9NFR | pdb_00009nfr

Crystal structure of CRBN-DDB1 and MRT-23227 in complex with VAV1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free: 
    0.271 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.211 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 
    0.214 (Depositor) 

Starting Models: experimental, in silico
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Mining the CRBN target space redefines rules for molecular glue-induced neosubstrate recognition.

Petzold, G.Gainza, P.Annunziato, S.Lamberto, I.Trenh, P.McAllister, L.A.DeMarco, B.Schwander, L.Bunker, R.D.Zlotosch, M.SriRamaratnam, R.Gilberto, S.Langousis, G.Donckele, E.J.Quan, C.Strande, V.De Donatis, G.M.Alabi, S.B.Alers, J.Matysik, M.Staehly, C.Dubois, A.Osmont, A.Garskovas, M.Lyon, D.Wiedmer, L.Oleinikovas, V.Lieberherr, R.Rubin, N.T.Lam, D.T.Lucas, X.Liardo, E.Widlund, N.I.Ritzen, A.Caceres, R.M.Vigil, D.Tsai, J.Wallace, O.Peluso, M.Sadok, A.Tiedt, R.Paterson, A.M.Zarayskiy, V.Fasching, B.Bonenfant, D.Warmuth, M.Castle, J.C.Townson, S.A.

(2025) Science 389: eadt6736-eadt6736

  • DOI: https://doi.org/10.1126/science.adt6736
  • Primary Citation of Related Structures:  
    9NFQ, 9NFR, 9NGT

  • PubMed Abstract: 

    The CRL4 CRBN E3 ubiquitin ligase is the target of molecular glue degrader compounds that reprogram ligase specificity to induce the degradation of clinically relevant neosubstrate proteins. Known cereblon (CRBN) neosubstrates share a generalizable β-hairpin G-loop recognition motif that allows for the systematic exploration of the CRBN target space. Computational mining approaches using structure- and surface-based matchmaking algorithms predict more than 1600 CRBN-compatible G-loop proteins across the human proteome, including the newly discovered helical G-loop motif, and identify the noncanonical neosubstrate binding mode of VAV1 that engages CRBN through a molecular surface mimicry mechanism. This work broadens the CRBN target space, redefines rules for neosubstrate recognition, and establishes a platform for the elimination of challenging drug targets by repurposing CRL4 CRBN through next-generation molecular glue degraders.


  • Organizational Affiliation
    • Monte Rosa Therapeutics Inc, Boston, MA, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA damage-binding protein 11,140Homo 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: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein cereblon442Homo sapiensMutation(s): 0 
Gene Names: CRBNAD-006
UniProt & NIH Common Fund Data Resources
Find proteins for Q96SW2 (Homo sapiens)
Explore Q96SW2 
Go to UniProtKB:  Q96SW2
PHAROS:  Q96SW2
GTEx:  ENSG00000113851 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96SW2
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Proto-oncogene vav59Homo sapiensMutation(s): 0 
Gene Names: VAV1VAV
UniProt & NIH Common Fund Data Resources
Find proteins for P15498 (Homo sapiens)
Explore P15498 
Go to UniProtKB:  P15498
PHAROS:  P15498
GTEx:  ENSG00000141968 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15498
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1BYX (Subject of Investigation/LOI)
Query on A1BYX

Download Ideal Coordinates CCD File 
E [auth B](3R)-3-{2-chloro-4'-[(1-methyl-1H-pyrazol-3-yl)methoxy][1,1'-biphenyl]-3-yl}piperidine-2,6-dione
C22 H20 Cl N3 O3
ATFVRCNMKWLFKW-LJQANCHMSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.40 Å
  • R-Value Free:  0.271 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.211 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 0.214 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 143.599α = 90
b = 143.599β = 90
c = 367.636γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-09
    Type: Initial release
  • Version 1.1: 2025-07-16
    Changes: Database references