MolNFT v1 · #185832 · protein
Crystal structure of cyclin-dependent kinase 2/CYCLIN a in complex with 3,5,7-substituted PYRAZOLO[4,3-D]PYRIMIDINE inhibitor 24
7QHL: “Crystal structure of cyclin-dependent kinase 2/CYCLIN a in complex with 3,5,7-substituted…”. X-ray diffraction, 1 ligand (D5P), 11 pockets (best druggability 0.80). MolNFT v1 #185832 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7QHL
- Type
- protein
- Length
- 1,086 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
- D5P
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-dependent kinase 2 (EC 2.7.11.22) | protein | 285 | 35% helix, 16% strand | P24941 |
| B | Cyclin-A2 | protein | 258 | 67% helix, 0% strand | P20248 |
| C | Cyclin-dependent kinase 2 (EC 2.7.11.22) | protein | 287 | 35% helix, 17% strand | P24941 |
| D | Cyclin-A2 | protein | 256 | 68% helix, 0% strand | P20248 |
Ligands and binding sites
- D5P · 5-(2-amino-1-ethyl)thio-3-cyclobutyl-7-[4-(pyrazol-1-yl)benzyl]amino-1(2)H-pyrazolo[4,3-d]pyrimidine · ligand · 2 copies · chains A, C
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains B, D
- SGM · Monothioglycerol · additive · 3 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 121 | 0.80 | 0.98 | 23 | empty |
| 2 | 117 | 0.80 | 0.98 | 22 | empty |
| 3 | 897 | 0.74 | 0.78 | 113 | GOL, EDO |
| 4 | 263 | 0.62 | 0.80 | 37 | empty |
| 5 | 258 | 0.62 | 0.80 | 31 | D5P |
Interfaces
5 interfaces between chains.
- C–D · 1638 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 1530 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 460 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 440 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 28 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent, 2 modified (additive adduct, phosphorylation).
Compared structures
- 7QHL · Crystal structure of Cyclin-dependent kinase 2/cyclin A in complex with 3,5,7-Substituted… · 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 0.92
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 7QHL · PDBe 7QHL · UniProt P24941 · UniProt P20248
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