MolNFT v1 · #163884 · protein

NEK2 kinase bound to inhibitor 96

6SGI · SERINE/THREONINE-protein kinase NEK2: “NEK2 kinase bound to inhibitor 96”. X-ray diffraction, 2 ligands (LCB, CL), 3 pockets (best druggability 0.70). MolNFT v1 #163884 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6SGI
Type: protein
Length: 252 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: LCB, CL
Pockets: 3 · best druggability 0.70

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	SERINE/THREONINE-protein kinase NEK2 (EC 2.7.11.1)	protein	252	40% helix, 18% strand	P51955

Ligands and binding sites

LCB · 4-[(6-ethyl-7~{H}-purin-2-yl)amino]benzenesulfonamide · ligand · chains A
CL · Chloride ion · ion · 3 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	569	0.70	0.78	54	LCB
2	91	0.35	0.75	19	empty
3	58	0.28	0.74	18	empty

Compared structures

6SGI · Nek2 kinase bound to inhibitor 96 · 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 0.97

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 6SGI · PDBe 6SGI · UniProt P51955

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