Research workbench
Structure of human SIRT2 in complex with 1,2,4-oxadiazole inhibitor and ADP ribose.
Analyse Structure of human SIRT2 in complex with 1,2,4-oxadiazole inhibitor and ADP… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MAR
- Type
- protein
- Length
- 604 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
- AR6, 7KE, ZN
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | NAD-dependent protein deacetylase sirtuin-2 (EC 3.5.1.-) | protein | 302 | 37% helix, 16% strand | Q8IXJ6 |
Ligands and binding sites
- AR6 · [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [hydroxy-[[(2R,3S,4R,5S)-3,4,5-trihydroxyoxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate · ligand · 2 copies · chains A, B
- 7KE · 3-[3-(4-chlorophenyl)-1,2,4-oxadiazol-5-yl]propan-1-ol · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 9 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
- ACT · Acetate ion · additive · chains 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 609 | 0.82 | 0.87 | 65 | AR6, 7KE, DMS |
| 2 | 596 | 0.79 | 0.85 | 69 | AR6, 7KE, DMS |
| 3 | 485 | 0.62 | 0.75 | 30 | DMS, GOL |
| 4 | 340 | 0.59 | 0.77 | 50 | empty |
| 5 | 188 | 0.48 | 0.76 | 35 | GOL |
Interfaces
1 interface between chains.
- A–B · 985 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 5MAR · Structure of human SIRT2 in complex with 1,2,4-Oxadiazole inhibitor and ADP ribose. · 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 5MAR · PDBe 5MAR · UniProt Q8IXJ6
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