Research workbench
Differential binding of inhibitors to active and inactive CDK2 provides insights for drug design
Analyse Differential binding of inhibitors to active and inactive CDK2 provides… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2C5O
- Type
- protein
- Length
- 1,108 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell division protein kinase 2; Cyclin A2
- EC
- 2.7.1.37
- UniProt
- P24941, P20248
- Ligands
- CK2
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cell division protein kinase 2 (EC 2.7.1.37) | protein | 296 | 33% helix, 17% strand | P24941 |
| B, D | Cyclin A2 | protein | 258 | 65% helix, 0% strand | P20248 |
Ligands and binding sites
- CK2 · 4-(2,4-dimethyl-1,3-thiazol-5-yl)pyrimidin-2-amine · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 135 | 0.81 | 0.98 | 25 | empty |
| 2 | 135 | 0.80 | 0.98 | 25 | empty |
| 3 | 732 | 0.75 | 0.80 | 71 | empty |
| 4 | 238 | 0.71 | 0.86 | 26 | CK2 |
| 5 | 226 | 0.69 | 0.85 | 28 | CK2 |
Interfaces
5 interfaces between chains.
- A–B · 1750 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1730 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 525 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 508 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 124 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2C5O · Differential Binding Of Inhibitors To Active And Inactive Cdk2 Provides Insights For Drug… · the same entry in another collection · chain D against D, TM-score 1.00
- P20248 · AlphaFold monomer V2.0 prediction for cyclin-A2 (P20248) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P24941 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinase 2 (P24941) · a predicted model of the same protein · chain C against A, TM-score 0.92
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
- Every structure of UniProt P20248
- Elsewhere: RCSB PDB 2C5O · PDBe 2C5O · UniProt P24941 · UniProt P20248
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