SMTL ID : 5bwx.1

X-RAY CRYSTAL STRUCTURE AT 1.70A RESOLUTION OF HUMAN MITOCHONDRIAL BRANCHED CHAIN AMINOTRANSFERASE (BCATM) COMPLEXED WITH A 4-CHLORO-2-FLUORO SUBSTITUTED PYRAZOLOPYRIMIDINONE COMPOUND AND AN INTERNAL ALDIMINE LINKED PLP COFACTOR.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 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: 4W4.2 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:K.206, A:L.270, 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.18: 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: 4W4.19 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 4W4: 5-butyl-2-[(4-chloro-2-fluorobenzyl)amino]-7-oxo-4,7-dihydropyrazolo[1,5-a]pyrimidine-3-carbonitrile(Non-covalent)

4W4.2: 23 residues within 4Å: Chain A: F.34, F.79, Y.145, R.147, V.186, K.206, Y.211, Q.228, V.242, G.243, T.244, M.245, G.316, A.318, C.319, C.322, V.324 Chain B: Y.74, L.157, G.158, V.159 Ligands: PLP.1, EDO.3 15 PLIP interactions: 13 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.79, A:V.186, A:Y.211, A:Q.228, A:V.242, A:A.318, B:V.159 Hydrogen bonds: A:A.318, A:C.319, B:V.159 Water bridges: A:T.244, A:T.317, A:T.317, A:T.317 Halogen bonds: A:T.244 4W4.19: 22 residues within 4Å: Chain A: Y.74, L.157, G.158, V.159 Chain B: F.79, Y.145, R.147, V.186, K.206, Y.211, Q.228, V.242, G.243, T.244, M.245, G.316, A.318, C.319, C.322, V.324 Ligands: PLP.18, EDO.21 14 PLIP interactions: 12 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.79, B:V.186, B:Y.211, B:V.242, 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 Halogen bonds: B:T.244

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

EDO.3: 3 residues within 4Å: Chain A: F.34, C.319 Ligands: 4W4.2 Ligand excluded by PLIP EDO.4: 7 residues within 4Å: Chain A: D.280, M.281, T.284, E.352, R.361, H.363, W.365 Ligand excluded by PLIP EDO.5: 5 residues within 4Å: Chain A: R.103, R.106, P.271, G.272, V.273 Ligand excluded by PLIP EDO.6: 5 residues within 4Å: Chain A: Y.250, R.310, E.344, L.345, R.348 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: E.46, L.63, T.64, L.166 Ligand excluded by PLIP EDO.8: 5 residues within 4Å: Chain A: V.199, Y.233, Q.238, N.266, T.294 Ligand excluded by PLIP EDO.9: 1 residues within 4Å: Chain A: W.98 Ligand excluded by PLIP EDO.10: 6 residues within 4Å: Chain A: R.110, W.198, G.200, G.201 Chain B: I.195, P.213 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: 4 residues within 4Å: Chain A: F.194, L.216, E.220 Chain B: R.110 Ligand excluded by PLIP EDO.13: 4 residues within 4Å: Chain A: W.98, D.102, K.118, L.119 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: R.106, N.204, Y.205 Ligands: CL.16 Ligand excluded by PLIP EDO.15: 6 residues within 4Å: Chain A: N.204, L.265, N.266, G.267 Ligands: CL.16, GOL.17 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain B: F.34, Y.177, C.319 Ligands: 4W4.19 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain B: D.280, T.284, E.352, H.363, W.365 Ligand excluded by PLIP EDO.23: 7 residues within 4Å: Chain B: Y.250, E.287, F.288, R.310, E.344, L.345, R.348 Ligand excluded by PLIP EDO.24: 2 residues within 4Å: Chain B: E.340, N.341 Ligand excluded by PLIP

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

CL.16: 3 residues within 4Å: Chain A: P.271 Ligands: EDO.14, EDO.15 Ligand excluded by PLIP CL.25: 1 residues within 4Å: Chain B: N.204 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.17: 4 residues within 4Å: Chain A: P.264, L.265, N.266 Ligands: EDO.15 1 PLIP interactions: 1 interactions with chain A Water bridges: A:L.265 GOL.26: 1 residues within 4Å: Chain B: W.98 No protein-ligand interaction detected (PLIP)

1 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.20: 4 residues within 4Å: Chain B: E.46, L.63, T.64, L.166 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.64 Water bridges: B:T.64 Salt bridges: B:E.46

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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