6BN7

Crystal structure of DDB1-CRBN-BRD4(BD1) complex bound to dBET23 PROTAC.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.501 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Plasticity in binding confers selectivity in ligand-induced protein degradation.

Nowak, R.P.DeAngelo, S.L.Buckley, D.He, Z.Donovan, K.A.An, J.Safaee, N.Jedrychowski, M.P.Ponthier, C.M.Ishoey, M.Zhang, T.Mancias, J.D.Gray, N.S.Bradner, J.E.Fischer, E.S.

(2018) Nat. Chem. Biol. 14: 706-714

  • DOI: 10.1038/s41589-018-0055-y
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Heterobifunctional small-molecule degraders that induce protein degradation through ligase-mediated ubiquitination have shown considerable promise as a new pharmacological modality. However, we currently lack a detailed understanding of the molecular ...

    Heterobifunctional small-molecule degraders that induce protein degradation through ligase-mediated ubiquitination have shown considerable promise as a new pharmacological modality. However, we currently lack a detailed understanding of the molecular basis for target recruitment and selectivity, which is critically required to enable rational design of degraders. Here we utilize a comprehensive characterization of the ligand-dependent CRBN-BRD4 interaction to demonstrate that binding between proteins that have not evolved to interact is plastic. Multiple X-ray crystal structures show that plasticity results in several distinct low-energy binding conformations that are selectively bound by ligands. We demonstrate that computational protein-protein docking can reveal the underlying interprotein contacts and inform the design of a BRD4 selective degrader that can discriminate between highly homologous BET bromodomains. Our findings that plastic interprotein contacts confer selectivity for ligand-induced protein dimerization provide a conceptual framework for the development of heterobifunctional ligands.


    Organizational Affiliation

    Department of Cell Biology, Harvard Medical School, Boston, MA, USA.,Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA. eric_fischer@dfci.harvard.edu.,Division of Genomic Stability and DNA Repair, Department of Radiation Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Novartis Institutes for Biomedical Research, Cambridge, MA, USA.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.,Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA. eric_fischer@dfci.harvard.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA damage-binding protein 1
A
864Homo sapiensMutation(s): 0 
Gene Names: DDB1 (XAP1)
Find proteins for Q16531 (Homo sapiens)
Go to Gene View: DDB1
Go to UniProtKB:  Q16531
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protein cereblon
B
463Homo sapiensMutation(s): 0 
Gene Names: CRBN
Find proteins for Q96SW2 (Homo sapiens)
Go to Gene View: CRBN
Go to UniProtKB:  Q96SW2
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Bromodomain-containing protein 4
C
127Homo sapiensMutation(s): 1 
Gene Names: BRD4 (HUNK1)
Find proteins for O60885 (Homo sapiens)
Go to Gene View: BRD4
Go to UniProtKB:  O60885
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
RN3
Query on RN3

Download SDF File 
Download CCD File 
B
methyl {(6S)-4-(4-chlorophenyl)-2-[(8-{[({2-[(3S)-2,6-dioxopiperidin-3-yl]-1,3-dioxo-2,3-dihydro-1H-isoindol-4-yl}oxy)acetyl]amino}octyl)carbamoyl]-3,9-dimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl}acetate
C43 H45 Cl N8 O9 S
ZIHIUFZFPMILIG-VMPREFPWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.501 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.212 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 115.571α = 90.00
b = 115.571β = 90.00
c = 596.315γ = 120.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
XDSdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer InstituteUnited StatesNCI R01CA214608
The Harvard University William F. Milton FundUnited States--
the Friends of Dana FarberUnited States--
Claudia Adams Barr Program for Innovative Cancer ResearchUnited States--
Linde Family FoundationUnited States--

Revision History 

  • Version 1.0: 2018-05-30
    Type: Initial release
  • Version 1.1: 2018-08-01
    Type: Data collection, Database references
  • Version 1.2: 2018-11-07
    Type: Data collection, Database references
  • Version 1.3: 2019-02-20
    Type: Author supporting evidence, Data collection