SMTL ID : 5i5x.1

X-RAY CRYSTAL STRUCTURE AT 1.65A RESOLUTION OF HUMAN MITOCHONDRIAL BRANCHED CHAIN AMINOTRANSFERASE (BCATM) COMPLEXED WITH A THIAZOLE COMPOUND AND PMP COFACTOR.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

2 x PMP: 4'-DEOXY-4'-AMINOPYRIDOXAL-5'-PHOSPHATE(Non-covalent)

PMP.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, S.315, G.316, T.317 Ligands: 68C.2 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.270 Hydrogen bonds: A:R.103, A:K.206, A:K.206, A:Y.211, A:V.273, A:V.274, A:T.317, A:T.317 Water bridges: A:R.275 Salt bridges: A:R.103 PMP.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, S.315, G.316, T.317 Ligands: 68C.17 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:L.270 Hydrogen bonds: B:R.103, B:K.206, B:K.206, B:Y.211, B:Y.211, B:E.241, B:V.273, B:V.274, B:T.317, B:T.317 Water bridges: B:G.81, B:R.275, B:T.317 Salt bridges: B:R.103

2 x 68C: 5-methyl-4-oxo-N-(1,3,4-thiadiazol-2-yl)-3,4-dihydrothieno[2,3-d]pyrimidine-6-carboxamide

68C.2: 12 residues within 4Å: Chain A: F.34, F.79, K.83, Y.145, V.174, Y.177, K.206, Y.211, A.318 Chain B: Y.74, V.159 Ligands: PMP.1 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.34, A:F.34, A:Y.145, A:A.318 Hydrogen bonds: A:K.83, A:Y.145, A:R.147, A:K.206 Water bridges: A:F.34, A:K.83, A:Y.145, A:G.175, A:G.175, A:A.318 pi-Stacking: A:F.34 pi-Cation interactions: A:R.147 68C.17: 11 residues within 4Å: Chain A: Y.74, V.159 Chain B: F.34, F.79, K.83, Y.145, Y.177, K.206, Y.211, A.318 Ligands: PMP.16 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:F.34, B:Y.145, B:A.318 Hydrogen bonds: B:K.83, B:Y.145, B:K.206 Water bridges: B:K.83, B:G.175, B:G.175, B:T.244 pi-Stacking: B:F.34, B:F.34 pi-Cation interactions: B:R.147

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

CL.3: 3 residues within 4Å: Chain A: K.83, A.318, Q.320 Ligand excluded by PLIP CL.4: 2 residues within 4Å: Chain A: N.204, P.271 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: R.96, W.98 Ligand excluded by PLIP CL.18: 3 residues within 4Å: Chain B: K.83, A.318, Q.320 Ligand excluded by PLIP CL.19: 2 residues within 4Å: Chain B: N.204, P.271 Ligand excluded by PLIP CL.20: 3 residues within 4Å: Chain B: R.96, W.98 Ligands: GOL.25 Ligand excluded by PLIP

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

EDO.6: 5 residues within 4Å: Chain A: Y.250, R.310, E.344, L.345, R.348 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.250, A:R.310, A:R.310, A:R.348 Water bridges: A:Y.250, A:Y.250, A:Y.250 EDO.7: 4 residues within 4Å: Chain A: E.46, L.63, T.64, L.166 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.64 Water bridges: A:E.46, A:E.46, A:E.46, A:T.64, A:T.64 EDO.8: 2 residues within 4Å: Chain A: Q.15, L.16 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.16, A:L.16 EDO.9: 3 residues within 4Å: Chain A: L.119, E.120, E.123 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.120 EDO.10: 4 residues within 4Å: Chain A: G.286, E.287, F.288, R.289 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.286 Water bridges: A:E.287 EDO.11: 4 residues within 4Å: Chain A: L.279, Q.283, V.290, E.292 3 PLIP interactions: 3 interactions with chain A Water bridges: A:Q.276, A:L.279, A:E.292 EDO.12: 6 residues within 4Å: Chain A: R.110, W.198, 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.13: 3 residues within 4Å: Chain A: H.253, R.293, Q.299 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.299 EDO.21: 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:R.348 Water bridges: B:R.310, B:E.344 EDO.22: 5 residues within 4Å: Chain B: E.46, R.56, L.63, T.64, L.166 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:E.46, B:E.46, B:R.56, B:T.64 Water bridges: B:Q.58, B:Q.58, B:T.64 EDO.23: 4 residues within 4Å: Chain B: G.286, E.287, F.288, R.289 6 PLIP interactions: 6 interactions with chain B Water bridges: B:E.287, B:F.288, B:R.289, B:R.289, B:R.289, B:V.290

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.14: 7 residues within 4Å: Chain A: D.280, M.281, T.284, E.352, R.361, H.363, W.365 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.284, A:T.284, A:R.361, A:R.361, A:H.363 GOL.15: 1 residues within 4Å: Chain A: W.98 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.364 GOL.24: 6 residues within 4Å: Chain B: L.304, E.305, R.332, N.333, L.334, H.335 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:L.304, B:N.333, B:H.335, B:H.335 Water bridges: B:R.332 GOL.25: 2 residues within 4Å: Chain B: W.98 Ligands: CL.20 No protein-ligand interaction detected (PLIP) GOL.26: 7 residues within 4Å: Chain B: D.280, M.281, T.284, E.352, I.356, H.363, W.365 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.280, B:E.352 Water bridges: B:T.284, B:E.352

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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