SMTL ID : 4xjp.1

Crystal structure of 7,8-diaminopelargonic acid synthase (BioA) from Mycobacterium tuberculosis, complexed with an inhibitor optimized from HTS lead

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)

PLP.1: 13 residues within 4Å: Chain A: S.143, G.144, S.145, Y.177, H.178, G.179, E.240, D.274, I.276, A.277, K.303 Chain B: P.337, T.338 14 PLIP interactions: 12 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:E.240, A:I.276, A:K.303 Hydrogen bonds: A:G.144, A:S.145, B:T.338, B:T.338 Water bridges: A:S.143, A:S.145, A:S.145, A:D.180, A:E.240 Salt bridges: A:K.303 pi-Stacking: A:Y.177 PLP.5: 14 residues within 4Å: Chain A: P.337, T.338 Chain B: S.143, G.144, S.145, Y.177, H.178, G.179, E.240, D.274, I.276, A.277, K.303 Ligands: EDO.8 17 PLIP interactions: 13 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:Y.177, B:E.240, B:I.276, B:K.303 Hydrogen bonds: B:G.144, B:S.145, B:S.145, A:T.338, A:T.338, A:T.338 Water bridges: B:S.143, B:S.145, B:D.180, B:E.240, A:F.339 Salt bridges: B:K.303 pi-Stacking: B:Y.177

2 x 41N: 1-{4-[4-(1,3-benzodioxol-5-ylcarbonyl)piperazin-1-yl]phenyl}ethanone(Non-covalent)

41N.2: 18 residues within 4Å: Chain A: P.44, Y.45, W.84, G.176, Y.177, C.188, D.189, G.192, G.193, A.246, G.247, F.422 Chain B: M.111, F.112, G.113, G.336, P.337, T.338 10 PLIP interactions: 2 interactions with chain B, 8 interactions with chain A Hydrogen bonds: B:F.112, B:G.113 Hydrophobic interactions: A:P.44, A:Y.45, A:W.84, A:F.422 Water bridges: A:D.189 pi-Stacking: A:W.84, A:W.84, A:Y.177 41N.6: 18 residues within 4Å: Chain A: M.111, F.112, G.113, G.336, P.337, T.338 Chain B: P.44, Y.45, W.84, G.176, Y.177, C.188, D.189, G.192, G.193, A.246, G.247, F.422 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:P.44, B:Y.45, B:W.84 Water bridges: B:G.192 pi-Stacking: B:W.84, B:W.84, B:Y.177 Hydrogen bonds: A:F.112, A:G.113

5 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 3 residues within 4Å: Chain A: L.405, F.422, R.423 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.423 Water bridges: A:L.405, A:P.421 EDO.7: 2 residues within 4Å: Chain B: W.65, E.76 1 PLIP interactions: 1 interactions with chain B Water bridges: B:E.76 EDO.8: 10 residues within 4Å: Chain A: D.142, F.339 Chain B: D.142, S.143, G.144, G.302, K.303, S.311, L.312 Ligands: PLP.5 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.302, B:L.312, A:D.142 Water bridges: B:G.144, B:L.305 EDO.9: 6 residues within 4Å: Chain B: G.375, T.378, T.440, T.443, S.444, V.447 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.443, B:S.444 Water bridges: B:T.440 EDO.11: 2 residues within 4Å: Chain B: R.266, Y.267 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.267

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.4: 6 residues within 4Å: Chain A: R.213, V.242, F.251, H.252, D.253, P.254 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.253 Water bridges: A:D.253, A:R.255 PEG.10: 7 residues within 4Å: Chain B: R.213, V.242, H.252, D.253, P.254, H.291, C.391 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.213

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, F. et al., Structure-Based Optimization of Pyridoxal 5'-Phosphate-Dependent Transaminase Enzyme (BioA) Inhibitors that Target Biotin Biosynthesis in Mycobacterium tuberculosis. J. Med. Chem. (2017)

Release Date

2016-01-20

Peptides

Adenosylmethionine-8-amino-7-oxononanoate aminotransferase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Adenosylmethionine-8-amino-7-oxononanoate aminotransferase

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