6H0F

Structure of DDB1-CRBN-pomalidomide complex bound to IKZF1(ZF2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history


Literature

Defining the human C2H2 zinc finger degrome targeted by thalidomide analogs through CRBN.

Sievers, Q.L.Petzold, G.Bunker, R.D.Renneville, A.Slabicki, M.Liddicoat, B.J.Abdulrahman, W.Mikkelsen, T.Ebert, B.L.Thoma, N.H.

(2018) Science 362: eaat0572

  • DOI: https://doi.org/10.1126/science.aat0572
  • Primary Citation of Related Structures:  
    6H0F, 6H0G

  • PubMed Abstract: 

    The small molecules thalidomide, lenalidomide, and pomalidomide induce the ubiquitination and proteasomal degradation of the transcription factors Ikaros (IKZF1) and Aiolos (IKZF3) by recruiting a Cys 2 -His 2 (C2H2) zinc finger domain to Cereblon (CRBN), the substrate receptor of the CRL4 CRBN E3 ubiquitin ligase. We screened the human C2H2 zinc finger proteome for degradation in the presence of thalidomide analogs, identifying 11 zinc finger degrons. Structural and functional characterization of the C2H2 zinc finger degrons demonstrates how diverse zinc finger domains bind the permissive drug-CRBN interface. Computational zinc finger docking and biochemical analysis predict that more than 150 zinc fingers bind the drug-CRBN complex in vitro, and we show that selective zinc finger degradation can be achieved through compound modifications. Our results provide a rationale for therapeutically targeting transcription factors that were previously considered undruggable.


  • Organizational Affiliation

    Friedrich Miescher Institute for Biomedical Research, 4058 Basel, Switzerland. benajmin_ebert@dfci.harvard.edu nicolas.thoma@fmi.ch.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1,DNA damage-binding protein 1
A, D, G, J
856Homo 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 cereblon
B, E, H, K
426Homo 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
DNA-binding protein Ikaros
C, F, I, L
38Homo sapiensMutation(s): 0 
Gene Names: IKZF1IK1IKAROSLYF1ZNFN1A1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13422 (Homo sapiens)
Explore Q13422 
Go to UniProtKB:  Q13422
PHAROS:  Q13422
GTEx:  ENSG00000185811 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13422
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Y70
Query on Y70

Download Ideal Coordinates CCD File 
N [auth B],
Q [auth E],
T [auth H],
W [auth K]
S-Pomalidomide
C13 H11 N3 O4
UVSMNLNDYGZFPF-QMMMGPOBSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
M [auth B]
O [auth C]
P [auth E]
R [auth F]
S [auth H]
M [auth B],
O [auth C],
P [auth E],
R [auth F],
S [auth H],
U [auth I],
V [auth K],
X [auth L]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
Y70 BindingDB:  6H0F Ki: 1.00e+4 (nM) from 1 assay(s)
IC50: min: 63.1, max: 2.58e+4 (nM) from 5 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.25 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 161.45α = 90
b = 177.86β = 90
c = 242.47γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European UnionHorizon 2020 No. 666068
European Molecular Biology OrganizationAdvanced Fellowship aALTF 761-2016
European UnionHuman Frontier Science Program Long-Term Fellowship LT000210/2014

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-07
    Type: Initial release
  • Version 1.1: 2018-11-14
    Changes: Data collection, Database references
  • Version 2.0: 2019-04-17
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2019-10-30
    Changes: Data collection, Database references
  • Version 2.2: 2024-01-17
    Changes: Data collection, Database references, Refinement description