SMTL ID : 7nxo.1

CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC BRANCHED-CHAIN AMINOTRANSFERASE (BCAT1) IN COMPLEX WITH PLP AND SMALL MOLECULE INHIBITOR COMPOUND 24(5-F)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.71 Å

Oligo State

homo-dimer

Ligands

2 x UU8: 4-[2,4-bis(oxidanylidene)-6-(phenylsulfonyl)-1H-pyrimidin-3-yl]-5-fluoranyl-2-(2-methylphenoxy)benzenecarbonitrile(Non-covalent)

UU8.1: 19 residues within 4Å: Chain A: F.52, F.98, Y.164, R.166, Y.196, F.197, K.225, Y.230, Q.237, V.241, Q.246, Q.247, T.263, A.337 Chain B: Y.93, L.176, G.177, V.178 Ligands: PLP.2 16 PLIP interactions: 3 interactions with chain B, 13 interactions with chain A Hydrophobic interactions: B:Y.93, B:V.178, A:F.52, A:F.98, A:Y.196, A:F.197, A:F.197, A:F.197, A:F.197, A:Y.230, A:Q.246 Hydrogen bonds: B:V.178, A:Q.237, A:Q.247, A:T.263, A:T.263 UU8.4: 19 residues within 4Å: Chain A: Y.93, L.176, G.177, V.178 Chain B: F.52, F.98, Y.164, R.166, Y.196, F.197, K.225, Y.230, Q.237, V.241, Q.246, Q.247, T.263, A.337 Ligands: PLP.5 15 PLIP interactions: 3 interactions with chain A, 12 interactions with chain B Hydrophobic interactions: A:Y.93, A:V.178, B:F.52, B:F.98, B:Y.196, B:F.197, B:Y.230, B:Q.246 Hydrogen bonds: A:V.178, B:Q.237, B:Q.247, B:T.263, B:T.263 Water bridges: B:Q.246 pi-Stacking: B:F.197

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

PLP.2: 15 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 Ligands: UU8.1 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:K.225, A:L.289, A:L.289 Hydrogen bonds: A:Y.230, A:V.292, A:T.293, A:T.336 Water bridges: A:G.100, A:R.294, A:T.336, A:T.336, A:T.336, A:A.337 Salt bridges: A:R.122, A:K.225 PLP.5: 15 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 Ligands: UU8.4 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:V.292, B:T.293, B:T.293, B:T.336 Water bridges: B:T.293, B:R.294, B:T.336, B:T.336, B:T.336, B:T.336, B:A.337 Salt bridges: B:R.122, B:K.225

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: L.118, P.290, G.291, V.292, R.295 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:P.290, A:R.295 Water bridges: A:R.294

1 x MG: MAGNESIUM ION(Non-covalent)

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.11, H2O.14

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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