SMTL ID : 5yjo.1

Crystal structure of SmyD3 in complex with covalent inhibitor 4

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.13 Å

Oligo State

monomer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.60, C.63, H.81, C.85 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.60, A:C.63, A:H.81, A:C.85 ZN.2: 4 residues within 4Å: Chain A: C.47, C.50, C.69, C.73 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.47, A:C.50, A:C.69, A:C.73 ZN.3: 4 residues within 4Å: Chain A: C.206, C.259, C.261, C.264 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.206, A:C.259, A:C.261, A:C.264

1 x 8W0: propyl (3~{S})-4-[[(6~{R})-6-(aminomethyl)-5,6,7,8-tetrahydroacridin-3-yl]carbonyl]-3-methyl-piperazine-1-carboxylate(Covalent)

8W0.4: 17 residues within 4Å: Chain A: C.178, N.179, S.180, F.181, T.182, C.184, M.188, I.212, F.214, I.235, C.236, Y.237, D.239, Y.255, D.330, V.366 Ligands: SAM.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.181, A:F.214, A:V.366 Hydrogen bonds: A:D.330 Water bridges: A:I.212, A:Y.356

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

SAM.5: 17 residues within 4Å: Chain A: R.12, G.13, N.14, Y.122, E.128, N.130, C.178, N.179, S.200, L.201, L.202, N.203, H.204, Y.237, Y.255, F.257 Ligands: 8W0.4 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:N.14, A:N.14, A:Y.122, A:E.128, A:N.130, A:N.203, A:N.203, A:H.204, A:H.204, A:Y.237, A:Y.255 Water bridges: A:E.128, A:E.128, A:S.200, A:D.260, A:D.260 pi-Stacking: A:F.257, A:F.257

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

2018-10-17

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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