MolNFT v1 · #120786 · protein
CDK8-cycc in complex with 8-[3-chloro-5-(1-methyl-2,2-dioxo-2, 3- dihydro-1H-2L6-BENZO[C]ISOTHIAZOL-5-yl)-pyridin- 4-yl]-1-oxa-3,8- diaza-SPIRO[4.5]DECAN-2-one
5HBE · Cyclin-dependent kinase 8: “CDK8-cycc in complex with 8-[3-chloro-5-(1-methyl-2,2-dioxo-2, 3…”. X-ray diffraction, 1 ligand (5Y6), 10 pockets (best druggability 0.75). MolNFT v1 #120786 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5HBE
- Type
- protein
- Length
- 610 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
- 5Y6
- Pockets
- 10 · best druggability 0.75
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 | 344 | 39% helix, 13% strand | P49336 |
| B | Cyclin-C | protein | 266 | 68% helix, 0% strand | P24863 |
Ligands and binding sites
- 5Y6 · 8-[3-chloranyl-5-[1-methyl-2,2-bis(oxidanylidene)-3~{H}-2,1-benzothiazol-5-yl]pyridin-4-yl]-1-oxa-3,8-diazaspiro[4.5]decan-2-one · ligand · chains A
- FMT · Formic acid · additive · 4 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · chains A
- EDO · 1,2-ethanediol · additive · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 611 | 0.75 | 0.81 | 63 | 5Y6, DMS |
| 2 | 405 | 0.69 | 0.80 | 51 | empty |
| 3 | 196 | 0.54 | 0.78 | 22 | empty |
| 4 | 235 | 0.52 | 0.76 | 31 | empty |
| 5 | 176 | 0.48 | 0.76 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1943 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 5HBE · CDK8-CYCC IN COMPLEX WITH 8-[3-Chloro-5-(1-methyl-2,2-dioxo-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 0.99
- 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 0.98
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 5HBE · PDBe 5HBE · UniProt P49336 · UniProt P24863
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