SMTL ID : 5kjk.1

SMYD2 in complex with AZ370

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.93 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: 6T1.6 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: 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, A:E.259 Salt bridges: A:R.15 pi-Stacking: A:F.256, A:F.256

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

BU3.2: 6 residues within 4Å: Chain A: T.243, E.244, N.247, R.251, T.257, K.266 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:T.243, A:E.244, A:N.247 Hydrogen bonds: A:N.247, A:R.251, A:R.251 Water bridges: A:K.266 BU3.3: 4 residues within 4Å: Chain A: W.352, R.386, L.387, G.390 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.352 BU3.4: 3 residues within 4Å: Chain A: G.1, R.118, K.123 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.118 Water bridges: A:R.118 BU3.5: 3 residues within 4Å: Chain A: R.63, Q.75, W.79 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.63, A:R.63

1 x 6T1: 2-[2-[1-[2-(3,4-dichlorophenyl)ethyl]azetidin-3-yl]oxyphenyl]-~{N}-(3-pyrrolidin-1-ylpropyl)pyridine-4-carboxamide(Non-covalent)

6T1.6: 17 residues within 4Å: Chain A: T.101, L.137, K.141, I.145, A.173, 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 13 PLIP interactions: 13 interactions with chain A Hydrophobic interactions: A:V.175, A:N.176, A:F.180, A:T.181, A:Y.236, A:Y.254, A:F.255 Hydrogen bonds: A:T.181, A:Y.236, A:Y.254 Water bridges: A:S.253 pi-Cation interactions: A:K.141 Halogen bonds: A:K.141

3 x ZN: ZINC ION(Non-covalent)

ZN.7: 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.8: 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.9: 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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