MolNFT v1 · #51258 · protein
Replace: a strategy for iterative design of cyclin binding groove inhibitors
2V22 · Cell division protein kinase 2: “Replace: a strategy for iterative design of cyclin binding groove inhibitors”. X-ray diffraction, 1 ligand (C35), 14 pockets (best druggability 0.81). MolNFT v1 #51258 on GenesisL1: 3D structure…
- PDB
- 2V22
- Type
- protein
- Length
- 1,108 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
- C35
- Pockets
- 14 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 48% 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 | 34% helix, 18% strand | P24941 |
| B, D | Cyclin-A2 | protein | 258 | 64% helix, 0% strand | P20248 |
Ligands and binding sites
- C35 · N~2~-{[1-(4-chlorophenyl)-5-methyl-1H-1,2,4-triazol-3-yl]carbonyl}-N~5~-(diaminomethylidene)-L-ornithyl-L-leucyl-L-isoleucyl-4-fluoro-L-phenylalaninamide · ligand · 2 copies · chains B, 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 | 136 | 0.81 | 0.98 | 24 | empty |
| 2 | 133 | 0.80 | 0.97 | 23 | empty |
| 3 | 1038 | 0.77 | 0.79 | 122 | empty |
| 4 | 213 | 0.69 | 0.86 | 22 | empty |
| 5 | 223 | 0.68 | 0.85 | 26 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1757 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 1722 Ų buried · 24 hydrogen bonds · protein-protein
- B–C · 512 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 440 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 123 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2V22 · REPLACE: A strategy for Iterative Design of Cyclin Binding Groove Inhibitors · 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 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 2V22 · PDBe 2V22 · UniProt P24941 · UniProt P20248
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