SMTL ID : 5i5w.1

X-RAY CRYSTAL STRUCTURE AT 2.40A RESOLUTION OF HUMAN MITOCHONDRIAL BRANCHED CHAIN AMINOTRANSFERASE (BCATM) COMPLEXED WITH A BIARYL AMIDE COMPOUND AND AN INTERNAL ALDIMINE LINKED PLP COFACTOR.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-dimer

Ligands

2 x 68B: N-(pyrimidin-5-yl)benzamide(Non-covalent)

68B.1: 11 residues within 4Å: Chain A: F.34, F.79, Y.145, R.147, K.206, T.244, A.318 Chain B: Y.74, V.159 Ligands: PLP.2, CL.12 9 PLIP interactions: 7 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.79, A:T.244, B:Y.74, B:V.159 Hydrogen bonds: A:K.83, A:Y.145 Water bridges: A:T.244, A:T.244 pi-Stacking: A:F.34 68B.10: 12 residues within 4Å: Chain A: Y.74, V.159 Chain B: F.34, F.79, Y.145, R.147, Y.177, K.206, T.244, A.318 Ligands: CL.3, PLP.11 6 PLIP interactions: 4 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.79, B:T.244, A:Y.74, A:V.159 Hydrogen bonds: B:A.318 pi-Stacking: B:F.34

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

PLP.2: 15 residues within 4Å: Chain A: R.103, R.196, K.206, Y.211, E.241, T.244, M.245, N.246, L.270, G.272, V.273, V.274, G.316, T.317 Ligands: 68B.1 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:K.206, A:Y.211, A:L.270 Hydrogen bonds: A:K.206, A:Y.211, A:V.273, A:V.274, A:T.317, A:T.317 Water bridges: A:R.103, A:R.103, A:R.103, A:R.103, A:R.275 Salt bridges: A:R.103, A:K.206 PLP.11: 15 residues within 4Å: Chain B: R.103, R.196, K.206, Y.211, E.241, T.244, M.245, N.246, L.270, G.272, V.273, V.274, G.316, T.317 Ligands: 68B.10 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:K.206 Hydrogen bonds: B:K.206, B:Y.211, B:Y.211, B:V.273, B:V.274, B:T.317, B:T.317 Water bridges: B:R.103, B:R.103, B:R.103, B:R.103, B:R.275 Salt bridges: B:R.103, B:K.206

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

CL.3: 2 residues within 4Å: Chain A: V.159 Ligands: 68B.10 Ligand excluded by PLIP CL.4: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP CL.12: 3 residues within 4Å: Chain B: G.158, V.159 Ligands: 68B.1 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain B: N.204, L.265 Ligand excluded by PLIP

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

EDO.5: 4 residues within 4Å: Chain A: Y.250, E.344, L.345, R.348 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.250, A:R.348, A:R.348 Water bridges: A:E.287 EDO.6: 4 residues within 4Å: Chain A: E.46, L.63, T.64, L.166 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.46, A:T.64 EDO.7: 3 residues within 4Å: Chain A: P.264, L.265, N.266 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.265 EDO.8: 2 residues within 4Å: Chain A: L.99, Q.276 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.96, A:Q.276 EDO.9: 3 residues within 4Å: Chain A: A.362, H.363, E.364 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.364 EDO.14: 6 residues within 4Å: Chain B: D.280, M.281, T.284, E.352, H.363, W.365 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.352 Water bridges: B:D.280, B:E.352, B:E.352, B:W.365 EDO.15: 5 residues within 4Å: Chain B: Y.250, R.310, E.344, L.345, R.348 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.250, B:R.310, B:R.348 Water bridges: B:R.310 EDO.16: 3 residues within 4Å: Chain B: E.46, T.64, L.166 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.64 Water bridges: B:R.56 EDO.17: 2 residues within 4Å: Chain B: H.363, E.364 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.364, B:E.364

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.18: 4 residues within 4Å: Chain B: G.286, E.287, F.288, R.289 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.286 Water bridges: B:R.289

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Borthwick, J.A. et al., Structurally Diverse Mitochondrial Branched Chain Aminotransferase (BCATm) Leads with Varying Binding Modes Identified by Fragment Screening. J.Med.Chem. (2016)

Release Date

2016-03-23

Peptides

Branched-chain-amino-acid aminotransferase, mitochondrial: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Branched-chain-amino-acid aminotransferase, mitochondrial

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