MolNFT v1 · #96765 · protein
Crystal structure of human SIRT3 with elt inhibitor 3 [14-(4-{2- [(METHYLSULFONYL)AMINO]ETHYL}PIPERIDIN-1-YL)THIENO[3,2-D]PYRIMIDINE- 6-carboxamide]
4JT9 · NAD-dependent protein deacetylase sirtuin-3, mitochondrial: “Crystal structure of human SIRT3 with elt inhibitor 3 [14-(4-{2…”. X-ray diffraction, 3 ligands (1NS, ZN, NA), 2 pockets (best druggability 0.67). MolNFT v1 #96765 on…
- PDB
- 4JT9
- Type
- protein
- Length
- 274 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent protein deacetylase sirtuin-3, mitochondrial
- EC
- 3.5.1.-
- UniProt
- Q9NTG7
- Ligands
- 1NS, ZN, NA
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | NAD-dependent protein deacetylase sirtuin-3, mitochondrial (EC 3.5.1.-) | protein | 274 | 41% helix, 17% strand | Q9NTG7 |
Ligands and binding sites
- 1NS · 4-(4-{2-[(methylsulfonyl)amino]ethyl}piperidin-1-yl)thieno[3,2-d]pyrimidine-6-carboxamide · ligand · chains A
- ZN · Zinc ion · metal · chains A
- NA · Sodium ion · metal · chains A
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 421 | 0.67 | 0.79 | 44 | 1NS, GOL |
| 2 | 114 | 0.38 | 0.74 | 24 | empty |
Compared structures
- 4JT9 · Crystal Structure of human SIRT3 with ELT inhibitor 3… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NTG7 · AlphaFold monomer V2.0 prediction for NAD-dependent protein deacetylase sirtuin-3… · a predicted model of the same protein · chain A against A, TM-score 0.94
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 Q9NTG7
- Elsewhere: RCSB PDB 4JT9 · PDBe 4JT9 · UniProt Q9NTG7
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