Research workbench
Crystal structure of human SIRT2 in complex with a brominated 2ND generation sirreal inhibitor and NAD+
Analyse Crystal structure of human SIRT2 in complex with a brominated 2ND generation… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DY4
- Type
- protein
- Length
- 301 residues
- Chains
- 1
- 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
- 5GN, NAD, ZN
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent protein deacetylase sirtuin-2 (EC 3.5.1.-) | protein | 301 | 40% helix, 17% strand | Q8IXJ6 |
Ligands and binding sites
- 5GN · N-{5-[(7-bromonaphthalen-1-yl)methyl]-1,3-thiazol-2-yl}-2-[(4,6-dimethylpyrimidin-2-yl)sulfanyl]acetamide · ligand · chains A
- NAD · Nicotinamide-adenine-dinucleotide · ligand · chains A
- ZN · Zinc ion · metal · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 684 | 0.76 | 0.81 | 51 | 5GN, NAD |
| 2 | 157 | 0.47 | 0.77 | 26 | empty |
| 3 | 125 | 0.40 | 0.75 | 27 | empty |
Compared structures
- 5DY4 · Crystal structure of human Sirt2 in complex with a brominated 2nd generation SirReal… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8IXJ6 · AlphaFold monomer V2.0 prediction for NAD-dependent protein deacetylase sirtuin-2 (Q8IXJ6) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 5DY4 · PDBe 5DY4 · UniProt Q8IXJ6
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