SMTL ID : 5oir.1

InhA (T2A mutant) complexed with 2,6-Dimethyl-3-(1-(pyrimidin-2-yl)piperidin-4-yl)pyridin-4(1H)-one

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 24 residues within 4Å: Chain A: G.14, I.15, I.16, S.20, I.21, F.41, L.63, D.64, V.65, S.94, I.95, G.96, I.122, M.147, D.148, F.149, M.161, K.165, A.191, G.192, P.193, I.194, T.196 Ligands: 9W8.2 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:I.21, A:F.149, A:A.191 Hydrogen bonds: A:G.14, A:S.20, A:I.21, A:D.64, A:V.65, A:I.95, A:G.96, A:K.165, A:I.194, A:T.196, A:T.196 Water bridges: A:A.22, A:F.41, A:F.41, A:I.95 pi-Stacking: A:F.41 NAD.8: 24 residues within 4Å: Chain B: G.14, I.15, I.16, S.20, I.21, F.41, L.63, D.64, V.65, S.94, I.95, G.96, I.122, M.147, D.148, F.149, M.161, K.165, A.191, G.192, P.193, I.194, T.196 Ligands: 9W8.9 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:I.21, B:F.149, B:A.191 Hydrogen bonds: B:G.14, B:S.20, B:I.21, B:D.64, B:V.65, B:I.95, B:G.96, B:K.165, B:I.194, B:T.196, B:T.196 Water bridges: B:A.22, B:F.41, B:F.41, B:I.95 pi-Stacking: B:F.41 NAD.15: 24 residues within 4Å: Chain C: G.14, I.15, I.16, S.20, I.21, F.41, L.63, D.64, V.65, S.94, I.95, G.96, I.122, M.147, D.148, F.149, M.161, K.165, A.191, G.192, P.193, I.194, T.196 Ligands: 9W8.16 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:I.21, C:F.149, C:A.191 Hydrogen bonds: C:G.14, C:S.20, C:I.21, C:D.64, C:D.64, C:V.65, C:I.95, C:G.96, C:K.165, C:I.194, C:T.196 Water bridges: C:A.22, C:F.41, C:F.41, C:I.95 pi-Stacking: C:F.41 NAD.22: 24 residues within 4Å: Chain D: G.14, I.15, I.16, S.20, I.21, F.41, L.63, D.64, V.65, S.94, I.95, G.96, I.122, M.147, D.148, F.149, M.161, K.165, A.191, G.192, P.193, I.194, T.196 Ligands: 9W8.23 19 PLIP interactions: 19 interactions with chain D Hydrophobic interactions: D:I.21, D:F.149, D:A.191 Hydrogen bonds: D:G.14, D:S.20, D:I.21, D:D.64, D:D.64, D:V.65, D:I.95, D:G.96, D:K.165, D:I.194, D:T.196 Water bridges: D:A.22, D:F.41, D:F.41, D:I.95 pi-Stacking: D:F.41

4 x 9W8: 2,6-dimethyl-3-(1-pyrimidin-2-ylpiperidin-4-yl)-1~{H}-pyridin-4-one(Non-covalent)

9W8.2: 11 residues within 4Å: Chain A: G.96, F.97, M.98, M.103, F.149, Y.158, M.161, K.165, M.199 Ligands: NAD.1, ETX.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.97, A:F.149, A:F.149, A:Y.158 Hydrogen bonds: A:M.98 9W8.9: 11 residues within 4Å: Chain B: G.96, F.97, M.98, M.103, F.149, Y.158, M.161, K.165, M.199 Ligands: NAD.8, ETX.10 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.97, B:F.149, B:F.149, B:Y.158 Hydrogen bonds: B:M.98 9W8.16: 11 residues within 4Å: Chain C: G.96, F.97, M.98, M.103, F.149, Y.158, M.161, K.165, M.199 Ligands: NAD.15, ETX.17 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:F.97, C:F.149, C:F.149, C:Y.158 Hydrogen bonds: C:M.98, C:Y.158 9W8.23: 11 residues within 4Å: Chain D: G.96, F.97, M.98, M.103, F.149, Y.158, M.161, K.165, M.199 Ligands: NAD.22, ETX.24 6 PLIP interactions: 6 interactions with chain D Hydrophobic interactions: D:F.97, D:F.149, D:F.149, D:Y.158 Hydrogen bonds: D:M.98, D:Y.158

16 x ETX: 2-ETHOXYETHANOL(Non-covalent)

ETX.3: 11 residues within 4Å: Chain A: M.103, G.104, F.149, M.155, A.157, Y.158, I.202, L.207, I.215, L.218 Ligands: 9W8.2 Ligand excluded by PLIP ETX.4: 4 residues within 4Å: Chain A: K.132 Chain C: F.109, D.110, A.111 Ligand excluded by PLIP ETX.5: 6 residues within 4Å: Chain A: S.152 Chain B: D.150, S.152, Y.259, H.265, T.266 Ligand excluded by PLIP ETX.6: 4 residues within 4Å: Chain A: F.97, P.99, Q.100, K.118 Ligand excluded by PLIP ETX.10: 11 residues within 4Å: Chain B: M.103, G.104, F.149, M.155, A.157, Y.158, I.202, L.207, I.215, L.218 Ligands: 9W8.9 Ligand excluded by PLIP ETX.11: 4 residues within 4Å: Chain B: K.132 Chain D: F.109, D.110, A.111 Ligand excluded by PLIP ETX.12: 6 residues within 4Å: Chain A: D.150, S.152, Y.259, H.265, T.266 Chain B: S.152 Ligand excluded by PLIP ETX.13: 4 residues within 4Å: Chain B: F.97, P.99, Q.100, K.118 Ligand excluded by PLIP ETX.17: 11 residues within 4Å: Chain C: M.103, G.104, F.149, M.155, A.157, Y.158, I.202, L.207, I.215, L.218 Ligands: 9W8.16 Ligand excluded by PLIP ETX.18: 4 residues within 4Å: Chain A: F.109, D.110, A.111 Chain C: K.132 Ligand excluded by PLIP ETX.19: 6 residues within 4Å: Chain C: S.152 Chain D: D.150, S.152, Y.259, H.265, T.266 Ligand excluded by PLIP ETX.20: 4 residues within 4Å: Chain C: F.97, P.99, Q.100, K.118 Ligand excluded by PLIP ETX.24: 11 residues within 4Å: Chain D: M.103, G.104, F.149, M.155, A.157, Y.158, I.202, L.207, I.215, L.218 Ligands: 9W8.23 Ligand excluded by PLIP ETX.25: 4 residues within 4Å: Chain B: F.109, D.110, A.111 Chain D: K.132 Ligand excluded by PLIP ETX.26: 6 residues within 4Å: Chain C: D.150, S.152, Y.259, H.265, T.266 Chain D: S.152 Ligand excluded by PLIP ETX.27: 4 residues within 4Å: Chain D: F.97, P.99, Q.100, K.118 Ligand excluded by PLIP

4 x SO4: SULFATE ION(Non-functional Binders)

SO4.7: 7 residues within 4Å: Chain A: S.19, H.24, I.194, R.195, T.196, K.233, A.235 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.235 Water bridges: A:H.24, A:K.233 Salt bridges: A:H.24 SO4.14: 7 residues within 4Å: Chain B: S.19, H.24, I.194, R.195, T.196, K.233, A.235 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.235 Water bridges: B:H.24, B:K.233 Salt bridges: B:H.24 SO4.21: 7 residues within 4Å: Chain C: S.19, H.24, I.194, R.195, T.196, K.233, A.235 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:A.235 Water bridges: C:H.24, C:K.233 Salt bridges: C:H.24 SO4.28: 7 residues within 4Å: Chain D: S.19, H.24, I.194, R.195, T.196, K.233, A.235 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:A.235 Water bridges: D:H.24, D:K.233 Salt bridges: D:H.24

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Prati, F. et al., Screening of a Novel Fragment Library with Functional Complexity against Mycobacterium tuberculosis InhA. ChemMedChem (2018)

Release Date

2018-02-14

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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