SMTL ID : 5kgt.1

Crystal structure of 7,8-diaminopelargonic acid synthase (BioA) from Mycobacterium tuberculosis, complexed with an inhibitor optimized from HTS lead: 1-[4-[4-(3-chlorophenyl)carbonylpiperidin-1-yl]phenyl]ethanone

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

homo-dimer

Ligands

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

PLP.1: 14 residues within 4Å: Chain A: W.85, 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: 11 interactions with chain A, 3 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.145, A:S.145, A:D.180, A:E.240, B:F.339 Salt bridges: A:K.303 pi-Stacking: A:Y.177 PLP.3: 13 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 15 PLIP interactions: 4 interactions with chain A, 11 interactions with chain B Hydrogen bonds: A:T.338, A:T.338, A:T.338, B:G.144, B:S.145, B:S.145 Water bridges: A:F.339, B:S.145, B:D.180, B:E.240 Hydrophobic interactions: B:E.240, B:I.276, B:K.303 Salt bridges: B:K.303 pi-Stacking: B:Y.177

1 x 6SQ: 1-[4-[4-(3-chlorophenyl)carbonylpiperidin-1-yl]phenyl]ethanone(Non-covalent)

6SQ.2: 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, D.189, G.192, G.193, A.246, G.247, F.422, R.423 10 PLIP interactions: 1 interactions with chain A, 9 interactions with chain B Hydrogen bonds: A:G.113, B:R.423 Hydrophobic interactions: B:P.44, B:Y.45, B:W.84, B:A.246 pi-Stacking: B:W.84, B:W.84, B:Y.177 Halogen bonds: B:G.176

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

2017-06-14

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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