9NFQ | pdb_00009nfq

Crystal structure of CRBN-DDB1 and MRT-3486 in complex with NEK7


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 
    0.261 (Depositor), 0.261 (DCC) 
  • R-Value Work: 
    0.212 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 
    0.214 (Depositor) 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 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
Serine/threonine-protein kinase Nek7304Homo sapiensMutation(s): 0 
Gene Names: NEK7
EC: 2.7.11.34
UniProt & NIH Common Fund Data Resources
Find proteins for Q8TDX7 (Homo sapiens)
Explore Q8TDX7 
Go to UniProtKB:  Q8TDX7
PHAROS:  Q8TDX7
GTEx:  ENSG00000151414 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8TDX7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1BX6 (Subject of Investigation/LOI)
Query on A1BX6

Download Ideal Coordinates CCD File 
D [auth B](3S)-N-{[(4R)-3-(2,4-dioxo-1,3-diazinan-1-yl)imidazo[1,2-a]pyridin-7-yl]methyl}-2-(phenylmethanesulfonyl)-1,2,3,4-tetrahydroisoquinoline-3-carboxamide
C29 H28 N6 O5 S
ZTRLXYYBDRZBSP-DEOSSOPVSA-N
ADP
Query on ADP

Download Ideal Coordinates CCD File 
F [auth C]ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
G [auth C]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free:  0.261 (Depositor), 0.261 (DCC) 
  • R-Value Work:  0.212 (Depositor), 0.211 (DCC) 
  • R-Value Observed: 0.214 (Depositor) 
Space Group: P 21 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.579α = 90
b = 121.857β = 90
c = 144.737γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
STARANISOdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



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
  • Version 1.2: 2025-07-23
    Changes: Derived calculations