MolNFT v1 · #53543 · protein
Structure of CDK2-cyclin a with a PYRAZOLO(4,3-H) quinazoline-3- carboxamide inhibitor
2WXV · Cell division protein kinase 2: “Structure of CDK2-cyclin a with a PYRAZOLO(4,3-H) quinazoline-3- carboxamide inhibitor”. X-ray diffraction, 2 ligands (WXV, SO4), 14 pockets (best druggability 0.81). MolNFT v1 #53543 on GenesisL1…
- PDB
- 2WXV
- Type
- protein
- Length
- 1,115 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
- WXV, SO4
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 43% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cell division protein kinase 2 (EC 2.7.1.37) | protein | 302 | 34% helix, 18% strand | P24941 |
| B, D | Cyclin-A2 | protein | 257 | 65% helix, 0% strand | P20248 |
| C | Cell division protein kinase 2 (EC 2.7.1.37) | protein | 299 | 34% helix, 19% strand | P24941 |
Ligands and binding sites
- WXV · N,1-dimethyl-8-{[1-(methylsulfonyl)piperidin-4-yl]amino}-1H-pyrazolo[4,3-h]quinazoline-3-carboxamide · 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
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 146 | 0.81 | 0.98 | 25 | empty |
| 2 | 139 | 0.81 | 0.98 | 22 | empty |
| 3 | 690 | 0.75 | 0.80 | 61 | empty |
| 4 | 654 | 0.70 | 0.78 | 68 | empty |
| 5 | 310 | 0.68 | 0.82 | 32 | WXV |
Interfaces
5 interfaces between chains.
- C–D · 1591 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1572 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 502 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 430 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 153 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 2WXV · Structure of CDK2-CYCLIN A with a Pyrazolo(4,3-h) quinazoline-3- carboxamide 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 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 2WXV · PDBe 2WXV · UniProt P24941 · UniProt P20248
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