Research workbench
CDK2/CYCLINA complexed with a pyrazolopyridazine inhibitor
Analyse CDK2/CYCLINA complexed with a pyrazolopyridazine inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EJ1
- Type
- protein
- Length
- 1,104 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell division protein kinase 2; Cyclin-A2
- EC
- 2.7.11.22
- UniProt
- P24941, P20248
- Ligands
- 5BP
- Pockets
- 14 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 47% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell division protein kinase 2 (EC 2.7.11.22) | protein | 295 | 31% helix, 18% strand | P24941 |
| B | Cyclin-A2 | protein | 258 | 64% helix, 0% strand | P20248 |
| C | Cell division protein kinase 2 (EC 2.7.11.22) | protein | 294 | 33% helix, 18% strand | P24941 |
| D | Cyclin-A2 | protein | 257 | 64% helix, 0% strand | P20248 |
Ligands and binding sites
- 5BP · N-cyclopropyl-4-pyrazolo[1,5-b]pyridazin-3-ylpyrimidin-2-amine · ligand · 2 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 110 | 0.80 | 0.99 | 22 | empty |
| 2 | 118 | 0.78 | 0.97 | 24 | empty |
| 3 | 892 | 0.77 | 0.80 | 83 | empty |
| 4 | 502 | 0.68 | 0.79 | 61 | empty |
| 5 | 243 | 0.68 | 0.84 | 27 | 5BP |
Interfaces
5 interfaces between chains.
- C–D · 1675 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1600 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 476 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 475 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 104 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3EJ1 · CDK2/CyclinA complexed with a pyrazolopyridazine inhibitor · 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 D 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 0.93
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 3EJ1 · PDBe 3EJ1 · UniProt P24941 · UniProt P20248
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