MolNFT v1 · #163880 · protein
NEK2 kinase covalently bound to 2-arylamino-6-ethynylpurine inhibitor 24
6SGD · SERINE/THREONINE-protein kinase NEK2: “NEK2 kinase covalently bound to 2-arylamino-6-ethynylpurine inhibitor 24”. X-ray diffraction, 3 ligands (LD5, NA, CL), 2 pockets (best druggability 0.61). MolNFT v1 #163880 on GenesisL1: 3D…
- PDB
- 6SGD
- Type
- protein
- Length
- 248 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
- LD5, NA, CL
- Pockets
- 2 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase NEK2 (EC 2.7.11.1) | protein | 248 | 41% helix, 17% strand | P51955 |
Ligands and binding sites
- LD5 · 4-[(6-ethenyl-7~{H}-purin-2-yl)amino]benzenesulfonamide · ligand · chains A
- NA · Sodium ion · metal · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 347 | 0.61 | 0.77 | 36 | LD5 |
| 2 | 62 | 0.27 | 0.72 | 17 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6SGD · Nek2 kinase covalently bound to 2-arylamino-6-ethynylpurine inhibitor 24 · 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 0.97
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 6SGD · PDBe 6SGD · UniProt P51955
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