218 Water bridges: C:A.42, C:F.61, C:F.61, C:F.61 NAD.25: 26 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, L.217, A.218 Ligands: F9T.26 20 PLIP interactions: 20 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:V.85, D:I.115, D:I.115, D:G.116, D:K.185, D:I.214, D:I.214, D:T.216, D:A.218 Water bridges: D:A.42, D:F.61, D:F.61, D:F.61

4 x F9T: 6-[4-(4-hexyl-2-oxidanyl-phenoxy)phenoxy]pyridin-2-ol(Non-covalent)

F9T.2: 15 residues within 4Å: Chain A: G.116, F.117, M.118, Q.120, M.123, F.169, P.176, A.177, Y.178, K.185, A.218, M.219, I.222, L.238 Ligands: NAD.1 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.169, A:F.169, A:A.177, A:Y.178, A:Y.178, A:A.218, A:M.219, A:I.222, A:I.222, A:L.238 Hydrogen bonds: A:M.118, A:Q.120, A:Q.120, A:Y.178, A:Y.178 pi-Stacking: A:F.169 F9T.10: 15 residues within 4Å: Chain B: G.116, F.117, M.118, Q.120, M.123, F.169, P.176, A.177, Y.178, K.185, A.218, M.219, I.222, L.238 Ligands: NAD.9 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:F.169, B:F.169, B:A.177, B:Y.178, B:Y.178, B:A.218, B:M.219, B:I.222, B:I.222, B:L.238 Hydrogen bonds: B:M.118, B:Q.120, B:Q.120, B:Y.178, B:Y.178 pi-Stacking: B:F.169 F9T.18: 15 residues within 4Å: Chain C: G.116, F.117, M.118, Q.120, M.123, F.169, P.176, A.177, Y.178, K.185, A.218, M.219, I.222, L.238 Ligands: NAD.17 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:F.169, C:F.169, C:A.177, C:Y.178, C:Y.178, C:A.218, C:M.219, C:I.222, C:I.222, C:L.238 Hydrogen bonds: C:M.118, C:Q.120, C:Q.120, C:Y.178 pi-Stacking: C:F.169 F9T.26: 15 residues within 4Å: Chain D: G.116, F.117, M.118, Q.120, M.123, F.169, P.176, A.177, Y.178, K.185, A.218, M.219, I.222, L.238 Ligands: NAD.25 15 PLIP interactions: 15 interactions with chain D Hydrophobic interactions: D:F.169, D:F.169, D:A.177, D:Y.178, D:Y.178, D:A.218, D:M.219, D:I.222, D:I.222, D:L.238 Hydrogen bonds: D:M.118, D:Q.120, D:Q.120, D:Y.178 pi-Stacking: D:F.169

20 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 2 residues within 4Å: Chain A: R.215, M.252 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: P.257, K.260 Chain C: P.271 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: L.81, E.82, R.97 Ligand excluded by PLIP CL.6: 3 residues within 4Å: Chain A: E.89, H.90, S.93 Ligand excluded by PLIP CL.7: 3 residues within 4Å: Chain A: D.62, L.64, R.65 Ligand excluded by PLIP CL.11: 2 residues within 4Å: Chain B: R.215, M.252 Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain B: P.257, K.260 Chain D: P.271 Ligand excluded by PLIP CL.13: 3 residues within 4Å: Chain B: L.81, E.82, R.97 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain B: E.89, H.90, S.93 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain B: D.62, L.64, R.65 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain C: R.215, M.252 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain A: P.271 Chain C: P.257, K.260 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain C: L.81, E.82, R.97 Ligand excluded by PLIP CL.22: 3 residues within 4Å: Chain C: E.89, H.90, S.93 Ligand excluded by PLIP CL.23: 3 residues within 4Å: Chain C: D.62, L.64, R.65 Ligand excluded by PLIP CL.27: 2 residues within 4Å: Chain D: R.215, M.252 Ligand excluded by PLIP CL.28: 3 residues within 4Å: Chain B: P.271 Chain D: P.257, K.260 Ligand excluded by PLIP CL.29: 3 residues within 4Å: Chain D: L.81, E.82, R.97 Ligand excluded by PLIP CL.30: 3 residues within 4Å: Chain D: E.89, H.90, S.93 Ligand excluded by PLIP CL.31: 3 residues within 4Å: Chain D: D.62, L.64, R.65 Ligand excluded by PLIP

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

NA.8: 3 residues within 4Å: Chain A: D.243, Q.244, A.246 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.244 NA.16: 3 residues within 4Å: Chain B: D.243, Q.244, A.246 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.246 NA.24: 3 residues within 4Å: Chain C: D.243, Q.244, A.246 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.244 NA.32: 3 residues within 4Å: Chain D: D.243, Q.244, A.246 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:D.243

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Eltschkner, S. et al., A Long Residence Time Enoyl-Reductase Inhibitor Explores an Extended Binding Region with Isoenzyme-Dependent Tautomer Adaptation and Differential Substrate-Binding Loop Closure. Acs Infect Dis. (2021)

Release Date

2021-03-24

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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