Research workbench
Crystal structure of human CDK8/CYCC in complex with compound 5 (1-[3- tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]-3-[3-(morpholin-4-yl) PROPYL]UREA)
Analyse Crystal structure of human CDK8/CYCC in complex with compound 5 (1-[3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4F6U
- Type
- protein
- Length
- 601 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
- 0SR, NA
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 53% 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 | 334 | 41% helix, 12% strand | P49336 |
| B | Cyclin-C | protein | 267 | 69% helix, 0% strand | P24863 |
Ligands and binding sites
- 0SR · 1-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]-3-[3-(morpholin-4-yl)propyl]urea · ligand · chains A
- NA · Sodium ion · metal · chains A
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B
- FMT · Formic acid · additive · 6 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 600 | 0.78 | 0.84 | 67 | 0SR, FMT |
| 2 | 346 | 0.69 | 0.82 | 40 | EDO |
| 3 | 186 | 0.55 | 0.79 | 22 | empty |
| 4 | 213 | 0.53 | 0.77 | 25 | FMT |
| 5 | 186 | 0.50 | 0.77 | 31 | EDO |
Interfaces
1 interface between chains.
- A–B · 1768 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 4F6U · Crystal structure of human CDK8/CYCC in complex with compound 5… · 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 0.98
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 4F6U · PDBe 4F6U · UniProt P49336 · UniProt P24863
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