MolNFT v1 · #17831 · protein
The structure of phospho-CDK2/CYCLIN a in complex with the inhibitor 4,5,6,7-tetrabromobenzotriazole (tbs)
1P5E · Cell division protein kinase 2: “The structure of phospho-CDK2/CYCLIN a in complex with the inhibitor 4,5,6,7-tetrabromobenzotriazole (tbs)”. X-ray diffraction, 1 ligand (TBS), 14 pockets (best druggability 0.81). MolNFT v1 #17831…
- PDB
- 1P5E
- Type
- protein
- Length
- 1,110 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.-
- UniProt
- P24941, P20248
- Ligands
- TBS
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cell division protein kinase 2 (EC 2.7.1.-) | protein | 297 | 34% helix, 17% strand | P24941 |
| B, D | Cyclin A2 | protein | 258 | 69% helix, 0% strand | P20248 |
Ligands and binding sites
- TBS · 4,5,6,7-tetrabromobenzotriazole · 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 123 | 0.81 | 0.99 | 25 | empty |
| 2 | 117 | 0.80 | 0.99 | 24 | empty |
| 3 | 232 | 0.66 | 0.83 | 25 | TBS |
| 4 | 226 | 0.65 | 0.83 | 25 | TBS |
| 5 | 290 | 0.60 | 0.79 | 35 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1747 Ų buried · 29 hydrogen bonds · protein-protein
- A–B · 1715 Ų buried · 33 hydrogen bonds · protein-protein
- A–D · 45 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 1P5E · The structure of phospho-CDK2/cyclin A in complex with the 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 B 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 0.91
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 1P5E · PDBe 1P5E · UniProt P24941 · UniProt P20248
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.