MolNFT v1 · #139846 · protein
CDK8-cycc in complex with compound 17:3-chloro-4-(4-pyridyl)-1H- pyrrole-2-carboxamide
5XS2 · Cyclin-dependent kinase 8: “CDK8-cycc in complex with compound 17:3-chloro-4-(4-pyridyl)-1H- pyrrole-2-carboxamide”. X-ray diffraction, 1 ligand (8D6), 11 pockets (best druggability 0.78). MolNFT v1 #139846 on GenesisL1: 3D…
- PDB
- 5XS2
- Type
- protein
- Length
- 629 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
- 8D6
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 50% 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 | 366 | 37% helix, 13% strand | P49336 |
| B | Cyclin-C | protein | 263 | 68% helix, 0% strand | P24863 |
Ligands and binding sites
- 8D6 · 3-chloranyl-4-pyridin-4-yl-1H-pyrrole-2-carboxamide · ligand · chains A
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 725 | 0.78 | 0.83 | 77 | 8D6 |
| 2 | 220 | 0.63 | 0.82 | 33 | empty |
| 3 | 207 | 0.59 | 0.81 | 23 | empty |
| 4 | 201 | 0.49 | 0.76 | 27 | GOL |
| 5 | 112 | 0.43 | 0.77 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 1983 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 5XS2 · CDK8-CYCC IN COMPLEX WITH COMPOUND 17:3-chloro-4-(4-pyridyl)-1H-pyrrole-2-carboxamide · 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 0.97
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 5XS2 · PDBe 5XS2 · UniProt P49336 · UniProt P24863
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