SMTL ID : 5v3h.1

Crystal structure of SMYD2 with SAM and EPZ033294

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.69 Å

Oligo State

monomer

Ligands

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

SAM.1: 16 residues within 4Å: Chain A: G.27, K.28, R.30, E.146, H.148, C.192, N.193, A.214, L.215, M.216, N.217, H.218, Y.251, Y.269, F.271 Ligands: 8WG.5 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:K.28, A:R.30, A:R.30, A:N.217, A:H.218, A:H.218, A:Y.269 Water bridges: A:E.146 Salt bridges: A:R.30 pi-Stacking: A:F.271, A:F.271

3 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.220, C.273, C.275, C.278 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.220, A:C.273, A:C.275, A:C.278 ZN.3: 4 residues within 4Å: Chain A: C.63, C.66, C.85, C.89 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.63, A:C.66, A:C.85, A:C.89 ZN.4: 4 residues within 4Å: Chain A: C.76, C.79, H.97, C.101 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.76, A:C.79, A:H.97, A:C.101

2 x 8WG: N-[1-({1-[(4-chlorophenyl)methyl]-1H-pyrazol-4-yl}methyl)azetidin-3-yl]-1-cyclopropyl-1H-1,2,3-triazole-4-carboxamide(Non-covalent)

8WG.5: 21 residues within 4Å: Chain A: C.192, G.194, F.195, T.196, E.198, D.199, E.200, L.202, V.226, Y.228, Y.251, Y.269, L.390, A.393, M.423, H.427 Ligands: SAM.1, 8WG.6, PEG.7, PEG.8, GOL.11 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:E.200, A:L.202, A:Y.251, A:Y.251, A:Y.269, A:L.390 Hydrogen bonds: A:T.196 Water bridges: A:Y.228 Salt bridges: A:E.198 8WG.6: 15 residues within 4Å: Chain A: T.116, L.119, V.190, N.191, G.194, F.195, T.196, S.207, Y.251, I.252, D.253, Y.256, R.264, H.352 Ligands: 8WG.5 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:V.190 Hydrogen bonds: A:D.253, A:R.264 Water bridges: A:R.264, A:R.264 pi-Cation interactions: A:R.264

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

PEG.7: 8 residues within 4Å: Chain A: P.222, V.224, V.226, T.249, S.250 Ligands: 8WG.5, PEG.8, GOL.11 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.249, A:S.250 Water bridges: A:T.249 PEG.8: 8 residues within 4Å: Chain A: I.225, V.226, S.389, L.390, N.391 Ligands: 8WG.5, PEG.7, GOL.11 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:V.226, A:V.226, A:S.389, A:L.390, A:N.391

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

EDO.9: 3 residues within 4Å: Chain A: A.49, Y.50, K.126 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:A.49, A:K.126 Water bridges: A:Y.52

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 3 residues within 4Å: Chain A: E.115, H.204, S.207 No protein-ligand interaction detected (PLIP) GOL.11: 7 residues within 4Å: Chain A: S.250, Y.251, I.252, D.253 Ligands: 8WG.5, PEG.7, PEG.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.250 Water bridges: A:N.391

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

2018-04-25

Peptides

N-lysine methyltransferase SMYD2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

N-lysine methyltransferase SMYD2