MolNFT v1 · #165260 · protein
CDK8/CYCLINC in complex with drug etp-50775
6TPA · Cyclin-dependent kinase 8: “CDK8/CYCLINC in complex with drug etp-50775”. X-ray diffraction, 2 ligands (NZ5, NZ8), 10 pockets (best druggability 0.75). MolNFT v1 #165260 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6TPA
- 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
- NZ5, NZ8
- Pockets
- 10 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 53% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cyclin-dependent kinase 8 (EC 2.7.11.22, 2.7.11.23) | protein | 336 | 40% helix, 13% strand | P49336 |
| B | Cyclin-C | protein | 265 | 70% helix, 0% strand | P24863 |
Ligands and binding sites
- NZ5 · (2~{R})-butane-1,2-diol · ligand · 4 copies · chains A, B
- NZ8 · 1-[4-chloranyl-3-(trifluoromethyl)phenyl]-3-(5-oxidanylidene-6-pyridin-4-yl-pyrido[2,3-B][1, 5]benzoxazepin-9-yl)urea · ligand · chains A
- FMT · Formic acid · additive · 12 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 367 | 0.75 | 0.85 | 46 | NZ8 |
| 2 | 290 | 0.59 | 0.78 | 34 | FMT |
| 3 | 159 | 0.50 | 0.78 | 16 | FMT |
| 4 | 56 | 0.42 | 0.82 | 15 | empty |
| 5 | 78 | 0.40 | 0.79 | 15 | FMT |
Interfaces
1 interface between chains.
- A–B · 1610 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6TPA · CDK8/CyclinC in complex with drug ETP-50775 · 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 0.96
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 6TPA · PDBe 6TPA · UniProt P49336 · UniProt P24863
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