MolNFT v1 · #94733 · protein
Crystal structure of the SIRT1 catalytic domain bound to NAD and an EX527 analog
4I5I · NAD-dependent protein deacetylase sirtuin-1: “Crystal structure of the SIRT1 catalytic domain bound to NAD and an EX527 analog”. X-ray diffraction, 3 ligands (4I5, NAD, ZN), 5 pockets (best druggability 0.81). MolNFT v1 #94733 on…
- PDB
- 4I5I
- Type
- protein
- Length
- 544 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- NAD-dependent protein deacetylase sirtuin-1
- EC
- 3.5.1.-
- UniProt
- Q96EB6
- Ligands
- 4I5, NAD, ZN
- Pockets
- 5 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 36% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | NAD-dependent protein deacetylase sirtuin-1 (EC 3.5.1.-) | protein | 272 | 36% helix, 18% strand | Q96EB6 |
Ligands and binding sites
- 4I5 · (6S)-2-chloro-5,6,7,8,9,10-hexahydrocyclohepta[b]indole-6-carboxamide · ligand · 2 copies · chains A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 476 | 0.81 | 0.88 | 61 | 4I5, NAD |
| 2 | 481 | 0.81 | 0.88 | 62 | 4I5, NAD |
| 3 | 712 | 0.68 | 0.76 | 92 | empty |
| 4 | 110 | 0.51 | 0.82 | 31 | empty |
| 5 | 51 | 0.26 | 0.73 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1057 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4I5I · Crystal structure of the SIRT1 catalytic domain bound to NAD and an EX527 analog · the same entry in another collection · chain A against A, TM-score 1.00
- Q96EB6 · AlphaFold monomer V2.0 prediction for NAD-dependent protein deacetylase sirtuin-1 (Q96EB6) · a predicted model of the same protein · chain A against A, TM-score 0.93
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 Q96EB6
- Elsewhere: RCSB PDB 4I5I · PDBe 4I5I · UniProt Q96EB6
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