Research workbench
Human SIRT2 in complex with myristoyl thiourea inhibitor, NO.23
Analyse Human SIRT2 in complex with myristoyl thiourea inhibitor, NO.23 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BOT
- Type
- protein
- Length
- 280 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent protein deacetylase sirtuin-2; Myristoyl thiourea inhibitor, NO.23
- EC
- 2.3.1.286
- UniProt
- Q8IXJ6
- Ligands
- P6S, F4R, ZN, NH2
- Pockets
- 2 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent protein deacetylase sirtuin-2 (EC 2.3.1.286) | protein | 277 | 40% helix, 17% strand | Q8IXJ6 |
| B | Myristoyl thiourea inhibitor, NO.23 | protein | 3 | 0% helix, 33% strand | — |
Ligands and binding sites
- P6S · benzyl hydrogen carbonate · ligand · chains A, B
- F4R · N-dodecylmethanethioamide · ligand · chains A, B
- ZN · Zinc ion · metal · chains A
- NH2 · Amino group · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 548 | 0.83 | 0.88 | 47 | F4R |
| 2 | 141 | 0.40 | 0.73 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 324 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 1 modified (covalent ligand, nonstandard).
Compared structures
- 7BOT · Human SIRT2 in complex with myristoyl thiourea inhibitor, No.23 · the same entry in another collection · 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 Q8IXJ6
- Elsewhere: RCSB PDB 7BOT · PDBe 7BOT · UniProt Q8IXJ6
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