Research workbench
CDK8-cycc in complex with 8-[3-(3-amino-1H-indazol-6-yl)-5-chloro- pyridine-4-yl]-2,8-diaza-SPIRO[4.5]DECAN-1-one
Analyse CDK8-cycc in complex with 8-[3-(3-amino-1H-indazol-6-yl)-5-chloro… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FGK
- Type
- protein
- Length
- 597 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
- 5XG
- Pockets
- 12 · best druggability 0.70
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 | 331 | 40% helix, 14% strand | P49336 |
| B | Cyclin-C | protein | 266 | 70% helix, 0% strand | P24863 |
Ligands and binding sites
- 5XG · 8-[3-(3-azanyl-2~{H}-indazol-6-yl)-5-chloranyl-pyridin-4-yl]-2,8-diazaspiro[4.5]decan-1-one · ligand · chains A
- FMT · Formic acid · additive · 7 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
- DMS · Dimethyl sulfoxide · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 365 | 0.70 | 0.82 | 35 | 5XG, DMS |
| 2 | 389 | 0.63 | 0.77 | 40 | empty |
| 3 | 196 | 0.57 | 0.80 | 20 | empty |
| 4 | 160 | 0.50 | 0.78 | 21 | empty |
| 5 | 97 | 0.46 | 0.80 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1731 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 5FGK · CDK8-CYCC IN COMPLEX WITH 8-[3-(3-Amino-1H-indazol-6-yl)-5-chloro… · 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 0.99
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 5FGK · PDBe 5FGK · UniProt P49336 · UniProt P24863
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