SMTL ID : 5i5v.1

X-RAY CRYSTAL STRUCTURE AT 1.94A RESOLUTION OF HUMAN MITOCHONDRIAL BRANCHED CHAIN AMINOTRANSFERASE (BCATM) COMPLEXED WITH A THIENOPYRIMIDINE COMPOUND AND AN INTERNAL ALDIMINE LINKED PLP COFACTOR.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

homo-dimer

Ligands

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

PLP.1: 16 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: EDO.4, EDO.5 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:K.206, 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.16: 16 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: EDO.6, EDO.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:G.81, B:R.103, B:R.103, B:R.103, B:R.275 Salt bridges: B:R.103, B:K.206

2 x 68A: 3,5-dimethyl-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-6-carboxylic acid(Non-covalent)

68A.2: 9 residues within 4Å: Chain A: F.34, K.83, Y.145, V.174, G.175, Y.177, A.318 Ligands: EDO.4, EDO.5 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.34, A:F.34, A:Y.145, A:A.318 Hydrogen bonds: A:K.83 Water bridges: A:Y.145 pi-Stacking: A:F.34 68A.17: 8 residues within 4Å: Chain B: F.34, K.83, Y.145, V.174, G.175, Y.177, A.318 Ligands: EDO.6 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:F.34, B:Y.145, B:A.318 Hydrogen bonds: B:K.83 Water bridges: B:F.34, B:Y.145, B:T.244 pi-Stacking: B:F.34

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

CL.3: 2 residues within 4Å: Chain A: N.204, P.271 Ligand excluded by PLIP CL.18: 1 residues within 4Å: Chain B: N.204 Ligand excluded by PLIP

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

EDO.4: 9 residues within 4Å: Chain A: F.79, R.147, K.206, T.244 Chain B: Y.74, V.159 Ligands: PLP.1, 68A.2, EDO.5 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:Y.74, A:R.147, A:K.206 Water bridges: A:Y.145 EDO.5: 9 residues within 4Å: Chain A: K.206, T.244, M.245, G.316, T.317, A.318 Ligands: PLP.1, 68A.2, EDO.4 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.244 Water bridges: A:V.242, A:T.244, A:T.244, A:T.317 EDO.6: 8 residues within 4Å: Chain A: Y.74, V.159 Chain B: F.79, R.147, K.206 Ligands: PLP.16, 68A.17, EDO.19 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Y.145, B:R.147, B:K.206, B:K.206 EDO.7: 6 residues within 4Å: Chain A: Y.250, F.288, 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, A:R.348 EDO.8: 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:N.62, A:T.64, A:T.64 EDO.9: 3 residues within 4Å: Chain A: P.264, L.265 Ligands: EDO.13 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.265 EDO.10: 1 residues within 4Å: Chain A: H.253 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:H.253 EDO.11: 6 residues within 4Å: Chain A: L.99, R.103, R.106, P.271, G.272, V.273 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.106 Water bridges: A:R.106, A:Q.276 EDO.12: 3 residues within 4Å: Chain A: L.119, E.120, E.123 2 PLIP interactions: 2 interactions with chain A Water bridges: A:A.11, A:A.11 EDO.13: 5 residues within 4Å: Chain A: N.204, L.265, N.266, G.267 Ligands: EDO.9 5 PLIP interactions: 5 interactions with chain A Water bridges: A:N.204, A:N.204, A:N.204, A:L.265, A:N.266 EDO.19: 7 residues within 4Å: Chain B: T.244, M.245, G.316, T.317, A.318 Ligands: EDO.6, PLP.16 1 PLIP interactions: 1 interactions with chain B Water bridges: B:T.244 EDO.20: 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.21: 5 residues within 4Å: Chain B: E.46, R.56, L.63, T.64, L.166 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.46, B:R.56, B:T.64, B:T.64 EDO.22: 4 residues within 4Å: Chain B: G.286, E.287, F.288, R.289 3 PLIP interactions: 3 interactions with chain B Water bridges: B:E.287, B:R.289, B:V.290

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

DMS.14: 5 residues within 4Å: Chain A: D.280, T.284, E.352, H.363, W.365 No protein-ligand interaction detected (PLIP) DMS.23: 6 residues within 4Å: Chain B: D.280, M.281, T.284, E.352, H.363, W.365 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.352 Salt bridges: B:E.352

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.15: 1 residues within 4Å: Chain A: W.98 No protein-ligand interaction detected (PLIP) GOL.24: 1 residues within 4Å: Chain B: W.98 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Borthwick, J.A. et al., Structurally Diverse Mitochondrial Branched Chain Aminotransferase (BCATm) Leads with Varying Binding Modes Identified by Fragment Screening. J.Med.Chem. (2016)

Release Date

2016-03-23

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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