SMTL ID : 5bwr.1

X-RAY CRYSTAL STRUCTURE AT 2.20A RESOLUTION OF HUMAN MITOCHONDRIAL BRANCHED CHAIN AMINOTRANSFERASE (BCATM) COMPLEXED WITH A PYRAZOLOPYRIMIDINONE FRAGMENT AND AN INTERNAL ALDIMINE LINKED PLP.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 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: 4VT.2 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:K.206, A:L.270 Hydrogen bonds: A:Y.211, 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.10: 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: 4VT.11 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:K.206, 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 4VT: 5-benzyl-7-oxo-4,7-dihydropyrazolo[1,5-a]pyrimidine-3-carbonitrile(Non-covalent)

4VT.2: 12 residues within 4Å: Chain A: F.34, F.79, K.206, Y.211, T.244, M.245, G.316, A.318, C.319 Chain B: Y.74, V.159 Ligands: PLP.1 11 PLIP interactions: 9 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.34, A:F.79, A:Y.211, A:T.244, A:A.318, B:Y.74, B:V.159 Hydrogen bonds: A:A.318, A:C.319 Water bridges: A:Q.228, A:Q.228 4VT.11: 14 residues within 4Å: Chain A: Y.74, V.159 Chain B: F.34, F.79, K.206, Y.211, T.244, M.245, G.316, T.317, A.318, C.319 Ligands: PLP.10, EDO.14 12 PLIP interactions: 10 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.79, B:F.79, B:Y.211, B:T.244, B:A.318, A:Y.74, A:V.159 Hydrogen bonds: B:Q.228, B:T.244, B:A.318, B:C.319 Water bridges: B:T.317

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

CL.3: 2 residues within 4Å: Chain A: R.96, W.98 Ligand excluded by PLIP CL.4: 3 residues within 4Å: Chain A: N.204, L.265 Ligands: EDO.7 Ligand excluded by PLIP CL.12: 2 residues within 4Å: Chain B: R.96, W.98 Ligand excluded by PLIP CL.13: 1 residues within 4Å: Chain B: N.204 Ligand excluded by PLIP

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

EDO.5: 4 residues within 4Å: Chain A: Y.250, E.344, L.345, R.348 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:Y.250, A:E.287, A:R.348 Water bridges: A:Y.250, A:E.287, A:E.344 EDO.6: 4 residues within 4Å: Chain A: E.46, L.63, T.64, L.166 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.46, A:E.46, A:T.64, A:T.64 EDO.7: 6 residues within 4Å: Chain A: N.204, L.265, N.266, G.267 Ligands: CL.4, EDO.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.204 EDO.8: 4 residues within 4Å: Chain A: P.264, L.265, N.266 Ligands: EDO.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.265 EDO.9: 4 residues within 4Å: Chain A: M.281, T.284, H.363, W.365 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.280, A:T.284, A:H.363 EDO.14: 3 residues within 4Å: Chain B: F.34, A.318 Ligands: 4VT.11 No protein-ligand interaction detected (PLIP) EDO.15: 6 residues within 4Å: Chain B: D.280, M.281, T.284, E.352, H.363, W.365 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:E.352, B:E.352 Water bridges: B:D.280, B:D.280, B:T.284, B:W.365 EDO.16: 5 residues within 4Å: Chain B: E.46, R.56, L.63, T.64, L.166 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.46, B:R.56, B:T.64 EDO.17: 5 residues within 4Å: Chain B: Y.250, R.310, E.344, L.345, R.348 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.250, B:Y.250, B:R.348 EDO.18: 1 residues within 4Å: Chain B: W.98 No protein-ligand interaction detected (PLIP)

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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