MolNFT v1 · #140719 · protein
Crystal structure of SMYD3 in complex with covalent inhibitor 4
5YJO · Histone-lysine N-methyltransferase SMYD3: “Crystal structure of SMYD3 in complex with covalent inhibitor 4”. X-ray diffraction, 3 ligands (8W0, SAM, ZN), 3 pockets (best druggability 0.79). MolNFT v1 #140719 on GenesisL1: 3D…
- PDB
- 5YJO
- Type
- protein
- Length
- 423 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
- 8W0, SAM, ZN
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase SMYD3 (EC 2.1.1.43) | protein | 423 | 50% helix, 13% strand | Q9H7B4 |
Ligands and binding sites
- 8W0 · propyl (3~{S})-4-[[(6~{R})-6-(aminomethyl)-5,6,7,8-tetrahydroacridin-3-yl]carbonyl]-3-methyl-piperazine-1-carboxylate · ligand · chains A
- SAM · S-adenosylmethionine · ligand · chains A
- ZN · Zinc ion · metal · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1090 | 0.79 | 0.81 | 101 | 8W0, SAM |
| 2 | 195 | 0.54 | 0.78 | 34 | empty |
| 3 | 101 | 0.44 | 0.79 | 26 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5YJO · Crystal structure of SmyD3 in complex with covalent inhibitor 4 · 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 5YJO · PDBe 5YJO · UniProt Q9H7B4
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