SMTL ID : 5arg.1

SMYD2 in complex with SGC probe BAY-598

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

monomer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 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.2: 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.3: 5 residues within 4Å: Chain A: C.65, R.67, 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

1 x H41: N-[1-(N'-CYANO-N-[3-(DIFLUOROMETHOXY)PHENYL]CARBAMIMIDOYL)-3-(3,4-DICHLOROPHENYL)-4,5-DIHYDRO-1H-PYRAZOL-4-YL]-N-ETHYL-2-HYDROXYACETAMIDE(Non-covalent)

H41.4: 20 residues within 4Å: Chain A: E.104, T.105, L.108, V.179, N.180, N.182, G.183, F.184, T.185, E.187, S.196, V.202, A.203, M.205, Y.217, T.238, S.239, Y.240, Y.258 Ligands: SAM.6 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:T.238, A:Y.240 Hydrogen bonds: A:G.183, A:T.185, A:T.185, A:E.187, A:S.196, A:Y.258 Water bridges: A:G.183 pi-Stacking: A:F.184 Halogen bonds: A:V.202

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 9 residues within 4Å: Chain A: C.209, L.243, R.250, E.266, 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.272, A:K.276, A:H.373

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

SAM.6: 17 residues within 4Å: Chain A: G.16, K.17, G.18, R.19, E.135, H.137, C.181, N.182, A.203, L.204, M.205, N.206, H.207, Y.240, Y.258, F.260 Ligands: H41.4 11 PLIP interactions: 11 interactions with chain A Hydrogen bonds: A:R.19, A:R.19, A:N.206, A:N.206, A:H.207, A:H.207, A:Y.258 Water bridges: A:E.135 Salt bridges: A:R.19 pi-Stacking: A:F.260, A:F.260

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Eggert, E. et al., Discovery and Characterization of a Highly Potent and Selective Aminopyrazoline-Based in Vivo Probe (Bay-598) for the Protein Lysine Methyltransferase Smyd2. J.Med.Chem. (2016)

Release Date

2016-04-27

Peptides

N-LYSINE METHYLTRANSFERASE SMYD2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

N-LYSINE METHYLTRANSFERASE SMYD2

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