MolNFT v1 · #54405 · protein
Structure of NEK2 bound to CCT243779
2XNO · SERINE/THREONINE-protein kinase NEK2: “Structure of NEK2 bound to CCT243779”. X-ray diffraction, 2 ligands (ED8, CL), 4 pockets (best druggability 0.59). MolNFT v1 #54405 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2XNO
- Type
- protein
- Length
- 251 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
- ED8, CL
- Pockets
- 4 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase NEK2 (EC 2.7.11.1) | protein | 251 | 41% helix, 18% strand | P51955 |
Ligands and binding sites
- ED8 · 5-{6-[(1-methylpiperidin-4-yl)oxy]-1H-benzimidazol-1-yl}-3-{[2-(trifluoromethyl)benzyl]oxy}thiophene-2-carboxamide · ligand · chains A
- CL · Chloride ion · ion · 2 copies · chains A
- EDO · 1,2-ethanediol · additive · 11 copies · chains A
- GOL · Glycerol · additive · chains A
- DMS · Dimethyl sulfoxide · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 316 | 0.59 | 0.77 | 35 | ED8, EDO |
| 2 | 87 | 0.35 | 0.75 | 23 | DMS |
| 3 | 87 | 0.34 | 0.74 | 22 | empty |
| 4 | 51 | 0.28 | 0.74 | 10 | empty |
Compared structures
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 2XNO · PDBe 2XNO · UniProt P51955
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