SMTL ID : 4uvd.1

Discovery of pyrimidine isoxazoles InhA in complex with compound 6

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 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: HRW.3 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:I.21, A:D.64, 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:F.41, A:I.95 pi-Stacking: A:F.41 NAD.4: 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: HRW.6 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:I.21, B:D.64, B:V.65, B:I.95, B:G.96, B:K.165, B:I.194, B:I.194, B:T.196 Water bridges: B:A.22, B:F.41, B:F.41, B:F.41, B:I.95 pi-Stacking: B:F.41 NAD.7: 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: HRW.9 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: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:F.41, C:I.95 pi-Stacking: C:F.41 NAD.10: 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: HRW.12 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:I.21, D:D.64, D:V.65, D:I.95, D:G.96, D:K.165, D:I.194, D:I.194, D:T.196 Water bridges: D:A.22, D:F.41, D:F.41, D:F.41, D:I.95 pi-Stacking: D:F.41

4 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 1 residues within 4Å: Chain A: D.52 5 PLIP interactions: 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: A:D.52, H2O.3, H2O.10, H2O.10, H2O.10 MG.5: 1 residues within 4Å: Chain B: D.52 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:D.52, H2O.13, H2O.20, H2O.20, H2O.20 MG.8: 1 residues within 4Å: Chain C: D.52 5 PLIP interactions: 1 interactions with chain C, 4 Ligand-Water interactions Metal complexes: C:D.52, H2O.23, H2O.29, H2O.29, H2O.29 MG.11: 1 residues within 4Å: Chain D: D.52 5 PLIP interactions: 1 interactions with chain D, 4 Ligand-Water interactions Metal complexes: D:D.52, H2O.32, H2O.39, H2O.39, H2O.39

4 x HRW: 2-[(4,6-dimethylpyrimidin-2-yl)sulfanyl]-N-[(2Z)-5-[3-(trifluoromethyl)benzyl]-1,3-thiazol-2(3H)-ylidene]acetamide(Non-covalent)

HRW.3: 12 residues within 4Å: Chain A: G.96, F.97, M.98, Q.100, F.149, A.198, M.199, A.201, I.202, A.206, L.207 Ligands: NAD.1 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Q.100, A:F.149, A:I.202, A:L.207 Hydrogen bonds: A:M.98 HRW.6: 12 residues within 4Å: Chain B: G.96, F.97, M.98, Q.100, F.149, A.198, M.199, A.201, I.202, A.206, L.207 Ligands: NAD.4 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:Q.100, B:F.149, B:I.202, B:L.207 Hydrogen bonds: B:M.98 HRW.9: 12 residues within 4Å: Chain C: G.96, F.97, M.98, Q.100, F.149, A.198, M.199, A.201, I.202, A.206, L.207 Ligands: NAD.7 5 PLIP interactions: 5 interactions with chain C Hydrophobic interactions: C:Q.100, C:F.149, C:I.202, C:L.207 Hydrogen bonds: C:M.98 HRW.12: 12 residues within 4Å: Chain D: G.96, F.97, M.98, Q.100, F.149, A.198, M.199, A.201, I.202, A.206, L.207 Ligands: NAD.10 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:Q.100, D:F.149, D:I.202, D:L.207 Hydrogen bonds: 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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