MolNFT v1 · #54289 · protein
Structure of NEK2 bound to aminopyrazine compound 15
2XK8 · SERINE/THREONINE-protein kinase NEK2: “Structure of NEK2 bound to aminopyrazine compound 15”. X-ray diffraction, 2 ligands (5R1, CL), 3 pockets (best druggability 0.54). MolNFT v1 #54289 on GenesisL1: 3D structure, binding sites and…
- PDB
- 2XK8
- Type
- protein
- Length
- 246 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
- 5R1, CL
- Pockets
- 3 · best druggability 0.54
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 | 246 | 41% helix, 18% strand | P51955 |
Ligands and binding sites
- 5R1 · 4-[3-amino-6-(3,4,5-trimethoxyphenyl)pyrazin-2-yl]-2-methoxybenzoic acid · ligand · chains A
- CL · Chloride ion · ion · 4 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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 154 | 0.54 | 0.80 | 22 | 5R1 |
| 2 | 69 | 0.29 | 0.73 | 18 | empty |
| 3 | 51 | 0.27 | 0.74 | 19 | CL |
Compared structures
- 2XK8 · Structure of Nek2 bound to aminopyrazine compound 15 · 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 2XK8 · PDBe 2XK8 · UniProt P51955
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