MolNFT v1 · #112909 · protein

SIRT1/ACTIVATOR/SUBSTRATE complex

4ZZJ · NAD-dependent protein deacetylase sirtuin-1: “SIRT1/ACTIVATOR/SUBSTRATE complex”. X-ray diffraction, 3 ligands (CNA, 4TQ, ZN), 3 pockets (best druggability 0.80). MolNFT v1 #112909 on GenesisL1: 3D structure, binding sites and…

PDB: 4ZZJ
Type: protein
Length: 351 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: NAD-dependent protein deacetylase sirtuin-1; Ac-P53
EC: 3.5.1.-
UniProt: Q96EB6
Ligands: CNA, 4TQ, ZN
Pockets: 3 · best druggability 0.80

Structure

x-ray diffraction · 2 distinct chains · 38% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	NAD-dependent protein deacetylase sirtuin-1 (EC 3.5.1.-)	protein	344	38% helix, 16% strand	Q96EB6
B	Ac-P53	protein	7	0% helix, 43% strand	—

Ligands and binding sites

CNA · Carba-nicotinamide-adenine-dinucleotide · ligand · chains A, B
4TQ · (3S)-1,3-dimethyl-N-[3-(1,3-oxazol-5-yl)phenyl]-6-[3-(trifluoromethyl)phenyl]-2,3-dihydropyrido[2,3-b]pyrazine-4(1H)-carboxamide · ligand · chains A
ZN · Zinc ion · metal · chains A
GOL · Glycerol · additive · 2 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	318	0.80	0.91	46	CNA
2	76	0.40	0.79	17	empty
3	50	0.30	0.76	10	GOL

Interfaces

1 interface between chains.

A–B · 655 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (acetylation, nonstandard).

Compared structures

4ZZJ · SIRT1/Activator/Substrate Complex · 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 0.87

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 4ZZJ · PDBe 4ZZJ · UniProt Q96EB6

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