SMTL ID : 5v37.1

Crystal structure of SMYD3 with SAM and EPZ028862

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.42 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 5 PLIP interactions: 4 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:C.49, A:C.52, A:C.71, A:C.75, H2O.3 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: 8WD.5 19 PLIP interactions: 19 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:R.14, A:R.14, A:R.14, A:E.130, A:E.130, A:D.262 pi-Stacking: A:F.259, A:F.259

1 x 8WD: N-{(3-endo)-8-[(trans-4-aminocyclohexyl)sulfonyl]-8-azabicyclo[3.2.1]octan-3-yl}-5-cyclopropyl-1,2-oxazole-3-carboxamide(Non-covalent)

8WD.5: 16 residues within 4Å: Chain A: C.180, N.181, S.182, F.183, T.184, M.190, E.192, I.237, C.238, Y.239, L.240, D.241, Y.257, V.368 Ligands: SAM.4, DMS.7 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.183, A:F.183, A:Y.239, A:Y.239, A:Y.257, A:V.368 Hydrogen bonds: A:T.184, A:Y.239, A:K.297, A:K.297 Water bridges: A:D.241, A:M.242, A:Y.358 pi-Stacking: A:F.183

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.6: 1 residues within 4Å: Chain A: E.318 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.318

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.7: 7 residues within 4Å: Chain A: S.182, F.183, T.184, V.195, Q.256, Y.257 Ligands: 8WD.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.256 DMS.8: 3 residues within 4Å: Chain A: P.99, L.147, T.150 No protein-ligand interaction detected (PLIP)

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

EDO.9: 5 residues within 4Å: Chain A: A.188, E.189, V.371, K.375, L.410 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.189 EDO.10: 3 residues within 4Å: Chain A: D.139, K.140, G.143 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.139 Water bridges: A:G.143 EDO.11: 3 residues within 4Å: Chain A: R.359, R.369, L.395 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.369, A:R.369

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thomenius, M.J. et al., Small molecule inhibitors and CRISPR/Cas9 mutagenesis demonstrate that SMYD2 and SMYD3 activity are dispensable for autonomous cancer cell proliferation. Plos One (2018)

Release Date

2018-03-07

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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