MolNFT v1 · #161929 · protein
Crystal structure of human CDK8/CYCC in complex with bi-1347
6QTG · Cyclin-dependent kinase 8: “Crystal structure of human CDK8/CYCC in complex with bi-1347”. X-ray diffraction, 1 ligand (JH8), 10 pockets (best druggability 0.67). MolNFT v1 #161929 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6QTG
- Type
- protein
- Length
- 593 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
- JH8
- Pockets
- 10 · best druggability 0.67
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 | 329 | 41% helix, 13% strand | P49336 |
| B | Cyclin-C | protein | 264 | 66% helix, 0% strand | P24863 |
Ligands and binding sites
- JH8 · 2-[4-(4-isoquinolin-4-ylphenyl)pyrazol-1-yl]-~{N},~{N}-dimethyl-ethanamide · ligand · chains A
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 | 290 | 0.67 | 0.82 | 41 | JH8 |
| 2 | 215 | 0.60 | 0.81 | 21 | empty |
| 3 | 276 | 0.59 | 0.78 | 35 | empty |
| 4 | 171 | 0.46 | 0.76 | 28 | empty |
| 5 | 92 | 0.39 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1600 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 6QTG · Crystal structure of human CDK8/CYCC in complex with BI-1347 · 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 6QTG · PDBe 6QTG · UniProt P49336 · UniProt P24863
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