Research workbench
Human SIRT2 in complex with a specific inhibitor, NPD11033
Analyse Human SIRT2 in complex with a specific inhibitor, NPD11033 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y0Z
- Type
- protein
- Length
- 577 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent protein deacetylase sirtuin-2
- EC
- 3.5.1.-
- UniProt
- Q8IXJ6
- Ligands
- 8K9, ZN
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent protein deacetylase sirtuin-2 (EC 3.5.1.-) | protein | 288 | 42% helix, 17% strand | Q8IXJ6 |
| B | NAD-dependent protein deacetylase sirtuin-2 (EC 3.5.1.-) | protein | 289 | 41% helix, 17% strand | Q8IXJ6 |
Ligands and binding sites
- 8K9 · (1~{R},9~{S})-11-[(2~{R})-3-[2,4-bis(2-methylbutan-2-yl)phenoxy]-2-oxidanyl-propyl]-7,11-diazatricyclo[7.3.1.0^{2,7}]trideca-2,4-dien-6-one · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 890 | 0.83 | 0.84 | 84 | 8K9 |
| 2 | 567 | 0.81 | 0.86 | 50 | 8K9 |
| 3 | 249 | 0.54 | 0.76 | 28 | empty |
| 4 | 71 | 0.38 | 0.79 | 21 | empty |
| 5 | 110 | 0.37 | 0.74 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 755 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5Y0Z · Human SIRT2 in complex with a specific inhibitor, NPD11033 · 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 5Y0Z · PDBe 5Y0Z · UniProt Q8IXJ6
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