MolNFT v1 · #121448 · protein
CDK8/CYCC in complex with compound 20
5HVY · Cyclin-dependent kinase 8: “CDK8/CYCC in complex with compound 20”. X-ray diffraction, 2 ligands (66X, CL), 10 pockets (best druggability 0.75). MolNFT v1 #121448 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5HVY
- Type
- protein
- Length
- 602 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cyclin-dependent kinase 8; Cyclin-C
- EC
- 2.7.11.22, 2.7.11.23
- UniProt
- P49336, P24863
- Ligands
- 66X, CL
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-dependent kinase 8 (EC 2.7.11.22, 2.7.11.23) | protein | 335 | 40% helix, 11% strand | P49336 |
| B | Cyclin-C | protein | 267 | 68% helix, 0% strand | P24863 |
Ligands and binding sites
- 66X · N-{(3S)-1-[2-(methylamino)pyrimidin-4-yl]pyrrolidin-3-yl}-N'-{4-[(morpholin-4-yl)methyl]-3-(trifluoromethyl)phenyl}urea · ligand · chains A
- CL · Chloride ion · ion · 2 copies · chains B
- FMT · Formic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 644 | 0.75 | 0.81 | 72 | 66X |
| 2 | 59 | 0.74 | 0.99 | 17 | CL |
| 3 | 299 | 0.67 | 0.82 | 33 | CL |
| 4 | 54 | 0.62 | 0.93 | 17 | empty |
| 5 | 194 | 0.55 | 0.79 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1718 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5HVY · CDK8/CYCC in complex with compound 20 · the same entry in another collection · chain A against A, TM-score 1.00
- P24863 · AlphaFold monomer V2.0 prediction for cyclin-C (P24863) · a predicted model of the same protein · chain B against A, TM-score 0.98
- P49336 · AlphaFold monomer V2.0 prediction for cyclin-dependent kinase 8 (P49336) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 P49336
- Every structure of UniProt P24863
- Elsewhere: RCSB PDB 5HVY · PDBe 5HVY · UniProt P49336 · UniProt P24863
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