SMTL ID : 4ynd.1

The Discovery of A-893, A New Cell-Active Benzoxazinone Inhibitor of Lysine Methyltransferase SMYD2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.79 Å

Oligo State

monomer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.80, C.83, C.102, C.106 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.80, A:C.83, A:C.102, A:C.106 ZN.2: 4 residues within 4Å: Chain A: C.237, C.290, C.292, C.295 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.237, A:C.290, A:C.292, A:C.295 ZN.3: 4 residues within 4Å: Chain A: C.93, C.96, H.114, C.118 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.93, A:C.96, A:H.114, A:C.118

1 x 4GQ: N-cyclohexyl-N~3~-[2-(3,4-dichlorophenyl)ethyl]-N-(2-{[(2R)-2-hydroxy-2-(3-oxo-3,4-dihydro-2H-1,4-benzoxazin-8-yl)ethyl]amino}ethyl)-beta-alaninamide(Non-covalent)

4GQ.4: 21 residues within 4Å: Chain A: T.133, L.169, K.173, I.177, A.205, V.207, N.208, C.209, N.210, G.211, F.212, T.213, S.224, A.231, T.266, S.267, Y.268, D.284, S.285, Y.286 Ligands: SAM.5 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:V.207, A:N.208, A:F.212, A:T.266, A:Y.268 Hydrogen bonds: A:Y.268, A:Y.286, A:Y.286 Water bridges: A:A.231, A:M.233 pi-Cation interactions: A:K.173 Halogen bonds: A:K.173

1 x SAM: S-ADENOSYLMETHIONINE(Non-covalent)

SAM.5: 15 residues within 4Å: Chain A: G.44, K.45, R.47, H.165, C.209, N.210, A.231, L.232, M.233, N.234, H.235, Y.268, Y.286, F.288 Ligands: 4GQ.4 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:R.47, A:N.234, A:H.235, A:H.235, A:Y.286 Water bridges: A:R.47 Salt bridges: A:R.47 pi-Stacking: A:F.288, A:F.288

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sweis, R.F. et al., Discovery of A-893, A New Cell-Active Benzoxazinone Inhibitor of Lysine Methyltransferase SMYD2. Acs Med.Chem.Lett. (2015)

Release Date

2015-05-20

Peptides

N-lysine methyltransferase SMYD2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

N-lysine methyltransferase SMYD2