SMTL ID : 5kgs.1

Crystal structure of 7,8-diaminopelargonic acid synthase (BioA) from Mycobacterium tuberculosis, complexed with an inhibitor optimized from HTS lead: 5-[4-(1,3-benzodioxol-5-ylcarbonyl)piperazin-1-yl]-2,3-dihydroinden-1-one

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.10 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 18 PLIP interactions: 14 interactions with chain A, 4 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, A:S.145, B:T.338, B:T.338, B:T.338 Water bridges: A:S.143, 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.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 14 PLIP interactions: 3 interactions with chain A, 11 interactions with chain B Hydrogen bonds: A:T.338, A:T.338, B:G.144, B:S.145 Water bridges: A:G.336, B:S.143, B:S.145, B:Y.177, B:E.240 Hydrophobic interactions: B:E.240, B:I.276, B:K.303 Salt bridges: B:K.303 pi-Stacking: B:Y.177

2 x 6SR: 5-[4-(1,3-benzodioxol-5-ylcarbonyl)piperazin-1-yl]-2,3-dihydroinden-1-one(Non-covalent)

6SR.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 11 PLIP interactions: 2 interactions with chain B, 9 interactions with chain A Hydrogen bonds: B:F.112, B:G.113 Hydrophobic interactions: A:P.44, A:P.44, A:Y.45, A:F.422 pi-Stacking: A:W.84, A:W.84, A:W.84, A:Y.177, A:Y.177 6SR.5: 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 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:P.44, B:P.44, B:Y.45, B:F.422 Water bridges: B:D.189 pi-Stacking: B:W.84, B:W.84, B:W.84, B:Y.177, B:Y.177 Hydrogen bonds: A:F.112, A:G.113

2 x PGE: TRIETHYLENE GLYCOL(Non-functional Binders)

PGE.3: 8 residues within 4Å: Chain A: R.213, D.214, F.251, H.252, D.253, P.254, H.291, C.391 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.214, A:D.253 PGE.6: 9 residues within 4Å: Chain B: R.213, D.214, V.242, F.251, H.252, D.253, P.254, H.291, C.391 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:D.214 Water bridges: B:D.214, B:R.255

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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