MolNFT v1 · #52588 · protein
Human NEK2 kinase ADP-bound
2W5A · SERINE/THREONINE-protein kinase NEK2: “Human NEK2 kinase ADP-bound”. X-ray diffraction, 2 ligands (ADP, MG), 4 pockets (best druggability 0.67). MolNFT v1 #52588 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 2W5A
- Type
- protein
- Length
- 267 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
- ADP, MG
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase NEK2 (EC 2.7.11.1) | protein | 267 | 45% helix, 18% strand | P51955 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 289 | 0.67 | 0.82 | 36 | ADP, MG |
| 2 | 107 | 0.65 | 0.89 | 22 | EDO |
| 3 | 447 | 0.59 | 0.74 | 33 | empty |
| 4 | 76 | 0.36 | 0.76 | 12 | 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 2W5A · PDBe 2W5A · UniProt P51955
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