Research workbench
CDK8-cycc in complex with [(S)-2-(4-chloro-phenyl)-pyrrolidin-1-yl]- (5-methyl-IMIDAZO[5,1-B][1,3,4]THIADIAZOL-2-yl)-methanone
Analyse CDK8-cycc in complex with [(S)-2-(4-chloro-phenyl)-pyrrolidin-1-yl]… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ICP
- Type
- protein
- Length
- 610 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
- 69Z
- Pockets
- 13 · best druggability 0.75
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 | 343 | 39% helix, 12% strand | P49336 |
| B | Cyclin-C | protein | 267 | 69% helix, 0% strand | P24863 |
Ligands and binding sites
- 69Z · [(2S)-2-(4-chlorophenyl)pyrrolidin-1-yl](5-methylimidazo[5,1-b][1,3,4]thiadiazol-2-yl)methanone · ligand · chains A
- FMT · Formic acid · additive · 9 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 640 | 0.75 | 0.81 | 77 | 69Z, EDO |
| 2 | 183 | 0.60 | 0.82 | 32 | FMT |
| 3 | 180 | 0.52 | 0.78 | 20 | empty |
| 4 | 101 | 0.48 | 0.80 | 19 | empty |
| 5 | 155 | 0.45 | 0.76 | 20 | EDO |
Interfaces
1 interface between chains.
- A–B · 1803 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 5ICP · CDK8-CYCC IN COMPLEX WITH [(S)-2-(4-Chloro-phenyl)-pyrrolidin-1-yl]-(5-methyl-imidazo[5,1… · 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 5ICP · PDBe 5ICP · UniProt P49336 · UniProt P24863
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