Research workbench
Structure of NEK2 bound to aminopyrazine compound 36
Analyse Structure of NEK2 bound to aminopyrazine compound 36 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XK6
- Type
- protein
- Length
- 243 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
- EQH, CL
- Pockets
- 2 · best druggability 0.49
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase NEK2 (EC 2.7.11.1) | protein | 243 | 42% helix, 18% strand | P51955 |
Ligands and binding sites
- EQH · cis-4-[3-amino-6-(3-cyclopropylthiophen-2-yl)pyrazin-2-yl]cyclohexanecarboxylic acid · ligand · chains A
- CL · Chloride ion · ion · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.49 | 0.79 | 17 | EQH |
| 2 | 62 | 0.28 | 0.74 | 20 | CL |
Compared structures
- 2XK6 · Structure of Nek2 bound to aminopyrazine compound 36 · 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 0.94
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 2XK6 · PDBe 2XK6 · UniProt P51955
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