Research workbench
Crystal structure of human CDK8/CYCC in complex with compound 7 (1-[3- tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-YL]UREA)
Analyse Crystal structure of human CDK8/CYCC in complex with compound 7 (1-[3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4F6S
- Type
- protein
- Length
- 594 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
- 0SQ
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-dependent kinase 8 (EC 2.7.11.22, 2.7.11.23) | protein | 328 | 40% helix, 13% strand | P49336 |
| B | Cyclin-C | protein | 266 | 68% helix, 0% strand | P24863 |
Ligands and binding sites
- 0SQ · 1-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]urea · ligand · chains A
- FMT · Formic acid · additive · 7 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 670 | 0.78 | 0.83 | 72 | 0SQ, EDO, FMT |
| 2 | 62 | 0.71 | 0.97 | 18 | EDO, FMT |
| 3 | 384 | 0.65 | 0.79 | 45 | EDO, FMT |
| 4 | 182 | 0.50 | 0.77 | 22 | empty |
| 5 | 202 | 0.49 | 0.76 | 33 | FMT |
Interfaces
1 interface between chains.
- A–B · 1678 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 4F6S · Crystal structure of human CDK8/CYCC in complex with compound 7… · 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 0.99
- 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 0.98
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 P49336
- Every structure of UniProt P24863
- Elsewhere: RCSB PDB 4F6S · PDBe 4F6S · UniProt P49336 · UniProt P24863
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