MolNFT v1 · #140916 · protein

Crystal structure of SIRT2 in complex with selective inhibitor L55

5YQN · NAD-dependent protein deacetylase sirtuin-2: “Crystal structure of SIRT2 in complex with selective inhibitor L55”. X-ray diffraction, 2 ligands (L55, ZN), 2 pockets (best druggability 0.77). MolNFT v1 #140916 on GenesisL1: 3D…

PDB: 5YQN
Type: protein
Length: 288 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: L55, ZN
Pockets: 2 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	NAD-dependent protein deacetylase sirtuin-2 (EC 3.5.1.-)	protein	288	38% helix, 17% strand	Q8IXJ6

Ligands and binding sites

L55 · N-[3-[[3-[2-(4,6-dimethylpyrimidin-2-yl) sulfanylethanoylamino]phenyl]methoxy]phenyl]-1-methyl-pyrazole-4-carboxamide · ligand · chains A
ZN · Zinc ion · metal · chains A
PEG · Di(hydroxyethyl)ether · additive · 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.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	468	0.77	0.85	53	L55
2	91	0.35	0.75	26	empty

Compared structures

5YQN · Crystal structure of Sirt2 in complex with selective inhibitor L55 · 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 5YQN · PDBe 5YQN · UniProt Q8IXJ6

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