SMTL ID : 5ccl.1

Crystal structure of SMYD3 with SAM and oxindole compound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.49, C.52, C.71, C.75 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.49, A:C.52, A:C.71, A:C.75 ZN.2: 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.3: 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.4: 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: 4ZW.5 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:R.14, 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:R.14, A:R.14, A:R.14, A:E.130, A:E.130 pi-Stacking: A:F.259, A:F.259

2 x 4ZW: 2-oxidanylidene-N-piperidin-4-yl-1,3-dihydroindole-5-carboxamide(Non-covalent)

4ZW.5: 12 residues within 4Å: Chain A: C.180, N.181, S.182, F.183, T.184, E.192, S.202, I.237, Y.239, D.241, Y.257 Ligands: SAM.4 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:F.183, A:F.183, A:I.237, A:Y.239 Hydrogen bonds: A:T.184, A:E.192, A:E.192, A:Y.239 Water bridges: A:Y.239 pi-Stacking: A:F.183 4ZW.6: 5 residues within 4Å: Chain A: E.7, R.19, V.21, V.231, G.232 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:V.21, A:V.231

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.7: 3 residues within 4Å: Chain A: L.344, H.382, Q.383 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.383

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mitchell, L.H. et al., Novel Oxindole Sulfonamides and Sulfamides: EPZ031686, the First Orally Bioavailable Small Molecule SMYD3 Inhibitor. Acs Med.Chem.Lett. (2016)

Release Date

2015-09-09

Peptides

Histone-lysine N-methyltransferase SMYD3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone-lysine N-methyltransferase SMYD3