SMTL ID : 5bww.1

X-RAY CRYSTAL STRUCTURE AT 1.82A RESOLUTION OF HUMAN MITOCHONDRIAL BRANCHED CHAIN AMINOTRANSFERASE (BCATM) COMPLEXED WITH A PYRROLIDINE AMIDE COMPOUND AND AN INTERNAL ALDIMINE LINKED PLP COFACTOR.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.82 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 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:K.206, A:Y.211, 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.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 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:K.206, B:Y.211, B:L.270, B:L.270 Hydrogen bonds: B:K.206, B:Y.211, B:Y.211, B:V.273, B:V.274, B:T.317, B:T.317 Water bridges: B:N.100, B:R.103, B:R.103, B:R.103, B:R.275 Salt bridges: B:R.103, B:K.206

2 x 4W6: 7-oxo-2-[2-oxo-2-(pyrrolidin-1-yl)ethyl]-5-propyl-4,7-dihydropyrazolo[1,5-a]pyrimidine-3-carbonitrile(Non-covalent)

4W6.2: 16 residues within 4Å: Chain A: F.79, Y.145, R.147, V.186, Q.228, V.242, G.243, T.244, M.245, A.318, C.319, C.322 Chain B: L.157, G.158, V.159 Ligands: EDO.3 14 PLIP interactions: 12 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:T.244, A:T.244, A:A.318, A:C.319, B:V.159 Water bridges: A:Q.228, A:T.317, A:T.317 4W6.13: 18 residues within 4Å: Chain A: Y.74, L.157, G.158, V.159 Chain B: F.79, Y.145, R.147, V.186, Q.228, V.242, G.243, T.244, M.245, G.316, A.318, C.319, C.322 Ligands: EDO.15 13 PLIP interactions: 11 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:T.244, B:A.318, B:C.319, A:V.159 Water bridges: B:Q.228, B:T.317, B:T.317

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

EDO.3: 4 residues within 4Å: Chain A: F.34, A.318, C.319 Ligands: 4W6.2 1 PLIP interactions: 1 interactions with chain A Water bridges: A:A.318 EDO.4: 8 residues within 4Å: Chain A: D.280, M.281, T.284, E.352, I.356, 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: Y.250, R.310, 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:R.310 EDO.6: 4 residues within 4Å: Chain A: E.46, L.63, T.64, L.166 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.46, A:T.64 EDO.7: 3 residues within 4Å: Chain A: H.253, R.293, Q.299 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Q.299 EDO.8: 4 residues within 4Å: Chain A: N.204, L.265, G.267, P.271 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.204, A:L.265, A:G.267 Water bridges: A:R.106, A:N.204 EDO.9: 2 residues within 4Å: Chain A: W.98 Ligands: CL.10 1 PLIP interactions: 1 interactions with chain A Water bridges: A:W.98 EDO.15: 3 residues within 4Å: Chain B: F.34, C.319 Ligands: 4W6.13 No protein-ligand interaction detected (PLIP) EDO.16: 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:D.280, B:E.352 Water bridges: B:T.284 EDO.17: 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:Y.250, B:R.310, B:E.344, B:R.348 Water bridges: B:R.310 EDO.18: 3 residues within 4Å: Chain B: L.14, Q.15, L.16 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:L.16, B:L.16 Water bridges: B:Q.15 EDO.19: 4 residues within 4Å: Chain B: E.17, Q.58, P.59, Q.61 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.58, B:Q.61 Water bridges: B:E.17 EDO.20: 4 residues within 4Å: Chain B: N.204, L.265, G.267, P.271 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.204, B:L.265 Water bridges: B:G.267 EDO.21: 5 residues within 4Å: Chain B: H.237, M.297, K.298, Y.329, K.330 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.329 Water bridges: B:D.236, B:M.297

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

CL.10: 3 residues within 4Å: Chain A: R.96, W.98 Ligands: EDO.9 Ligand excluded by PLIP CL.22: 2 residues within 4Å: Chain B: R.96, W.98 Ligand excluded by PLIP

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.11: 3 residues within 4Å: Chain A: P.264, L.265, N.266 3 PLIP interactions: 3 interactions with chain A Water bridges: A:L.265, A:N.266, A:E.292 GOL.23: 1 residues within 4Å: Chain B: W.98 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.364

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

DMS.14: 4 residues within 4Å: Chain B: E.46, L.63, T.64, L.166 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: 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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