Research workbench
Structure of NEK2 bound to aminopyrazine compound 2
Analyse Structure of NEK2 bound to aminopyrazine compound 2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XKF
- Type
- protein
- Length
- 250 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
- BX1, CL
- Pockets
- 4 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase NEK2 (EC 2.7.11.1) | protein | 250 | 44% helix, 18% strand | P51955 |
Ligands and binding sites
- BX1 · 1-[3-amino-6-(3,4,5-trimethoxyphenyl)pyrazin-2-yl]piperidine-4-carboxylic 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
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 | 163 | 0.55 | 0.80 | 22 | BX1 |
| 2 | 122 | 0.42 | 0.76 | 19 | empty |
| 3 | 91 | 0.32 | 0.73 | 23 | empty |
| 4 | 50 | 0.28 | 0.75 | 16 | CL |
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 2XKF · PDBe 2XKF · UniProt P51955
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.