MolNFT v1 · #173677 · protein
CDK2/CYCLIN A2 in complex with 3H-PYRAZOLO[4,3-F]QUINOLINE-based derivative HSD1368
7B7S · Cyclin-dependent kinase 2: “CDK2/CYCLIN A2 in complex with 3H-PYRAZOLO[4,3-F]QUINOLINE-based derivative HSD1368”. X-ray diffraction, 3 ligands (T1T, NO3, SO4), 12 pockets (best druggability 0.81). MolNFT v1 #173677 on GenesisL1: 3D…
- PDB
- 7B7S
- Type
- protein
- Length
- 1,083 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
- T1T, NO3, SO4
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-dependent kinase 2 (EC 2.7.11.22) | protein | 287 | 33% helix, 16% strand | P24941 |
| B | Cyclin-A2 | protein | 254 | 66% helix, 0% strand | P20248 |
| C | Cyclin-dependent kinase 2 (EC 2.7.11.22) | protein | 288 | 33% helix, 17% strand | P24941 |
| D | Cyclin-A2 | protein | 254 | 67% helix, 0% strand | P20248 |
Ligands and binding sites
- T1T · 7-(3-(trifluoromethyl)-1H-pyrazol-4yl)-3,8,10,11-tetrahydropyrazolo[4,3-f]thiopyrano[3,4-c]quinoline 9-oxide · ligand · 2 copies · chains A, C
- NO3 · Nitrate ion · ion · 2 copies · chains A, D, B, C
- SO4 · Sulfate ion · ion · chains A, D
- SGM · Monothioglycerol · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 129 | 0.81 | 0.99 | 24 | empty |
| 2 | 118 | 0.80 | 0.99 | 24 | empty |
| 3 | 1093 | 0.75 | 0.77 | 120 | NO3, SO4 |
| 4 | 329 | 0.67 | 0.81 | 38 | T1T |
| 5 | 318 | 0.65 | 0.80 | 34 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1549 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1538 Ų buried · 20 hydrogen bonds · protein-protein
- B–C · 441 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 424 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified, 1 covalent (phosphorylation, additive adduct).
Compared structures
- 7B7S · CDK2/cyclin A2 in complex with 3H-pyrazolo[4,3-f]quinoline-based derivative HSD1368 · 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 0.92
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 7B7S · PDBe 7B7S · UniProt P24941 · UniProt P20248
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