SMTL ID : 6ijl.1

Crystal structure of SmyD3 in complex with covalent inhibitor 5

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

monomer

Ligands

1 x A8U: propyl (2~{R})-4-[2-[4-(1-azanylcyclopropyl)phenyl]quinolin-7-yl]carbonyl-2-methyl-piperazine-1-carboxylate(Covalent)

A8U.1: 17 residues within 4Å: Chain A: S.182, F.183, T.184, C.186, M.190, I.214, F.216, I.237, C.238, Y.239, D.241, L.243, Y.257, D.332, Y.358, V.368 Ligands: SAM.5 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.183, A:F.183, A:M.190, A:F.216, A:L.243, A:V.368, A:V.368 Hydrogen bonds: A:Y.257, A:Y.358, A:Y.358 Water bridges: A:I.214

3 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.49, C.52, C.71, C.75 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.49, A:C.52, A:C.75 ZN.3: 4 residues within 4Å: Chain A: C.208, C.261, C.263, C.266 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.208, A:C.261, A:C.263, A:C.266 ZN.4: 4 residues within 4Å: Chain A: C.62, C.65, H.83, C.87 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.62, A:C.65, A:H.83, A:C.87

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

SAM.5: 17 residues within 4Å: Chain A: R.14, G.15, N.16, Y.124, E.130, N.132, C.180, N.181, S.202, L.203, L.204, N.205, H.206, Y.239, Y.257, F.259 Ligands: A8U.1 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:N.16, A:N.16, A:Y.124, A:E.130, A:N.132, A:N.132, A:N.205, A:N.205, A:H.206, A:H.206, A:Y.239 Water bridges: A:K.135 pi-Stacking: A:F.259, A:F.259

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, C. et al., Discovery of Irreversible Inhibitors Targeting Histone Methyltransferase, SMYD3. Acs Med.Chem.Lett. (2019)

Release Date

2019-08-14

Peptides

Histone-lysine N-methyltransferase SMYD3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone-lysine N-methyltransferase SMYD3

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