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
- 3EID
- Type
- protein
- Length
- 1,094 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
- PO5
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell division protein kinase 2 (EC 2.7.11.22) | protein | 292 | 34% helix, 18% strand | P24941 |
| B | Cyclin-A2 | protein | 257 | 66% helix, 0% strand | P20248 |
| C | Cell division protein kinase 2 (EC 2.7.11.22) | protein | 290 | 35% helix, 18% strand | P24941 |
| D | Cyclin-A2 | protein | 255 | 69% helix, 0% strand | P20248 |
Ligands and binding sites
- PO5 · (2S)-1-(dimethylamino)-3-(4-{[4-(6-morpholin-4-ylpyrazolo[1,5-b]pyridazin-3-yl)pyrimidin-2-yl]amino}phenoxy)propan-2-ol · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 127 | 0.81 | 0.98 | 22 | empty |
| 2 | 140 | 0.77 | 0.95 | 24 | empty |
| 3 | 959 | 0.76 | 0.79 | 104 | empty |
| 4 | 564 | 0.66 | 0.76 | 53 | empty |
| 5 | 520 | 0.66 | 0.77 | 54 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1483 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 1416 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 485 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 443 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 67 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 3EID · 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 3EID · PDBe 3EID · UniProt P24941 · UniProt P20248
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.