SMTL ID : 5oip.1

InhA (T2A mutant) complexed with 1-(Pyridin-3-ylmethyl)-3-(1-(pyrimidin-2-yl)piperidin-4-yl)urea

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.71 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 25 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, M.199 Ligands: 9WE.2 20 PLIP interactions: 20 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:I.194 Water bridges: A:A.22, A:F.41, A:F.41, A:I.95, A:T.196, A:T.196 pi-Stacking: A:F.41 NAD.4: 25 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, M.199 Ligands: 9WE.5 20 PLIP interactions: 20 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:I.194 Water bridges: B:A.22, B:F.41, B:F.41, B:I.95, B:T.196, B:T.196 pi-Stacking: B:F.41 NAD.7: 25 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, M.199 Ligands: 9WE.8 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:I.194 Water bridges: C:A.22, C:F.41, C:F.41, C:I.95 pi-Stacking: C:F.41 NAD.10: 25 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, M.199 Ligands: 9WE.11 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:I.194 Water bridges: D:A.22, D:F.41, D:F.41, D:I.95 pi-Stacking: D:F.41

4 x 9WE: 1-(pyridin-3-ylmethyl)-3-(1-pyrimidin-2-ylpiperidin-4-yl)urea(Non-covalent)

9WE.2: 15 residues within 4Å: Chain A: G.96, F.97, M.98, M.103, F.149, M.155, Y.158, M.161, P.193, A.198, M.199, I.215, L.218, E.219 Ligands: NAD.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:F.97, A:Y.158, A:L.218 Hydrogen bonds: A:M.98 pi-Stacking: A:F.149 9WE.5: 15 residues within 4Å: Chain B: G.96, F.97, M.98, M.103, F.149, M.155, Y.158, M.161, P.193, A.198, M.199, I.215, L.218, E.219 Ligands: NAD.4 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:F.97, B:Y.158, B:L.218 Hydrogen bonds: B:M.98 pi-Stacking: B:F.149 9WE.8: 15 residues within 4Å: Chain C: G.96, F.97, M.98, M.103, F.149, M.155, Y.158, M.161, P.193, A.198, M.199, I.215, L.218, E.219 Ligands: NAD.7 7 PLIP interactions: 7 interactions with chain C Hydrophobic interactions: C:F.97, C:Y.158, C:L.218 Hydrogen bonds: C:M.98, C:Y.158, C:E.219 pi-Stacking: C:F.149 9WE.11: 15 residues within 4Å: Chain D: G.96, F.97, M.98, M.103, F.149, M.155, Y.158, M.161, P.193, A.198, M.199, I.215, L.218, E.219 Ligands: NAD.10 7 PLIP interactions: 7 interactions with chain D Hydrophobic interactions: D:F.97, D:Y.158, D:L.218 Hydrogen bonds: D:M.98, D:Y.158, D:E.219 pi-Stacking: D:F.149

4 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 7 residues within 4Å: Chain A: S.19, H.24, I.194, R.195, K.233, D.234, A.235 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.195, A:A.235 Water bridges: A:S.19 Salt bridges: A:H.24 PO4.6: 7 residues within 4Å: Chain B: S.19, H.24, I.194, R.195, K.233, D.234, A.235 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.195, B:A.235 Water bridges: B:S.19 Salt bridges: B:H.24 PO4.9: 7 residues within 4Å: Chain C: S.19, H.24, I.194, R.195, K.233, D.234, A.235 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.195, C:A.235 Water bridges: C:S.19 Salt bridges: C:H.24 PO4.12: 7 residues within 4Å: Chain D: S.19, H.24, I.194, R.195, K.233, D.234, A.235 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:R.195, D:A.235 Water bridges: D:S.19 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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