SMTL ID : 5hne.1

X-RAY CRYSTAL STRUCTURE OF HUMAN MITOCHONDRIAL BRANCHED CHAIN AMINOTRANSFERASE (BCATM) COMPLEXED WITH A 2-ARYL BENZIMIDAZOLE COMPOUND AND AN INTERNAL ALDIMINE LINKED PLP COFACTOR

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.04 Å

Oligo State

homo-dimer

Ligands

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

PLP.1: 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: EL2.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:K.206, A:L.270 Hydrogen bonds: 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: EL2.12 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:K.206, B:Y.211, B:L.270, B:L.270 Hydrogen bonds: 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

2 x EL2: 1-[(1R,3S)-3-{[(5-bromothiophen-2-yl)carbonyl]amino}cyclohexyl]-N-methyl-2-(pyridin-2-yl)-1H-benzimidazole-5-carboxamide(Non-covalent)

EL2.2: 20 residues within 4Å: Chain A: F.34, F.79, K.83, V.174, G.175, Y.177, V.186, K.206, Y.211, Q.228, V.242, G.243, T.244, M.245, A.318, C.322, V.324 Chain B: Y.74, V.159 Ligands: PLP.1 21 PLIP interactions: 19 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.34, A:F.79, A:Y.177, A:V.186, A:Y.211, A:Q.228, A:T.244, A:A.318, B:Y.74, B:V.159 Hydrogen bonds: A:K.83, A:T.244 Water bridges: A:Y.145, A:Y.145, A:Y.177, A:Q.228, A:T.244, A:T.244 pi-Stacking: A:F.34, A:F.34 pi-Cation interactions: A:R.147 EL2.12: 21 residues within 4Å: Chain A: Y.74, V.159 Chain B: F.34, F.79, K.83, V.174, G.175, Y.177, V.186, K.206, Y.211, Q.228, V.242, G.243, T.244, M.245, G.314, A.318, C.322, V.324 Ligands: PLP.11 14 PLIP interactions: 12 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.79, B:Y.177, B:Y.211, B:Q.228, B:A.318, A:Y.74, A:V.159 Hydrogen bonds: B:K.83, B:Y.145, B:Q.228, B:T.244, B:T.244 pi-Stacking: B:F.34 pi-Cation interactions: B:R.147

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

CL.3: 2 residues within 4Å: Chain A: R.96, W.98 Ligand excluded by PLIP CL.13: 2 residues within 4Å: Chain B: R.96, W.98 Ligand excluded by PLIP

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

EDO.4: 5 residues within 4Å: Chain A: N.204, L.265, N.266, G.267 Ligands: EDO.9 6 PLIP interactions: 6 interactions with chain A Water bridges: A:N.204, A:N.204, A:N.204, A:L.265, A:N.266, A:G.267 EDO.5: 5 residues within 4Å: Chain A: Y.250, R.310, E.344, L.345, R.348 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.310, A:R.348 Water bridges: A:Y.250, A:R.310 EDO.6: 6 residues within 4Å: Chain A: D.280, M.281, T.284, E.352, H.363, W.365 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.280, A:T.284, A:H.363 EDO.7: 2 residues within 4Å: Chain A: Q.15, L.16 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.16 EDO.8: 4 residues within 4Å: Chain A: E.46, L.63, T.64, L.166 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.46, A:T.64 Water bridges: A:T.64 EDO.9: 4 residues within 4Å: Chain A: P.264, L.265, N.266 Ligands: EDO.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.265 EDO.10: 9 residues within 4Å: Chain A: R.110, W.198, G.200, G.201 Chain B: F.194, I.195, R.196, P.213, V.217 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:I.195, A:R.110 EDO.14: 5 residues within 4Å: Chain B: Y.250, R.310, E.344, L.345, R.348 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Y.250, B:R.310, B:E.344, B:E.344, B:R.348 Water bridges: B:R.310 EDO.15: 6 residues within 4Å: Chain B: D.280, M.281, T.284, E.352, H.363, W.365 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.280, B:E.352, B:H.363 Water bridges: B:T.284

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.16: 6 residues within 4Å: Chain B: E.46, R.56, N.62, L.63, T.64, L.166 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.46, B:R.56, B:N.62, B:T.64

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Deng, H. et al., Discovery and Optimization of Potent, Selective, and in Vivo Efficacious 2-Aryl Benzimidazole BCATm Inhibitors. Acs Med.Chem.Lett. (2016)

Release Date

2016-05-04

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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