MolNFT v1 · #32959 · protein
Differential binding of inhibitors to active and inactive CDK2 provides insights for drug design
2C5V · Cell division protein kinase 2: “Differential binding of inhibitors to active and inactive CDK2 provides insights for drug design”. X-ray diffraction, 2 ligands (CK4, NH2), 15 pockets (best druggability 0.81). MolNFT v1 #32959 on…
- PDB
- 2C5V
- Type
- protein
- Length
- 1,124 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cell division protein kinase 2; Cyclin A2; Ala-ala-aba-arg-ser-leu-ile-pff-NH2
- EC
- 2.7.1.37
- UniProt
- P24941, P20248
- Ligands
- CK4, NH2
- Pockets
- 15 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 8% 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, 16% strand | P24941 |
| B, D | Cyclin A2 | protein | 258 | 66% helix, 0% strand | P20248 |
| F, H | Ala-ala-aba-arg-ser-leu-ile-pff-NH2 | protein | 8 | 0% helix, 0% strand | — |
Ligands and binding sites
- CK4 · 4-(2,4-dimethyl-1,3-thiazol-5-yl)-N-[4-(trifluoromethyl)phenyl]pyrimidin-2-amine · ligand · 2 copies · chains A, C
- NH2 · Amino group · ion · 2 copies · chains F, D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 135 | 0.81 | 0.98 | 25 | empty |
| 2 | 132 | 0.80 | 0.98 | 24 | empty |
| 3 | 883 | 0.77 | 0.80 | 87 | empty |
| 4 | 200 | 0.68 | 0.86 | 26 | CK4 |
| 5 | 206 | 0.66 | 0.84 | 23 | CK4 |
Interfaces
7 interfaces between chains.
- A–B · 1659 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 1607 Ų buried · 23 hydrogen bonds · protein-protein
- B–F · 553 Ų buried · 11 hydrogen bonds · protein-protein
- D–H · 520 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 477 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (nonstandard).
Compared structures
- 2C5V · Differential Binding Of Inhibitors To Active And Inactive Cdk2 Provides Insights For Drug… · the same entry in another collection · chain H against H, 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 0.92
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 2C5V · PDBe 2C5V · UniProt P24941 · UniProt P20248
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