Research workbench
Human CDK8-cycc in complex with compound 4: N-methyl-4-(4-pyridyl)-1H- pyrrole-2-carboxamide
Analyse Human CDK8-cycc in complex with compound 4: N-methyl-4-(4-pyridyl)-1H… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XQX
- Type
- protein
- Length
- 603 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
- 8CC
- Pockets
- 8 · best druggability 0.74
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 | 340 | 40% helix, 14% strand | P49336 |
| B | Cyclin-C | protein | 263 | 70% helix, 0% strand | P24863 |
Ligands and binding sites
- 8CC · N-methyl-4-pyridin-4-yl-1H-pyrrole-2-carboxamide · ligand · chains A
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 470 | 0.74 | 0.83 | 54 | GOL, 8CC |
| 2 | 269 | 0.63 | 0.81 | 35 | empty |
| 3 | 186 | 0.56 | 0.80 | 20 | empty |
| 4 | 181 | 0.49 | 0.77 | 25 | GOL |
| 5 | 144 | 0.43 | 0.75 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1842 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 5XQX · Human CDK8-CYCC in complex with compound 4: N-methyl-4-(4-pyridyl)-1H-pyrrole-2-carboxamid… · 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 1.00
- 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 5XQX · PDBe 5XQX · UniProt P49336 · UniProt P24863
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