Research workbench
X-ray structure of human CDK6-vcyclin in complex with the inhibitor PD0332991
Analyse X-ray structure of human CDK6-vcyclin in complex with the inhibitor PD0332991 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2EUF
- Type
- protein
- Length
- 526 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Viral cyclin; Cell division protein kinase 6
- EC
- 2.7.1.37
- UniProt
- Q01043, Q00534
- Ligands
- LQQ, CA
- Pockets
- 9 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Viral cyclin | protein | 244 | 67% helix, 1% strand | Q01043 |
| B | Cell division protein kinase 6 (EC 2.7.1.37) | protein | 282 | 34% helix, 16% strand | Q00534 |
Ligands and binding sites
- LQQ · 6-acetyl-8-cyclopentyl-5-methyl-2-[(5-piperazin-1-ylpyridin-2-yl)amino]pyrido[2,3-d]pyrimidin-7(8H)-one · ligand · chains B
- CA · Calcium ion · metal · chains A, B
- ACT · Acetate ion · additive · chains B
- DMS · Dimethyl sulfoxide · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 178 | 0.70 | 0.88 | 30 | empty |
| 2 | 188 | 0.66 | 0.85 | 29 | LQQ |
| 3 | 126 | 0.46 | 0.78 | 28 | empty |
| 4 | 56 | 0.46 | 0.84 | 14 | DMS |
| 5 | 55 | 0.45 | 0.84 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 2207 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 2EUF · X-ray structure of human CDK6-Vcyclin in complex with the inhibitor PD0332991 · 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 B 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 Q01043
- Every structure of UniProt Q00534
- Elsewhere: RCSB PDB 2EUF · PDBe 2EUF · UniProt Q01043 · UniProt Q00534
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