MolNFT v1 · #126705 · protein
Structure of human sirtuin 2 in complex with a selective thienopyrimidinone based inhibitor
5MAT · NAD-dependent protein deacetylase sirtuin-2: “Structure of human sirtuin 2 in complex with a selective thienopyrimidinone based inhibitor”. X-ray diffraction, 3 ligands (7KJ, ZN, SO4), 6 pockets (best druggability 0.81). MolNFT v1…
- PDB
- 5MAT
- Type
- protein
- Length
- 598 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
- 7KJ, ZN, SO4
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent protein deacetylase sirtuin-2 (EC 3.5.1.-) | protein | 300 | 39% helix, 17% strand | Q8IXJ6 |
| C | NAD-dependent protein deacetylase sirtuin-2 (EC 3.5.1.-) | protein | 298 | 38% helix, 17% strand | Q8IXJ6 |
Ligands and binding sites
- 7KJ · (7~{R})-7-[(3,5-dimethyl-1,2-oxazol-4-yl)methylamino]-3-[(4-methoxynaphthalen-1-yl)methyl]-5,6,7,8-tetrahydro-[1]benzothiolo[2,3-d]pyrimidin-4-one · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A, C
- SO4 · Sulfate ion · ion · 14 copies · chains A, C
- PG4 · Tetraethylene glycol · additive · chains A
- P6G · Hexaethylene glycol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 649 | 0.81 | 0.85 | 56 | 7KJ, SO4 |
| 2 | 754 | 0.80 | 0.83 | 62 | SO4 |
| 3 | 171 | 0.50 | 0.77 | 16 | empty |
| 4 | 126 | 0.38 | 0.74 | 26 | empty |
| 5 | 90 | 0.35 | 0.75 | 23 | empty |
Interfaces
1 interface between chains.
- A–C · 1065 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 5MAT · Structure of human Sirtuin 2 in complex with a selective thienopyrimidi based inhibitor · 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 5MAT · PDBe 5MAT · UniProt Q8IXJ6
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