8BDX image
Entry Detail
PDB ID:
8BDX
Keywords:
Title:
Ternary complex between VCB, BRD4-BD2 and PROTAC 48
Biological Source:
Source Organism:
Host Organism:
PDB Version:
Deposition Date:
2022-10-20
Release Date:
2023-02-15
Method Details:
Experimental Method:
Resolution:
2.93 Å
R-Value Free:
0.25
R-Value Work:
0.18
R-Value Observed:
0.18
Space Group:
P 32
Macromolecular Entities
Polymer Type:polypeptide(L)
Description:Bromodomain-containing protein 4
Chain IDs:A, E
Chain Length:129
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Elongin-B
Chain IDs:B, F
Chain Length:104
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:Elongin-C
Chain IDs:C, G
Chain Length:97
Number of Molecules:2
Biological Source:Homo sapiens
Polymer Type:polypeptide(L)
Description:von Hippel-Lindau disease tumor suppressor
Chain IDs:D, H
Chain Length:162
Number of Molecules:2
Biological Source:Homo sapiens
Ligand Molecules
Primary Citation
Systematic Potency and Property Assessment of VHL Ligands and Implications on PROTAC Design.
Chemmedchem 18 e202200615 e202200615 (2023)
PMID: 36749883 DOI: 10.1002/cmdc.202200615

Abstact

Herein, we describe a systematic SAR- and SPR-investigation of the peptidomimetic hydroxy-proline based VHL-ligand VH032, from which most to-date published VHL-targeting PROTACs have been derived. This study provides for the first time a consistent data set which allows for direct comparison of structural variations including those which were so far hidden in patent literature. The gained knowledge about improved VHL binders was used to design a small library of highly potent BRD4-degraders comprising different VHL exit vectors. Newly designed degraders showed favorable molecular properties and significantly improved degradation potency compared to MZ1.

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Protein

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Primary Citation of related structures