8ROY

Structure of the human DDB1-DDA1-DCAF15 E3 ubiquitin ligase bound to compound furan 24


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


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Literature

Optimization of Potent Ligands for the E3 Ligase DCAF15 and Evaluation of Their Use in Heterobifunctional Degraders.

Lucas, S.C.C.Ahmed, A.Ashraf, S.N.Argyrou, A.Bauer, M.R.De Donatis, G.M.Demanze, S.Eisele, F.Fusani, L.Hock, A.Kadamur, G.Li, S.Macmillan-Jones, A.Michaelides, I.N.Phillips, C.Rehnstrom, M.Richter, M.Rodrigo-Brenni, M.C.Shilliday, F.Wang, P.Storer, R.I.

(2024) J Med Chem 

  • DOI: https://doi.org/10.1021/acs.jmedchem.3c02136
  • Primary Citation of Related Structures:  
    8ROX, 8ROY

  • PubMed Abstract: 

    Unlocking novel E3 ligases for use in heterobifunctional PROTAC degraders is of high importance to the pharmaceutical industry. Over-reliance on the current suite of ligands used to recruit E3 ligases could limit the potential of their application. To address this, potent ligands for DCAF15 were optimized using cryo-EM supported, structure-based design to improve on micromolar starting points. A potent binder, compound 24 , was identified and subsequently conjugated into PROTACs against multiple targets. Following attempts on degrading a number of proteins using DCAF15 recruiting PROTACs, only degradation of BRD4 was observed. Deconvolution of the mechanism of action showed that this degradation was not mediated by DCAF15, thereby highlighting both the challenges faced when trying to expand the toolbox of validated E3 ligase ligands for use in PROTAC degraders and the pitfalls of using BRD4 as a model substrate.


  • Organizational Affiliation

    Hit Discovery, Discovery Sciences, R&D, AstraZeneca, Cambridge CB2 0AA, U.K.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DDB1- and CUL4-associated factor 15603Homo sapiensMutation(s): 0 
Gene Names: DCAF15C19orf72
UniProt & NIH Common Fund Data Resources
Find proteins for Q66K64 (Homo sapiens)
Explore Q66K64 
Go to UniProtKB:  Q66K64
PHAROS:  Q66K64
GTEx:  ENSG00000132017 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ66K64
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA damage-binding protein 1836Homo sapiensMutation(s): 0 
Gene Names: DDB1XAP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16531 (Homo sapiens)
Explore Q16531 
Go to UniProtKB:  Q16531
PHAROS:  Q16531
GTEx:  ENSG00000167986 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16531
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
DET1- and DDB1-associated protein 1C [auth D]102Homo sapiensMutation(s): 0 
Gene Names: DDA1C19orf58PCIA1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BW61 (Homo sapiens)
Explore Q9BW61 
Go to UniProtKB:  Q9BW61
PHAROS:  Q9BW61
GTEx:  ENSG00000130311 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BW61
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1H18 (Subject of Investigation/LOI)
Query on A1H18

Download Ideal Coordinates CCD File 
D [auth A]1-[5-[[3,4-bis(chloranyl)-1~{H}-indol-7-yl]sulfamoyl]-3-methyl-furan-2-yl]carbonyl-~{N}-methyl-piperidine-4-carboxamide
C21 H22 Cl2 N4 O5 S
IUAIKPCCBLHWMQ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.21rc1_5084:

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-03
    Type: Initial release