SMTL ID : 5bwv.1

X-RAY CRYSTAL STRUCTURE AT 1.86A RESOLUTION OF HUMAN MITOCHONDRIAL BRANCHED CHAIN AMINOTRANSFERASE (BCATM) COMPLEXED WITH A PYRAZOLOPYRIMIDINONE COMPOUND AND AN INTERNAL ALDIMINE LINKED PLP COFACTOR.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.86 Å

Oligo State

homo-dimer

Ligands

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

PLP.1: 14 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 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:K.206, A:Y.211, 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.18: 14 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 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:K.206, B:Y.211, 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 775: 2-[(4-chlorobenzyl)amino]-7-oxo-5-propyl-4,7-dihydropyrazolo[1,5-a]pyrimidine-3-carbonitrile(Non-covalent)

775.2: 19 residues within 4Å: Chain A: F.79, Y.145, R.147, Y.177, V.186, Q.228, V.242, T.244, M.245, G.316, T.317, A.318, C.319, C.322, V.324 Chain B: Y.74, L.157, V.159 Ligands: EDO.5 13 PLIP interactions: 11 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.79, A:V.186, A:Q.228, A:V.242, A:A.318, B:V.159 Hydrogen bonds: A:Y.177, A:A.318, A:C.319, B:V.159 Water bridges: A:T.244, A:T.317, A:T.317 775.19: 19 residues within 4Å: Chain A: Y.74, L.157, V.159 Chain B: F.79, Y.145, R.147, Y.177, V.186, Q.228, V.242, T.244, M.245, G.316, T.317, A.318, C.319, C.322, V.324 Ligands: EDO.6 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.79, B:V.186, B:Q.228, B:A.318, A:V.159 Hydrogen bonds: B:T.244, B:A.318, B:C.319, A:V.159 Water bridges: B:T.244, B:T.317, B:T.317

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

CL.3: 2 residues within 4Å: Chain A: N.204, P.271 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: R.96, W.98 Ligands: EDO.15 Ligand excluded by PLIP CL.20: 2 residues within 4Å: Chain B: N.204, P.271 Ligand excluded by PLIP CL.21: 2 residues within 4Å: Chain B: R.96, W.98 Ligand excluded by PLIP

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

EDO.5: 5 residues within 4Å: Chain A: Y.177, Q.228, T.244 Chain B: V.159 Ligands: 775.2 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: V.159 Chain B: Y.177, Q.228, T.244 Ligands: 775.19 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: M.281, T.284, H.363, W.365 Ligand excluded by PLIP EDO.8: 6 residues within 4Å: Chain A: L.99, R.103, R.106, P.271, G.272, V.273 Ligand excluded by PLIP EDO.9: 5 residues within 4Å: Chain A: Y.250, R.310, E.344, L.345, R.348 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: V.199, Y.233, Q.238, N.266, T.294 Ligand excluded by PLIP EDO.11: 4 residues within 4Å: Chain A: I.195, Y.233, G.234 Chain B: W.198 Ligand excluded by PLIP EDO.12: 7 residues within 4Å: Chain A: G.87, K.88, D.89, Q.91, R.93, Y.358, G.359 Ligand excluded by PLIP EDO.13: 2 residues within 4Å: Chain A: H.253, Q.299 Ligand excluded by PLIP EDO.14: 2 residues within 4Å: Chain A: E.120, E.123 Ligand excluded by PLIP EDO.15: 2 residues within 4Å: Chain A: W.98 Ligands: CL.4 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain A: D.191, A.193, F.194, E.220, R.224 Ligand excluded by PLIP EDO.22: 6 residues within 4Å: Chain B: D.280, M.281, T.284, E.352, H.363, W.365 Ligand excluded by PLIP EDO.23: 5 residues within 4Å: Chain B: Y.250, R.310, E.344, L.345, R.348 Ligand excluded by PLIP EDO.24: 5 residues within 4Å: Chain B: E.46, R.56, L.63, T.64, L.166 Ligand excluded by PLIP EDO.25: 3 residues within 4Å: Chain B: L.119, E.120, E.123 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.17: 4 residues within 4Å: Chain A: E.340, N.341, G.342, E.344 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.344 Water bridges: A:N.341

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bertrand, S.M. et al., The Discovery of in Vivo Active Mitochondrial Branched-Chain Aminotransferase (BCATm) Inhibitors by Hybridizing Fragment and HTS Hits. J.Med.Chem. (2015)

Release Date

2015-07-01

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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