Research workbench
Crystal structure of the CDK2 in complex with oxindole inhibitor
Analyse Crystal structure of the CDK2 in complex with oxindole inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4FKU
- Type
- protein
- Length
- 293 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclin-dependent kinase 2
- EC
- 2.7.11.22
- UniProt
- P24941
- Ligands
- 60K, ACE
- Pockets
- 4 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 33% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-dependent kinase 2 (EC 2.7.11.22) | protein | 293 | 33% helix, 16% strand | P24941 |
Ligands and binding sites
- 60K · (3Z)-2-oxo-3-[2-(4-sulfamoylphenyl)hydrazinylidene]-2,3-dihydro-1H-indole-5-carboxylic acid · ligand · 2 copies · chains A
- ACE · Acetyl group · ligand · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 490 | 0.72 | 0.81 | 55 | 60K |
| 2 | 106 | 0.45 | 0.78 | 17 | empty |
| 3 | 69 | 0.41 | 0.80 | 18 | empty |
| 4 | 58 | 0.37 | 0.79 | 13 | empty |
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4FKU · Crystal structure of the cdk2 in complex with oxindole inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- P24941 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinase 2 (P24941) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 4FKU · PDBe 4FKU · UniProt P24941
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