SMTL ID : 5kjn.1

SMYD2 in complex with AZ506

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.72 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: 6TL.10 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:R.15, A:E.131, A:N.202, A:N.202, A:H.203, A:H.203, A:Y.254 Salt bridges: A:R.15 pi-Stacking: A:F.256, A:F.256

6 x BU3: (R,R)-2,3-BUTANEDIOL(Non-covalent)

BU3.2: 4 residues within 4Å: Chain A: A.34, Y.35, Y.37, K.111 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.37 Hydrogen bonds: A:K.111, A:K.111 Water bridges: A:A.34, A:K.111 BU3.3: 2 residues within 4Å: Chain A: W.352, G.390 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.352 BU3.4: 4 residues within 4Å: Chain A: R.118, T.119, P.120, K.123 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:P.120 Hydrogen bonds: A:T.119, A:K.123 BU3.5: 2 residues within 4Å: Chain A: R.63, W.79 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.79 Hydrogen bonds: A:R.63, A:R.63 BU3.6: 5 residues within 4Å: Chain A: E.100, T.101, T.181, S.192 Ligands: 6TL.10 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.181 Hydrogen bonds: A:S.192, A:S.192 BU3.7: 6 residues within 4Å: Chain A: R.54, D.184, E.185, E.186, S.188, R.386 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.184, A:E.185, A:R.386

2 x NA: SODIUM ION(Non-functional Binders)

NA.8: 1 residues within 4Å: Chain A: E.186 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.186 NA.9: 3 residues within 4Å: Chain A: D.238, Y.366, Y.370 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.241, A:Y.366

1 x 6TL: 5-[2-[4-[2-(1~{H}-indol-3-yl)ethyl]piperazin-1-yl]phenyl]-~{N}-(3-pyrrolidin-1-ylpropyl)pyridine-3-carboxamide(Non-covalent)

6TL.10: 17 residues within 4Å: Chain A: K.141, I.145, V.175, N.176, C.177, N.178, G.179, F.180, T.181, S.192, Y.236, D.252, S.253, Y.254, F.255 Ligands: SAM.1, BU3.6 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:K.141, A:K.141, A:I.145, A:I.145, A:V.175, A:N.176, A:F.180, A:T.181 Hydrogen bonds: A:T.181, A:Y.254

3 x ZN: ZINC ION(Non-covalent)

ZN.11: 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.12: 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.13: 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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