MolNFT v1 · #126509 · protein
NEK2 bound to arylaminopurine inhibitor 11
5M53 · SERINE/THREONINE-protein kinase NEK2: “NEK2 bound to arylaminopurine inhibitor 11”. X-ray diffraction, 2 ligands (7GJ, PO4), 2 pockets (best druggability 0.78). MolNFT v1 #126509 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 5M53
- Type
- protein
- Length
- 255 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
- 7GJ, PO4
- Pockets
- 2 · best druggability 0.78
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 | 255 | 41% helix, 18% strand | P51955 |
Ligands and binding sites
- 7GJ · 3-[[6-(cyclohexylmethoxy)-7~{H}-purin-2-yl]amino]-~{N}, ~{N}-dimethyl-benzamide · ligand · chains A
- PO4 · Phosphate ion · ion · 4 copies · chains A
- EDO · 1,2-ethanediol · additive · 6 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · 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 | 130 | 0.78 | 0.95 | 19 | EDO |
| 2 | 141 | 0.48 | 0.78 | 25 | 7GJ, EDO |
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 5M53 · PDBe 5M53 · UniProt P51955
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