MolNFT v1 · #140914 · protein

Crystal structure of SIRT2 in complex with selective inhibitor A2I

5YQL · NAD-dependent protein deacetylase sirtuin-2: “Crystal structure of SIRT2 in complex with selective inhibitor A2I”. X-ray diffraction, 2 ligands (A2I, ZN), 3 pockets (best druggability 0.77). MolNFT v1 #140914 on GenesisL1: 3D…

PDB: 5YQL
Type: protein
Length: 296 residues
Chains: 1
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: A2I, ZN
Pockets: 3 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	NAD-dependent protein deacetylase sirtuin-2 (EC 3.5.1.-)	protein	296	36% helix, 17% strand	Q8IXJ6

Ligands and binding sites

A2I · 2-(4,6-dimethylpyrimidin-2-yl)sulfanyl-N-[3-(phenoxymethyl)phenyl]ethanamide · ligand · chains A
ZN · Zinc ion · metal · chains A
BME · Beta-mercaptoethanol · additive · 2 copies · chains A

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	428	0.77	0.85	46	A2I
2	111	0.47	0.79	21	BME
3	74	0.32	0.75	22	empty

Compared structures

5YQL · Crystal structure of Sirt2 in complex with selective inhibitor A2I · 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 5YQL · PDBe 5YQL · UniProt Q8IXJ6

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