› 6paf

X-ray diffraction
1.24Å resolution

Co-crystal Structure of human SMYD3 with Isoxazole Amides Inhibitors

Released:
DOI: 10.2210/pdb6paf/pdb
PDB entry 6paf coloured by chain, front view.
PDB entry 6paf coloured by chain, side view.
PDB entry 6paf coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Discovery of Isoxazole Amides as Potent and Selective SMYD3 Inhibitors.
Su DS, Qu J, Schulz M, Blackledge CW, Yu H, Zeng J, Burgess J, Reif A, Stern M, Nagarajan R, Pappalardi MB, Wong K, Graves AP, Bonnette W, Wang L, Elkins P, Knapp-Reed B, Carson JD, McHugh C, Mohammad H, Kruger R, Luengo J, Heerding DA, Creasy CL
ACS Med Chem Lett 11 133-140 (2020)
PMID: 32071679

Function and Biology Details

Reaction catalysed: 
(1a) S-adenosyl-L-methionine + a [histone H3]-L-lysine(4) = S-adenosyl-L-homocysteine + a [histone H3]-N(6)-methyl-L-lysine(4)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-190659 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Histone-lysine N-methyltransferase SMYD3 Chain: A
Molecule details ›
Chain: A
Length: 432 amino acids
Theoretical weight: 49.54 KDa
Source organism: Homo sapiens
Expression system: unidentified baculovirus
UniProt:
  • Canonical: Q9H7B4 (Residues: 1-428; Coverage: 100%)
Gene names: SMYD3, ZMYND1, ZNFN3A1
Sequence domains:

Ligands and Environments

5 bound ligands:
Ligand ZN 3 x ZN
Ligand MG 2 x MG
Ligand GOL 2 x GOL
Ligand SAM 1 x SAM
Ligand O6A 1 x O6A
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 21-ID-D
Spacegroup: P212121
Unit cell:
a: 60.971Å b: 65.991Å c: 106.544Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.173 0.172 0.188
Expression system: unidentified baculovirus

Quick links

Citations

2 review citations

Lysine methyltransferase inhibitors: where we are now.
Feoli et al. (2022)
1 more