MolNFT v1 · #52908 · protein
Truncation and optimisation of peptide inhibitors of CDK2, cyclin a through structure guided design
2WEV · Cell division protein kinase 2: “Truncation and optimisation of peptide inhibitors of CDK2, cyclin a through structure guided design”. X-ray diffraction, 3 ligands (ACE, CK7, NH2), 17 pockets (best druggability 0.80). MolNFT v1…
- PDB
- 2WEV
- 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-B3L-mea
- EC
- 2.7.1.37
- UniProt
- P24941, P20248
- Ligands
- ACE, CK7, NH2
- Pockets
- 17 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cell division protein kinase 2 (EC 2.7.1.37) | protein | 296 | 33% helix, 18% strand | P24941 |
| B, D | Cyclin-A2 | protein | 258 | 64% helix, 0% strand | P20248 |
| E, F | Arg-arg-B3L-mea | protein | 4 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 2 copies · chains B, E, D, F
- CK7 · [4-(2-amino-4-methyl-thiazol-5-yl)-pyrimidin-2-yl]-(3-nitro-phenyl)-amine · ligand · 2 copies · chains A, C
- NH2 · Amino group · ion · 2 copies · chains B, E, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 128 | 0.80 | 0.98 | 24 | empty |
| 2 | 121 | 0.80 | 0.98 | 23 | empty |
| 3 | 1098 | 0.73 | 0.76 | 92 | empty |
| 4 | 191 | 0.69 | 0.87 | 28 | CK7 |
| 5 | 201 | 0.66 | 0.85 | 28 | CK7 |
Interfaces
7 interfaces between chains.
- A–B · 1740 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1684 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 519 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 492 Ų buried · 4 hydrogen bonds · protein-protein
- D–F · 438 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified, 2 covalent (nonstandard, covalent ligand).
Compared structures
- 2WEV · Truncation and Optimisation of Peptide Inhibitors of CDK2, Cyclin A Through Structure… · the same entry in another collection · chain A against A, 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 0.92
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 2WEV · PDBe 2WEV · UniProt P24941 · UniProt P20248
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