MolNFT v2 · #129974 · protein
Cdk2(WT) covalent adduct with D28 at C177
5OO0 · Cyclin-dependent kinase 2: “Cdk2(WT) covalent adduct with D28 at C177”. X-ray diffraction at 1.6, 1 ligand (9YZ), 3 pockets (best druggability 0.63). MolNFT v2 #129974 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5OO0
- Type
- protein
- Length
- 288 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.6
- Source
- Homo sapiens
- Molecule
- Cyclin-dependent kinase 2
- EC
- 2.7.11.22
- UniProt
- P24941
- Ligands
- 9YZ
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · resolution 1.6 · 1 distinct chain · 35% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-dependent kinase 2 (EC 2.7.11.22) | protein | 288 | 35% helix, 17% strand | P24941 |
Ligands and binding sites
- 9YZ · methyl 4-propanoyl-2,3-dihydroquinoxaline-1-carboxylate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 160 | 0.63 | 0.85 | 25 | empty |
| 2 | 119 | 0.46 | 0.78 | 27 | empty |
| 3 | 50 | 0.30 | 0.76 | 13 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
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 P24941
- Elsewhere: RCSB PDB 5OO0 · PDBe 5OO0 · UniProt P24941
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