SMTL ID : 6p6k.1

Co-crystal Structure of human SMYD3 with Isoxazole Amides Inhibitors

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.55 Å

Oligo State

monomer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.212, C.265, C.267, C.270 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.212, A:C.265, A:C.267, A:C.270 ZN.2: 4 residues within 4Å: Chain A: C.66, C.69, H.87, C.91 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.66, A:C.69, A:H.87, A:C.91 ZN.3: 4 residues within 4Å: Chain A: C.53, C.56, C.75, C.79 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.53, A:C.56, A:C.75, A:C.79

2 x MG: MAGNESIUM ION(Non-functional Binders)(Non-covalent)

MG.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.5: 1 residues within 4Å: Chain A: N.138 No protein-ligand interaction detected (PLIP)

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.6: 5 residues within 4Å: Chain A: S.217, C.242, H.370, P.371 Ligands: L0J.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:C.242, A:C.242 Water bridges: A:I.218

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

SAM.7: 17 residues within 4Å: Chain A: R.18, G.19, N.20, Y.128, E.134, N.136, C.184, N.185, S.206, L.207, L.208, N.209, H.210, Y.243, Y.261, F.263 Ligands: L0J.8 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:N.20, A:N.20, A:N.20, A:E.134, A:N.136, A:N.209, A:N.209, A:H.210, A:H.210, A:Y.261 Water bridges: A:R.18, A:R.18, A:Y.128, A:Y.128, A:D.266, A:D.266 pi-Stacking: A:F.263, A:F.263

1 x L0J: N-{1-[(2-aminoethyl)sulfonyl]piperidin-4-yl}-5-cyclopropyl-1,2-oxazole-3-carboxamide(Non-covalent)

L0J.8: 16 residues within 4Å: Chain A: C.184, N.185, S.186, F.187, T.188, C.190, M.194, I.218, I.241, Y.243, L.244, D.245, Y.261, V.372 Ligands: EDO.6, SAM.7 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:F.187, A:F.187, A:Y.243, A:Y.261 Hydrogen bonds: A:T.188, A:T.188, A:M.194 Water bridges: A:C.242, A:M.246, A:Y.261 pi-Stacking: A:F.187

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Su, D.S. et al., Discovery of Isoxazole Amides as Potent and Selective SMYD3 Inhibitors. Acs Med.Chem.Lett. (2020)

Release Date

2020-01-15

Peptides

Histone-lysine N-methyltransferase SMYD3: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Histone-lysine N-methyltransferase SMYD3

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