Research workbench
Structure of CDK2-cyclin a complexed with 8-anilino-1-methyl-4,5-dihydro- 1H-PYRAZOLO[4,3-H] quinazoline-3-carboxylic acid
Analyse Structure of CDK2-cyclin a complexed with 8-anilino-1-methyl-4,5-dihydro… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WIP
- Type
- protein
- Length
- 1,102 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.8
- Source
- HOMO SAPIENS
- Molecule
- Cell division protein kinase 2; Cyclin-A2
- EC
- 2.7.1.37
- UniProt
- P24941, P20248
- Ligands
- P49, SO4
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · resolution 2.8 · 4 distinct chains · 50% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell division protein kinase 2 (EC 2.7.1.37) | protein | 297 | 36% helix, 16% strand | P24941 |
| B | Cyclin-A2 | protein | 258 | 67% helix, 0% strand | P20248 |
| C | Cell division protein kinase 2 (EC 2.7.1.37) | protein | 292 | 36% helix, 17% strand | P24941 |
| D | Cyclin-A2 | protein | 255 | 67% helix, 0% strand | P20248 |
Ligands and binding sites
- P49 · 1-methyl-8-(phenylamino)-4,5-dihydro-1H-pyrazolo[4,3-h]quinazoline-3-carboxylic acid · ligand · 2 copies · chains A, C
- SO4 · Sulfate ion · ion · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 150 | 0.81 | 0.98 | 24 | empty |
| 2 | 147 | 0.81 | 0.98 | 27 | empty |
| 3 | 528 | 0.75 | 0.82 | 54 | empty |
| 4 | 601 | 0.69 | 0.77 | 65 | empty |
| 5 | 212 | 0.63 | 0.82 | 21 | P49 |
Interfaces
5 interfaces between chains.
- A–B · 1575 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1551 Ų buried · 22 hydrogen bonds · protein-protein
- A–D · 536 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 467 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 149 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2WIP · Structure of CDK2-cyclin a complexed with 8-anilino-1-methyl-4,5- dihydro… · 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 C against A, TM-score 0.91
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 2WIP · PDBe 2WIP · UniProt P24941 · UniProt P20248
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