MolNFT v1 · #111320 · protein
The discovery of a-893, a new cell-active benzoxazinone inhibitor of lysine methyltransferase SMYD2
4YND · N-lysine methyltransferase SMYD2: “The discovery of a-893, a new cell-active benzoxazinone inhibitor of lysine methyltransferase SMYD2”. X-ray diffraction, 3 ligands (4GQ, SAM, ZN), 4 pockets (best druggability 0.81). MolNFT v1…
- PDB
- 4YND
- Type
- protein
- Length
- 428 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- N-lysine methyltransferase SMYD2
- EC
- 2.1.1.-, 2.1.1.43
- UniProt
- Q9NRG4
- Ligands
- 4GQ, SAM, ZN
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | N-lysine methyltransferase SMYD2 (EC 2.1.1.-, 2.1.1.43) | protein | 428 | 50% helix, 14% strand | Q9NRG4 |
Ligands and binding sites
- 4GQ · N-cyclohexyl-N~3~-[2-(3,4-dichlorophenyl)ethyl]-N-(2-{[(2R)-2-hydroxy-2-(3-oxo-3,4-dihydro-2H-1,4-benzoxazin-8-yl)ethyl]amino}ethyl)-beta-alaninamide · 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
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 | 723 | 0.81 | 0.85 | 78 | SAM |
| 2 | 119 | 0.53 | 0.82 | 25 | 4GQ |
| 3 | 104 | 0.46 | 0.79 | 17 | empty |
| 4 | 99 | 0.41 | 0.77 | 15 | empty |
Compared structures
- 4YND · The Discovery of A-893, A New Cell-Active Benzoxazi Inhibitor of Lysine Methyltransferase… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NRG4 · AlphaFold monomer V2.0 prediction for N-lysine methyltransferase SMYD2 (Q9NRG4) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q9NRG4
- Elsewhere: RCSB PDB 4YND · PDBe 4YND · UniProt Q9NRG4
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