MolNFT v1 · #120790 · protein
CDK8-cycc in complex with 8-[2-amino-3-chloro-5-(1-methyl-1H-indazol- 5-yl)-pyridin-4-yl]-2,8-diaza-SPIRO[4.5]DECAN-1-one
5HBJ · Cyclin-dependent kinase 8: “CDK8-cycc in complex with 8-[2-amino-3-chloro-5-(1-methyl-1H-indazol…”. X-ray diffraction, 1 ligand (5Y8), 13 pockets (best druggability 0.74). MolNFT v1 #120790 on GenesisL1: 3D structure, binding sites…
- PDB
- 5HBJ
- Type
- protein
- Length
- 609 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
- 5Y8
- Pockets
- 13 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 51% 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 | 342 | 39% helix, 13% strand | P49336 |
| B | Cyclin-C | protein | 267 | 67% helix, 0% strand | P24863 |
Ligands and binding sites
- 5Y8 · 8-[2-azanyl-3-chloranyl-5-(1-methylindazol-5-yl)pyridin-4-yl]-2,8-diazaspiro[4.5]decan-1-one · ligand · chains A
- EDO · 1,2-ethanediol · additive · chains A
- FMT · Formic acid · additive · chains 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 635 | 0.74 | 0.81 | 68 | 5Y8 |
| 2 | 56 | 0.73 | 0.99 | 15 | FMT |
| 3 | 413 | 0.69 | 0.80 | 46 | empty |
| 4 | 193 | 0.56 | 0.79 | 23 | empty |
| 5 | 186 | 0.48 | 0.76 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1813 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 5HBJ · CDK8-CYCC IN COMPLEX WITH 8-[2-Amino-3-chloro-5-(1-methyl-1H-indazol-5-yl)-pyridin-4-yl]-2… · 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 5HBJ · PDBe 5HBJ · UniProt P49336 · UniProt P24863
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.