SMTL ID : 4wuy.1

Crystal Structure of Protein Lysine Methyltransferase SMYD2 in complex with LLY-507, a Cell-Active, Potent and Selective Inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.63 Å

Oligo State

monomer

Ligands

1 x 3UJ: 5-cyano-2'-{4-[2-(3-methyl-1H-indol-1-yl)ethyl]piperazin-1-yl}-N-[3-(pyrrolidin-1-yl)propyl]biphenyl-3-carboxamide(Non-covalent)

3UJ.1: 19 residues within 4Å: Chain A: T.105, S.136, L.141, K.145, I.149, A.177, V.179, N.180, C.181, N.182, G.183, F.184, T.185, A.203, Y.240, S.257, Y.258, F.259 Ligands: SAH.2 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:L.141, A:K.145, A:K.145, A:K.145, A:I.149, A:I.149, A:N.180, A:F.184, A:T.185, A:A.203, A:Y.240, A:Y.240, A:F.259 Hydrogen bonds: A:T.185, A:Y.240, A:Y.258 Water bridges: A:Y.217 pi-Cation interactions: A:K.145

1 x SAH: S-ADENOSYL-L-HOMOCYSTEINE(Non-covalent)

SAH.2: 16 residues within 4Å: Chain A: G.16, K.17, G.18, R.19, E.135, H.137, N.182, A.203, L.204, M.205, N.206, H.207, Y.240, Y.258, F.260 Ligands: 3UJ.1 13 PLIP interactions: 13 interactions with chain A Hydrogen bonds: A:R.19, A:R.19, A:H.137, A:N.206, A:H.207, A:H.207 Water bridges: A:R.19, A:E.135, A:E.263, A:E.263 Salt bridges: A:R.19 pi-Stacking: A:F.260, A:F.260

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 2 residues within 4Å: Chain A: K.140, F.259 No protein-ligand interaction detected (PLIP) GOL.4: 5 residues within 4Å: Chain A: A.38, Y.39, Y.41, Y.54, K.115 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.38, A:Y.41, A:K.115, A:K.115 GOL.5: 8 residues within 4Å: Chain A: C.209, L.243, R.250, K.272, K.276, H.373, Y.374, P.375 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.250, A:K.272, A:K.276, A:H.373 Water bridges: A:K.272

4 x ZN: ZINC ION(Non-covalent)

ZN.6: 4 residues within 4Å: Chain A: C.65, C.68, H.86, C.90 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.65, A:C.68, A:H.86, A:C.90 ZN.7: 4 residues within 4Å: Chain A: C.209, C.262, C.264, C.267 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.209, A:C.262, A:C.264, A:C.267 ZN.8: 4 residues within 4Å: Chain A: C.52, C.55, C.74, C.78 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.52, A:C.55, A:C.74, A:C.78 ZN.9: 2 residues within 4Å: Chain A: C.210, E.266 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.210

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nguyen, H. et al., LLY-507, a Cell-active, Potent, and Selective Inhibitor of Protein-lysine Methyltransferase SMYD2. J.Biol.Chem. (2015)

Release Date

2015-04-08

Peptides

N-lysine methyltransferase SMYD2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

N-lysine methyltransferase SMYD2