Research workbench
CDK8-cycc in complex with 8-(1-methyl-2,2-dioxo-2,3-dihydro-1H-2L6- BENZO[C]ISOTHIAZOL-5-yl)-[1,6]NAPHTHYRIDINE-2-carboxylic acid methylamide
Analyse CDK8-cycc in complex with 8-(1-methyl-2,2-dioxo-2,3-dihydro-1H-2L6… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5I5Z
- Type
- protein
- Length
- 611 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
- 68U
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 52% 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 | 345 | 39% helix, 13% strand | P49336 |
| B | Cyclin-C | protein | 266 | 69% helix, 0% strand | P24863 |
Ligands and binding sites
- 68U · N-methyl-8-(1-methyl-2,2-dioxo-2,3-dihydro-1H-2lambda~6~,1-benzothiazol-5-yl)-1,6-naphthyridine-2-carboxamide · ligand · chains A
- FMT · Formic acid · additive · 2 copies · 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 490 | 0.73 | 0.82 | 54 | 68U |
| 2 | 403 | 0.71 | 0.82 | 46 | FMT |
| 3 | 215 | 0.55 | 0.78 | 21 | empty |
| 4 | 158 | 0.52 | 0.79 | 24 | empty |
| 5 | 223 | 0.51 | 0.76 | 30 | FMT |
Interfaces
1 interface between chains.
- A–B · 1977 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 5I5Z · CDK8-CYCC IN COMPLEX WITH 8-(1-Methyl-2,2-dioxo-2,3-dihydro-1H-2l6-benzo[c]isothiazol-5-yl… · 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 0.97
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 5I5Z · PDBe 5I5Z · UniProt P49336 · UniProt P24863
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