MolNFT v1 · #32954 · protein
Differential binding of inhibitors to active and inactive CDK2 provides insights for drug design
2C5O · Cell division protein kinase 2: “Differential binding of inhibitors to active and inactive CDK2 provides insights for drug design”. X-ray diffraction, 1 ligand (CK2), 16 pockets (best druggability 0.81). MolNFT v1 #32954 on…
- 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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