SMTL ID : 7ny9.1

CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC BRANCHED-CHAIN AMINOTRANSFERASE (BCAT1) IN COMPLEX WITH PLP AND SMALL MOLECULE INHIBITOR COMPOUND 38

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

homo-dimer

Ligands

2 x UV5: 3-[2,6-bis(oxidanylidene)-4-(trifluoromethyl)-5~{H}-pyrimidin-1-yl]-~{N}-methyl-2-pyridin-2-yl-imidazo[1,2-a]pyridine-7-carboxamide(Non-covalent)

UV5.1: 15 residues within 4Å: Chain A: F.52, Y.164, R.166, Y.196, Q.237, A.240, Q.246, Q.247, V.248, G.262, T.263, A.337 Chain B: Y.93, G.177, V.178 13 PLIP interactions: 10 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:F.52, A:F.52, A:F.52, A:A.337, B:V.178 Hydrogen bonds: A:Q.247, A:V.248, B:V.178 Water bridges: A:T.263, A:T.263, A:A.337 pi-Stacking: A:Y.196 Halogen bonds: B:Y.93 UV5.4: 16 residues within 4Å: Chain A: Y.93, L.176, G.177, V.178 Chain B: F.52, Y.164, R.166, Y.196, Q.237, A.240, Q.246, Q.247, V.248, G.262, T.263, A.337 14 PLIP interactions: 11 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.52, B:F.52, B:F.52, B:T.263, B:A.337, A:V.178 Hydrogen bonds: B:Q.247, B:V.248, A:V.178 Water bridges: B:T.263, B:T.263, B:A.337 pi-Stacking: B:Y.196 Halogen bonds: A:Y.93

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

PLP.2: 14 residues within 4Å: Chain A: R.122, R.215, K.225, Y.230, E.260, T.263, M.264, N.265, L.289, G.291, V.292, T.293, G.335, T.336 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:K.225, A:L.289, A:L.289 Hydrogen bonds: A:Y.230, A:Y.230, A:V.292, A:T.293, A:T.293, A:T.336, A:T.336 Water bridges: A:R.122, A:R.122, A:R.122, A:R.294, A:T.336 Salt bridges: A:R.122, A:K.225 PLP.5: 14 residues within 4Å: Chain B: R.122, R.215, K.225, Y.230, E.260, T.263, M.264, N.265, L.289, G.291, V.292, T.293, G.335, T.336 17 PLIP interactions: 17 interactions with chain B Hydrophobic interactions: B:K.225, B:L.289, B:L.289 Hydrogen bonds: B:Y.230, B:Y.230, B:V.292, B:T.293, B:T.336, B:T.336 Water bridges: B:R.122, B:R.122, B:R.122, B:R.122, B:R.294, B:A.337 Salt bridges: B:R.122, B:K.225

2 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.6: 1 residues within 4Å: Chain B: D.136 3 PLIP interactions: 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.136, H2O.17, H2O.18

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Gunther, J. et al., BAY-069, a Novel (Trifluoromethyl)pyrimidinedione-Based BCAT1/2 Inhibitor and Chemical Probe. J.Med.Chem. (2022)

Release Date

2022-11-02

Peptides

Branched-chain-amino-acid aminotransferase, cytosolic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Branched-chain-amino-acid aminotransferase, cytosolic

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