MolNFT v1 · #76840 · protein
Crystal structure of histone lysine methyltransferase SMYD2 in complex with the methyltransferase inhibitor sinefungin
3QWW · Set and mynd domain-containing protein 2: “Crystal structure of histone lysine methyltransferase SMYD2 in complex with the methyltransferase inhibitor…”. X-ray diffraction, 2 ligands (SFG, ZN), 3 pockets (best druggability 0.77).…
- PDB
- 3QWW
- Type
- protein
- Length
- 430 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Set and mynd domain-containing protein 2
- UniProt
- Q8R5A0
- Ligands
- SFG, ZN
- Pockets
- 3 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Set and mynd domain-containing protein 2 | protein | 430 | 50% helix, 13% strand | Q8R5A0 |
Ligands and binding sites
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 | 999 | 0.77 | 0.78 | 96 | empty |
| 2 | 152 | 0.60 | 0.83 | 25 | SFG |
| 3 | 63 | 0.35 | 0.78 | 15 | empty |
Compared structures
- 3QWW · Crystal structure of histone lysine methyltransferase SmyD2 in complex with the… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8R5A0 · AlphaFold monomer V2.0 prediction for N-lysine methyltransferase SMYD2 (Q8R5A0) · 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 Q8R5A0
- Elsewhere: RCSB PDB 3QWW · PDBe 3QWW · UniProt Q8R5A0
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