SMTL ID : 4uvg.1

Discovery of pyrimidine isoxazoles InhA in complex with compound 15

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 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, K.165, A.191, G.192, P.193, I.194, T.196, M.199 Ligands: A0C.4 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:I.21, A:F.149, A:F.149, A:A.191 Hydrogen bonds: A:G.14, A:I.21, A:D.64, A:D.64, A:V.65, A:I.95, A:G.96, A:K.165, A:I.194, A:T.196 Water bridges: A:G.14, A:A.22, A:F.41, A:F.41, A:I.95 pi-Stacking: A:F.41 NAD.5: 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, K.165, A.191, G.192, P.193, I.194, T.196, M.199 Ligands: A0C.8 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:I.21, B:F.149, B:F.149, B:A.191 Hydrogen bonds: B:G.14, 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:G.14, B:A.22, B:F.41, B:F.41, B:I.95 pi-Stacking: B:F.41 NAD.9: 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, K.165, A.191, G.192, P.193, I.194, T.196, M.199 Ligands: A0C.12 20 PLIP interactions: 20 interactions with chain C Hydrophobic interactions: C:I.21, C:F.149, C:F.149, C:A.191 Hydrogen bonds: C:G.14, 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:G.14, C:A.22, C:F.41, C:F.41, C:I.95 pi-Stacking: C:F.41 NAD.13: 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, K.165, A.191, G.192, P.193, I.194, T.196, M.199 Ligands: A0C.16 20 PLIP interactions: 20 interactions with chain D Hydrophobic interactions: D:I.21, D:F.149, D:F.149, D:A.191 Hydrogen bonds: D:G.14, D:I.21, D:D.64, D:V.65, D:I.95, D:G.96, D:K.165, D:I.194, D:T.196, D:T.196 Water bridges: D:G.14, D:A.22, D:F.41, D:F.41, D:I.95 pi-Stacking: D:F.41

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 2 residues within 4Å: Chain A: D.52 Ligands: 1PE.3 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.52, H2O.13 MG.6: 2 residues within 4Å: Chain B: D.52 Ligands: 1PE.7 2 PLIP interactions: 1 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:D.52, H2O.25 MG.10: 2 residues within 4Å: Chain C: D.52 Ligands: 1PE.11 2 PLIP interactions: 1 interactions with chain C, 1 Ligand-Water interactions Metal complexes: C:D.52, H2O.37 MG.14: 2 residues within 4Å: Chain D: D.52 Ligands: 1PE.15 2 PLIP interactions: 1 interactions with chain D, 1 Ligand-Water interactions Metal complexes: D:D.52, H2O.49

4 x 1PE: PENTAETHYLENE GLYCOL(Non-functional Binders)

1PE.3: 5 residues within 4Å: Chain A: D.52, R.53, L.54, P.55 Ligands: MG.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:L.54, A:P.55, A:K.57 1PE.7: 5 residues within 4Å: Chain B: D.52, R.53, L.54, P.55 Ligands: MG.6 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.54, B:P.55, B:K.57 1PE.11: 5 residues within 4Å: Chain C: D.52, R.53, L.54, P.55 Ligands: MG.10 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:L.54, C:P.55, C:K.57 1PE.15: 5 residues within 4Å: Chain D: D.52, R.53, L.54, P.55 Ligands: MG.14 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:L.54, D:P.55, D:K.57

4 x A0C: 5-[(4,6-dimethylpyrimidin-2-yl)sulfanylmethyl]isoxazole-3-carboxamide(Non-covalent)

A0C.4: 8 residues within 4Å: Chain A: G.96, F.97, M.98, F.149, M.161, M.199, I.202 Ligands: NAD.1 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.149, A:I.202 Hydrogen bonds: A:M.98, A:M.98 A0C.8: 8 residues within 4Å: Chain B: G.96, F.97, M.98, F.149, M.161, M.199, I.202 Ligands: NAD.5 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.149, B:I.202 Hydrogen bonds: B:M.98, B:M.98 A0C.12: 8 residues within 4Å: Chain C: G.96, F.97, M.98, F.149, M.161, M.199, I.202 Ligands: NAD.9 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.149, C:I.202 Hydrogen bonds: C:M.98, C:M.98 A0C.16: 8 residues within 4Å: Chain D: G.96, F.97, M.98, F.149, M.161, M.199, I.202 Ligands: NAD.13 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:F.149, D:I.202 Hydrogen bonds: D:M.98, D:M.98

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Madhavapeddi, P. et al., Hitting the Target in More Than One Way: Novel, Direct Inhibitors of Mycobacterium Tuberculosis Enoyl Acp Reductase. To be Published

Release Date

2015-09-30

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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