MolNFT v1 · #113839 · protein
SMYD2 in complex with small molecule inhibitor compound-2
5ARF · N-lysine methyltransferase SMYD2: “SMYD2 in complex with small molecule inhibitor compound-2”. X-ray diffraction, 3 ligands (I9H, SAM, ZN), 4 pockets (best druggability 0.80). MolNFT v1 #113839 on GenesisL1: 3D structure, binding…
- PDB
- 5ARF
- Type
- protein
- Length
- 425 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
- I9H, SAM, ZN
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 51% 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 | 425 | 51% helix, 14% strand | Q9NRG4 |
Ligands and binding sites
- I9H · N-[3-(4-chlorophenyl)-1-{N'-cyano-N-[3-(difluoromethoxy)phenyl]carbamimidoyl}-4,5-dihydro-1H- pyrazol-4-yl]-N-ethyl-2-hydroxyacetamide · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 942 | 0.80 | 0.82 | 100 | I9H, SAM |
| 2 | 107 | 0.40 | 0.76 | 22 | empty |
| 3 | 85 | 0.38 | 0.77 | 15 | empty |
| 4 | 53 | 0.25 | 0.72 | 14 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5ARF · SMYD2 in complex with small molecule inhibitor compound-2 · 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 0.99
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 5ARF · PDBe 5ARF · UniProt Q9NRG4
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