SMTL ID : 4xjo.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 1.50 Å

Oligo State

homo-dimer

Ligands

2 x PLP: PYRIDOXAL-5'-PHOSPHATE(Covalent)(Non-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 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:Y.177, 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.4: 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: 11 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:Y.177, B:E.240, B:I.276 Hydrogen bonds: B:G.144, B:S.145, B:S.145, B:K.303, A:T.338, A:T.338, A:T.338 Water bridges: B:S.145, B:D.180, B:E.240, A:F.339 pi-Stacking: B:Y.177

2 x 41O: 5-[4-(3-chlorobenzoyl)piperazin-1-yl]-1H-inden-1-one(Non-covalent)

41O.2: 15 residues within 4Å: Chain A: P.44, Y.45, W.84, G.176, Y.177, G.192, G.193, A.246, G.247 Chain B: M.111, F.112, G.113, G.336, P.337, T.338 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:P.44, A:P.44, A:Y.45 Water bridges: A:R.423 pi-Stacking: A:W.84, A:W.84, A:W.84, A:Y.177 Halogen bonds: A:G.176 Hydrogen bonds: B:F.112, B:G.113 41O.5: 16 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 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:P.44, B:P.44, B:Y.45 pi-Stacking: B:W.84, B:W.84, B:W.84, B:Y.177 Halogen bonds: B:G.176 Hydrogen bonds: A:F.112, A:G.113

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

EDO.3: 5 residues within 4Å: Chain A: R.364, I.433, C.434, T.435, P.436 No protein-ligand interaction detected (PLIP)

1 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 8 residues within 4Å: Chain B: Y.158, W.159, R.261, C.264, E.268, V.269, L.270, D.297 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Y.158, B:Y.158, B:R.261, B:C.264, B:V.269

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.7: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP

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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