MolNFT v1 · #164006 · protein

NEK2 bound to purine compound 51

6SK9 · SERINE/THREONINE-protein kinase NEK2: “NEK2 bound to purine compound 51”. X-ray diffraction, 1 ligand (F9N), 2 pockets (best druggability 0.54). MolNFT v1 #164006 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6SK9
Type: protein
Length: 240 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: SERINE/THREONINE-protein kinase NEK2
EC: 2.7.11.1
UniProt: P51955
Ligands: F9N
Pockets: 2 · best druggability 0.54

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	SERINE/THREONINE-protein kinase NEK2 (EC 2.7.11.1)	protein	240	42% helix, 18% strand	P51955

Ligands and binding sites

F9N · 3-[[6-(cyclohexylmethoxy)-7~{H}-purin-2-yl]amino]-~{N}-[3-(dimethylamino)propyl]benzenesulfonamide · ligand · chains A
GOL · Glycerol · 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	203	0.54	0.78	37	F9N
2	60	0.28	0.74	19	empty

Compared structures

6SK9 · Nek2 bound to purine compound 51 · the same entry in another collection · chain A against A, TM-score 1.00
P51955 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase NEK2 (P51955) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 P51955
Elsewhere: RCSB PDB 6SK9 · PDBe 6SK9 · UniProt P51955

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