MolNFT v1 · #163883 · protein
NEK2 kinase covalently bound to 2-arylamino-6-ethynylpurine inhibitor 66
6SGH · SERINE/THREONINE-protein kinase NEK2: “NEK2 kinase covalently bound to 2-arylamino-6-ethynylpurine inhibitor 66”. X-ray diffraction, 1 ligand (LCW), 2 pockets (best druggability 0.56). MolNFT v1 #163883 on GenesisL1: 3D structure…
- PDB
- 6SGH
- Type
- protein
- Length
- 238 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
- LCW
- Pockets
- 2 · best druggability 0.56
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 | 238 | 42% helix, 18% strand | P51955 |
Ligands and binding sites
- LCW · 2-[4-[(6-ethenyl-9~{H}-purin-2-yl) amino]phenyl]ethanamide · ligand · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 297 | 0.56 | 0.76 | 44 | LCW |
| 2 | 68 | 0.28 | 0.73 | 17 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6SGH · Nek2 kinase covalently bound to 2-arylamino-6-ethynylpurine inhibitor 66 · 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 6SGH · PDBe 6SGH · UniProt P51955
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