MolNFT v2 · #223379 · protein
CDK2-CyclinE1 in complex with allosteric inhibitor I-198.
8VQ3 · Cyclin-dependent kinase 2: “CDK2-CyclinE1 in complex with allosteric inhibitor I-198.”. X-ray diffraction at 1.84, 1 ligand (A1AC4), 4 pockets (best druggability 0.82). MolNFT v2 #223379 on GenesisL1: 3D structure, binding sites and…
- PDB
- 8VQ3
- Type
- protein
- Length
- 567 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.84
- Source
- Homo sapiens
- Molecule
- Cyclin-dependent kinase 2; G1/S-specific cyclin-E1
- EC
- 2.7.11.22
- UniProt
- P24941, P24864
- Ligands
- A1AC4
- Pockets
- 4 · best druggability 0.82
Structure
x-ray diffraction · resolution 1.84 · 2 distinct chains · 50% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-dependent kinase 2 (EC 2.7.11.22) | protein | 297 | 35% helix, 18% strand | P24941 |
| B | G1/S-specific cyclin-E1 | protein | 270 | 66% helix, 1% strand | P24864 |
Ligands and binding sites
- A1AC4 · (8R)-N-[(2S,3R)-3-(cyclohexylmethoxy)-1-(morpholin-4-yl)-1-oxobutan-2-yl]-2-[(1S)-2,2-dimethylcyclopropane-1-carbonyl]-6-(1,3-thiazole-5-carbonyl)-2,6-diazaspiro[3.4]octane-8-carboxamide · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1101 | 0.82 | 0.83 | 104 | empty |
| 2 | 486 | 0.66 | 0.77 | 51 | A1AC4 |
| 3 | 88 | 0.48 | 0.81 | 19 | empty |
| 4 | 85 | 0.36 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1530 Ų buried · 21 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (phosphorylation).
Compared structures
- 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 0.99
- 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 8VQ3 · PDBe 8VQ3 · UniProt P24941 · UniProt P24864
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