MolNFT v1 · #54403 · protein

Structure of NEK2 bound to cct

2XNM · SERINE/THREONINE-protein kinase NEK2: “Structure of NEK2 bound to cct”. X-ray diffraction, 2 ligands (WGZ, CL), 3 pockets (best druggability 0.58). MolNFT v1 #54403 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2XNM
Type: protein
Length: 258 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: WGZ, CL
Pockets: 3 · best druggability 0.58

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	SERINE/THREONINE-protein kinase NEK2 (EC 2.7.11.1)	protein	258	43% helix, 19% strand	P51955

Ligands and binding sites

WGZ · 5-{6-[(1-methylpiperidin-4-yl)oxy]-1H-benzimidazol-1-yl}-3-{(1R)-1-[2-(trifluoromethyl)phenyl]ethoxy}thiophene-2-carboxamide · ligand · chains A
CL · Chloride ion · ion · 3 copies · chains A
EDO · 1,2-ethanediol · additive · 8 copies · chains A
TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · 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	196	0.58	0.80	22	WGZ
2	148	0.41	0.74	37	empty
3	79	0.32	0.74	21	CL

Compared structures

2XNM · Structure of NEK2 bound to CCT · 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 0.92

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 2XNM · PDBe 2XNM · UniProt P51955

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