MolNFT v1 · #158950 · protein
Crystal structure of SMYD3 with potent and selective isoxazole amide inhibitor 1
6O9O · Histone-lysine N-methyltransferase SMYD3: “Crystal structure of SMYD3 with potent and selective isoxazole amide inhibitor 1”. X-ray diffraction, 4 ligands (SAH, LUP, ZN), 4 pockets (best druggability 0.81). MolNFT v1 #158950 on…
- PDB
- 6O9O
- Type
- protein
- Length
- 426 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase SMYD3
- EC
- 2.1.1.43
- UniProt
- Q9H7B4
- Ligands
- SAH, LUP, ZN, MG
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase SMYD3 (EC 2.1.1.43) | protein | 426 | 51% helix, 13% strand | Q9H7B4 |
Ligands and binding sites
- SAH · S-adenosyl-L-homocysteine · ligand · chains A
- LUP · 5-cyclopropyl-N-{1-[({trans-4-[(4,4,4-trifluorobutyl) amino]cyclohexyl}methyl)sulfonyl]piperidin-4-yl}-1,2-oxazole-3-carboxamide · ligand · chains A
- ZN · Zinc ion · metal · 3 copies · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1156 | 0.81 | 0.82 | 101 | GOL, SAH, LUP |
| 2 | 142 | 0.51 | 0.79 | 21 | empty |
| 3 | 138 | 0.49 | 0.79 | 26 | empty |
| 4 | 52 | 0.32 | 0.77 | 13 | empty |
Compared structures
- 6O9O · Crystal Structure of SMYD3 with Potent and Selective Isoxazole Amide Inhibitor 1 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9H7B4 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase SMYD3 (Q9H7B4) · a predicted model of the same protein · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q9H7B4
- Elsewhere: RCSB PDB 6O9O · PDBe 6O9O · UniProt Q9H7B4
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