MolNFT v1 · #121170 · protein
CDK8-cycc in complex with [6-hydroxy-3-(3-methyl-benzyl)-1H-indazol-5- yl]-((S)-3-hydroxy-pyrrolidin-1-yl)-methanone
5HNB · Cyclin-dependent kinase 8: “CDK8-cycc in complex with [6-hydroxy-3-(3-methyl-benzyl)-1H-indazol-5…”. X-ray diffraction, 1 ligand (62M), 11 pockets (best druggability 0.71). MolNFT v1 #121170 on GenesisL1: 3D structure, binding sites…
- PDB
- 5HNB
- Type
- protein
- Length
- 608 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
- 62M
- Pockets
- 11 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 53% 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 | 342 | 40% helix, 13% strand | P49336 |
| B | Cyclin-C | protein | 266 | 68% helix, 0% strand | P24863 |
Ligands and binding sites
- 62M · [6-hydroxy-3-(3-methylbenzyl)-1H-indazol-5-yl][(3S)-3-hydroxypyrrolidin-1-yl]methanone · ligand · chains A
- FMT · Formic acid · additive · 6 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 2 copies · chains 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 397 | 0.71 | 0.83 | 40 | 62M, FMT |
| 2 | 418 | 0.71 | 0.82 | 39 | FMT |
| 3 | 197 | 0.59 | 0.81 | 34 | FMT |
| 4 | 216 | 0.53 | 0.77 | 27 | empty |
| 5 | 210 | 0.52 | 0.77 | 34 | FMT |
Interfaces
1 interface between chains.
- A–B · 2015 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 5HNB · CDK8-CYCC IN COMPLEX WITH [6-Hydroxy-3-(3-methyl-benzyl)-1H-indazol-5-yl]-((S)-3-hydroxy-p… · 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 5HNB · PDBe 5HNB · UniProt P49336 · UniProt P24863
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