Research workbench
Truncation and optimisation of peptide inhibitors of CDK2, cyclin a through structure guided design
Analyse Truncation and optimisation of peptide inhibitors of CDK2, cyclin a through… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2WHB
- Type
- protein
- Length
- 1,116 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell division protein kinase 2; Cyclin-A2; Arg-arg-L3O-pff
- EC
- 2.7.1.37
- UniProt
- P24941, P20248
- Ligands
- NH2
- Pockets
- 16 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cell division protein kinase 2 (EC 2.7.1.37) | protein | 296 | 34% helix, 18% strand | P24941 |
| B, D | Cyclin-A2 | protein | 258 | 62% helix, 0% strand | P20248 |
| E, F | Arg-arg-L3O-pff | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- NH2 · Amino group · ion · 2 copies · chains E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 144 | 0.81 | 0.97 | 22 | empty |
| 2 | 145 | 0.80 | 0.97 | 23 | empty |
| 3 | 834 | 0.78 | 0.81 | 81 | empty |
| 4 | 203 | 0.68 | 0.86 | 25 | empty |
| 5 | 232 | 0.66 | 0.84 | 27 | empty |
Interfaces
7 interfaces between chains.
- C–D · 1679 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1644 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 488 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 442 Ų buried · 2 hydrogen bonds · protein-protein
- D–F · 419 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 2WHB · Truncation and Optimisation of Peptide Inhibitors of CDK2, Cyclin A Through Structure… · the same entry in another collection · chain F against F, 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 0.99
- 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 2WHB · PDBe 2WHB · UniProt P24941 · UniProt P20248
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