Research workbench
CDK6 in complex with CPD24 N-(5-(6-ethyl-2,6-DIAZASPIRO[3.3]HEPTAN-2- YL)PYRIDIN-2-yl)-5-fluoro-4-(4-methyl-5,6,7,8-tetrahydro-4H- PYRAZOLO[1,5-A]AZEPIN-3-YL)PYRIMIDIN-2-amine
Analyse CDK6 in complex with CPD24 N-(5-(6-ethyl-2,6-DIAZASPIRO[3.3]HEPTAN-2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OQO
- Type
- protein
- Length
- 269 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclin-dependent kinase 6
- EC
- 2.7.11.22
- UniProt
- Q00534
- Ligands
- N1J
- Pockets
- 2 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-dependent kinase 6 (EC 2.7.11.22) | protein | 269 | 38% helix, 17% strand | Q00534 |
Ligands and binding sites
- N1J · N-[5-(6-ethyl-2,6-diazaspiro[3.3]heptan-2-yl)pyridin-2-yl]-5-fluoro-4-[(4R)-4-methyl-5,6,7,8-tetrahydro-4H-pyrazolo[1,5-a]azepin-3-yl]pyrimidin-2-amine · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 188 | 0.64 | 0.84 | 21 | N1J |
| 2 | 84 | 0.34 | 0.74 | 17 | empty |
Compared structures
- 6OQO · CDK6 in complex with Cpd24 N-(5-(6-ethyl-2,6-diazaspiro[3.3]heptan-2-yl)pyridin-2-yl)-5-fl… · the same entry in another collection · chain A against A, TM-score 1.00
- Q00534 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinase 6 (Q00534) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q00534
- Elsewhere: RCSB PDB 6OQO · PDBe 6OQO · UniProt Q00534
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