SMTL ID : 5bwu.1

X-RAY CRYSTAL STRUCTURE AT 2.17A RESOLUTION OF HUMAN MITOCHONDRIAL BRANCHED CHAIN AMINOTRANSFERASE (BCATM) COMPLEXED WITH A TRIAZOLOPYRIMIDINONE COMPOUND AND AN INTERNAL ALDIMINE LINKED PLP COFACTOR.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.17 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.12: 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 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 4VR: 2-[(4-bromobenzyl)amino]-5-propyl[1,2,4]triazolo[1,5-a]pyrimidin-7(4H)-one(Non-covalent)

4VR.2: 18 residues within 4Å: Chain A: F.79, Y.145, R.147, V.186, Q.228, V.242, T.244, M.245, G.314, A.318, C.319, C.322, V.324 Chain B: Y.74, L.157, G.158, V.159 Ligands: EDO.3 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: A:F.79, A:V.186, A:Q.228, A:V.242, B:V.159 Water bridges: A:T.244, A:A.318, A:A.318, A:C.319 Hydrogen bonds: B:V.159 4VR.13: 16 residues within 4Å: Chain A: Y.74, L.157, V.159 Chain B: F.79, Y.145, R.147, V.186, Q.228, V.242, T.244, M.245, A.318, C.319, C.322, V.324 Ligands: EDO.14 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:F.79, B:Q.228, A:V.159 Hydrogen bonds: B:T.244, A:V.159 Water bridges: B:T.244, B:A.318, B:A.318, B:C.319 pi-Stacking: B:F.34

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

EDO.3: 4 residues within 4Å: Chain A: F.34, A.318, C.319 Ligands: 4VR.2 No protein-ligand interaction detected (PLIP) EDO.4: 7 residues within 4Å: Chain A: D.280, M.281, T.284, E.352, R.361, H.363, W.365 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.280, A:T.284, A:R.361, A:H.363 EDO.5: 5 residues within 4Å: Chain A: N.204, L.265, N.266, G.267 Ligands: EDO.11 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.204 Water bridges: A:L.265 EDO.6: 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.310, A:R.348 Water bridges: A:E.344 EDO.7: 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 Water bridges: A:T.64 EDO.8: 1 residues within 4Å: Chain A: W.98 1 PLIP interactions: 1 interactions with chain A Water bridges: A:W.98 EDO.9: 5 residues within 4Å: Chain A: R.110, G.200, G.201 Chain B: I.195, P.213 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:I.195, A:R.110 Water bridges: B:R.196 EDO.10: 3 residues within 4Å: Chain A: P.264, L.265, N.266 2 PLIP interactions: 2 interactions with chain A Water bridges: A:L.265, A:L.265 EDO.11: 5 residues within 4Å: Chain A: N.204, L.265, G.267, P.271 Ligands: EDO.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.204, A:G.267 EDO.14: 4 residues within 4Å: Chain B: F.34, Y.177, C.319 Ligands: 4VR.13 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Y.177 EDO.15: 6 residues within 4Å: Chain B: D.280, M.281, T.284, E.352, H.363, W.365 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.352 Water bridges: B:D.280, B:T.284 EDO.16: 6 residues within 4Å: Chain B: Y.250, F.288, R.310, E.344, L.345, R.348 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.250, B:E.287, B:R.310, B:R.348 EDO.17: 6 residues within 4Å: Chain B: M.44, E.46, R.56, L.63, T.64, L.166 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:E.46, B:R.56, B:T.64, B:T.64 Water bridges: B:T.64 EDO.18: 4 residues within 4Å: Chain B: N.204, L.265, G.267, P.271 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.204, B:L.265, B:G.267 Water bridges: B:R.106

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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