MolNFT v1 · #164634 · protein
CDK8/CYCLIN C in complex with N-(4-CHLOROBENZYL)ISOQUINOLIN-4-amine
6T41 · Cyclin-dependent kinase 8: “CDK8/CYCLIN C in complex with N-(4-CHLOROBENZYL)ISOQUINOLIN-4-amine”. X-ray diffraction, 1 ligand (MFE), 15 pockets (best druggability 0.71). MolNFT v1 #164634 on GenesisL1: 3D structure, binding sites…
- PDB
- 6T41
- Type
- protein
- Length
- 613 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
- MFE
- Pockets
- 15 · best druggability 0.71
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 | 346 | 40% helix, 12% strand | P49336 |
| B | Cyclin-C | protein | 267 | 68% helix, 0% strand | P24863 |
Ligands and binding sites
- MFE · ~{N}-[(4-chlorophenyl)methyl]quinazolin-4-amine · ligand · chains A
- FMT · Formic acid · additive · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 52 | 0.71 | 0.98 | 17 | empty |
| 2 | 288 | 0.71 | 0.85 | 38 | MFE |
| 3 | 191 | 0.67 | 0.86 | 30 | FMT |
| 4 | 196 | 0.54 | 0.78 | 20 | empty |
| 5 | 118 | 0.52 | 0.82 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1969 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 6T41 · CDK8/Cyclin C in complex with N-(4-chlorobenzyl)isoquinolin-4-amine · 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 0.97
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 6T41 · PDBe 6T41 · UniProt P49336 · UniProt P24863
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