Research workbench
The X-ray co-crystal structure of human CDK2/CYCLINE and dinaciclib.
Analyse The X-ray co-crystal structure of human CDK2/CYCLINE and dinaciclib. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5L2W
- Type
- protein
- Length
- 568 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclin-dependent kinase 2; G1/S-specific cyclin-E1
- EC
- 2.7.11.22
- UniProt
- P24941, P24864
- Ligands
- 1QK
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-dependent kinase 2 (EC 2.7.11.22) | protein | 298 | 34% helix, 16% strand | P24941 |
| B | G1/S-specific cyclin-E1 | protein | 270 | 61% helix, 1% strand | P24864 |
Ligands and binding sites
- 1QK · 3-[({3-ethyl-5-[(2S)-2-(2-hydroxyethyl)piperidin-1-yl]pyrazolo[1,5-a]pyrimidin-7-yl}amino)methyl]-1-hydroxypyridinium · ligand · chains A
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 271 | 0.81 | 0.93 | 43 | empty |
| 2 | 200 | 0.70 | 0.87 | 26 | 1QK |
| 3 | 201 | 0.62 | 0.82 | 38 | empty |
| 4 | 152 | 0.43 | 0.75 | 29 | empty |
| 5 | 112 | 0.38 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1922 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 5L2W · The X-ray co-crystal structure of human CDK2/CyclinE and Dinaciclib. · the same entry in another collection · chain A against A, TM-score 1.00
- P24864 · AlphaFold monomer V2.0 prediction for G1/S-specific cyclin-E1 (P24864) · 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 A against A, TM-score 0.88
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 P24864
- Elsewhere: RCSB PDB 5L2W · PDBe 5L2W · UniProt P24941 · UniProt P24864
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