MolNFT v1 · #140179 · protein
Human SIRT6 in complex with allosteric activator mdl-801
5Y2F · NAD-dependent protein deacetylase sirtuin-6: “Human SIRT6 in complex with allosteric activator mdl-801”. X-ray diffraction, 5 ligands (AR6, 8L9, HDR), 3 pockets (best druggability 0.79). MolNFT v1 #140179 on GenesisL1: 3D structure…
- PDB
- 5Y2F
- Type
- protein
- Length
- 305 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent protein deacetylase sirtuin-6; 9-mer peptide qtarkstgg
- EC
- 3.5.1.-
- UniProt
- Q8N6T7
- Ligands
- AR6, 8L9, HDR, ZN, SO4
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent protein deacetylase sirtuin-6 (EC 3.5.1.-) | protein | 297 | 29% helix, 15% strand | Q8N6T7 |
| C | 9-mer peptide qtarkstgg | protein | 8 | 0% helix, 25% strand | — |
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 · chains A, C
- 8L9 · 5-[[3,5-bis(chloranyl)phenyl]sulfonylamino]-2-[(5-bromanyl-4-fluoranyl-2-methyl-phenyl)sulfamoyl]benzoic acid · ligand · chains A
- HDR · Hexadecane-1-sulfinic acid · ligand · chains A, C
- ZN · Zinc ion · metal · chains A
- SO4 · Sulfate ion · ion · 7 copies · chains A, C
- GOL · Glycerol · additive · 5 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 567 | 0.79 | 0.85 | 66 | AR6, 8L9, SO4, HDR |
| 2 | 207 | 0.55 | 0.78 | 30 | empty |
| 3 | 51 | 0.28 | 0.75 | 20 | empty |
Interfaces
1 interface between chains.
- A–C · 586 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5Y2F · Human SIRT6 in complex with allosteric activator MDL-801 · 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 Q8N6T7
- Elsewhere: RCSB PDB 5Y2F · PDBe 5Y2F · UniProt Q8N6T7
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