MolNFT v1 · #126106 · protein
Structure of the epigenetic oncogene mmset and inhibition by N-alkyl sinefungin derivatives
5LSX · Histone-lysine N-methyltransferase SETD2: “Structure of the epigenetic oncogene mmset and inhibition by N-alkyl sinefungin derivatives”. X-ray diffraction, 2 ligands (76O, ZN), 3 pockets (best druggability 0.69). MolNFT v1 #126106…
- PDB
- 5LSX
- Type
- protein
- Length
- 231 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone-lysine N-methyltransferase SETD2
- EC
- 2.1.1.43
- UniProt
- Q9BYW2
- Ligands
- 76O, ZN
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 18% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone-lysine N-methyltransferase SETD2 (EC 2.1.1.43) | protein | 231 | 18% helix, 26% strand | Q9BYW2 |
Ligands and binding sites
- 76O · [(2~{R},5~{S})-1-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]-5-azaniumyl-6-oxidanyl-6-oxidanylidene-hexan-2-yl]-(phenylmethyl)azanium · 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 | 260 | 0.69 | 0.84 | 34 | 76O |
| 2 | 99 | 0.62 | 0.88 | 18 | empty |
| 3 | 140 | 0.45 | 0.76 | 21 | empty |
Compared structures
- 5LSX · Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9BYW2 · AlphaFold monomer V2.0 prediction for histone-lysine N-methyltransferase SETD2 (Q9BYW2) · 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 Q9BYW2
- Elsewhere: RCSB PDB 5LSX · PDBe 5LSX · UniProt Q9BYW2
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