Research workbench
CDK2/CYCLIN A2 in complex with an IMIDAZO[1,2-C]PYRIMIDIN-5-one inhibitor
Analyse CDK2/CYCLIN A2 in complex with an IMIDAZO[1,2-C]PYRIMIDIN-5-one inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7ACK
- Type
- protein
- Length
- 1,103 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclin-dependent kinase 2; Cyclin-A2
- EC
- 2.7.11.22
- UniProt
- P24941, P20248
- Ligands
- R7B, NA, NO3
- Pockets
- 11 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 55% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cyclin-dependent kinase 2 (EC 2.7.11.22) | protein | 295 | 35% helix, 17% strand | P24941 |
| B | Cyclin-A2 | protein | 258 | 66% helix, 0% strand | P20248 |
| D | Cyclin-A2 | protein | 255 | 68% helix, 0% strand | P20248 |
Ligands and binding sites
- R7B · 8-cyclohexyl-6~{H}-imidazo[1,2-c]pyrimidin-5-one · ligand · 2 copies · chains A, C
- NA · Sodium ion · metal · 2 copies · chains B, D
- NO3 · Nitrate ion · ion · chains D
- EDO · 1,2-ethanediol · additive · 12 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 133 | 0.81 | 0.98 | 22 | empty |
| 2 | 135 | 0.81 | 0.98 | 24 | EDO |
| 3 | 1114 | 0.76 | 0.78 | 123 | EDO |
| 4 | 191 | 0.71 | 0.88 | 27 | R7B |
| 5 | 216 | 0.69 | 0.86 | 26 | R7B |
Interfaces
4 interfaces between chains.
- C–D · 1554 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1552 Ų buried · 26 hydrogen bonds · protein-protein
- A–D · 439 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 439 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (phosphorylation).
Compared structures
- 7ACK · CDK2/cyclin A2 in complex with an imidazo[1,2-c]pyrimidin-5-one 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 D 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 7ACK · PDBe 7ACK · UniProt P24941 · UniProt P20248
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