SMTL ID : 5kjm.1

SMYD2 in complex with AZ931

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.19 Å

Oligo State

monomer

Ligands

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

SAM.1: 17 residues within 4Å: Chain A: G.12, K.13, G.14, R.15, E.131, H.133, C.177, N.178, A.199, L.200, M.201, N.202, H.203, Y.236, Y.254, F.256 Ligands: 6TM.2 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:R.15, A:R.15, A:H.133, A:N.202, A:N.202, A:H.203, A:H.203 Water bridges: A:E.131, A:E.259 Salt bridges: A:R.15 pi-Stacking: A:F.256, A:F.256

1 x 6TM: 6-[2-[4-[2-(3,4-dichlorophenyl)ethyl]piperazin-1-yl]phenyl]-~{N}-(3-pyrrolidin-1-ylpropyl)-2~{H}-pyrazolo[3,4-b]pyridine-4-carboxamide(Non-covalent)

6TM.2: 17 residues within 4Å: Chain A: T.101, L.104, L.137, K.141, I.145, V.175, N.176, C.177, N.178, G.179, F.180, T.181, Y.236, S.253, Y.254, F.255 Ligands: SAM.1 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:L.104, A:V.175, A:N.176, A:F.180, A:T.181, A:Y.236 Hydrogen bonds: A:T.181, A:Y.254, A:Y.254 Water bridges: A:T.181, A:T.181, A:Y.213 pi-Cation interactions: A:K.141 Halogen bonds: A:K.141

3 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: C.48, C.51, C.70, C.74 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.48, A:C.51, A:C.70, A:C.74 ZN.4: 4 residues within 4Å: Chain A: C.61, C.64, H.82, C.86 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.61, A:C.64, A:H.82, A:C.86 ZN.5: 4 residues within 4Å: Chain A: C.205, C.258, C.260, C.263 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.205, A:C.258, A:C.260, A:C.263

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cowen, S.D. et al., Design, Synthesis, and Biological Activity of Substrate Competitive SMYD2 Inhibitors. J. Med. Chem. (2016)

Release Date

2016-12-07

Peptides

N-lysine methyltransferase SMYD2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

N-lysine methyltransferase SMYD2

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