Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 165.44 kDa 
• Atom Count: 10,373 
• Modelled Residue Count: 1,310 
• Deposited Residue Count: 1,454 
• Unique protein chains: 3

 6BOY

Crystal structure of DDB1-CRBN-BRD4(BD1) complex bound to dBET6 PROTAC.

• PDB DOI:  https://doi.org/10.2210/pdb6BOY/pdb

• Classification: LIGASE
• Organism(s): Homo sapiens
• Expression System: Trichoplusia ni, Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-11-21 Released: 2018-05-30 
• Deposition Author(s): Nowak, R.P., DeAngelo, S.L., Buckley, D., Bradner, J.E., Fischer, E.S.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI), The Harvard University William F. Milton Fund, the Friends of Dana Farber, the Claudia Adams Barr Program for Innovative Cancer Research, the Linde Family Foundation

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.33 Å
• R-Value Free: 0.234 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 

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

• PubMed: 29892083 
• DOI: https://doi.org/10.1038/s41589-018-0055-y
• Primary Citation of Related Structures:  
  6BN7, 6BN8, 6BN9, 6BNB, 6BOY


• 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 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.

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Organizational Affiliation: 

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA damage-binding protein 1	A	864	Homo sapiens	Mutation(s): 0  Gene Names: DDB1, XAP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q16531 (Homo sapiens) Explore Q16531  Go to UniProtKB:  Q16531
PHAROS:  Q16531

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein cereblon	B	463	Homo sapiens	Mutation(s): 0  Gene Names: CRBN, AD-006
UniProt & NIH Common Fund Data Resources
Find proteins for Q96SW2 (Homo sapiens) Explore Q96SW2  Go to UniProtKB:  Q96SW2
PHAROS:  Q96SW2

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	C	127	Homo sapiens	Mutation(s): 1  Gene Names: BRD4, HUNK1
UniProt & NIH Common Fund Data Resources
Find proteins for O60885 (Homo sapiens) Explore O60885  Go to UniProtKB:  O60885
PHAROS:  O60885

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RN6 (Subject of Investigation/LOI)	E [auth B]	2-[(6S)-4-(4-chlorophenyl)-2,3,9-trimethyl-6H-thieno[3,2-f][1,2,4]triazolo[4,3-a][1,4]diazepin-6-yl]-N-(8-{[({2-[(3S)-2,6-dioxopiperidin-3-yl]-1,3-dioxo-2,3-dihydro-1H-isoindol-4-yl}oxy)acetyl]amino}octyl)acetamide C42 H45 Cl N8 O7 S JGQPZPLJOBHHBK-KYJUHHDHSA-N
ZN	D [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.33 Å
• R-Value Free: 0.234 
• R-Value Work: 0.199 
• R-Value Observed: 0.201 
• Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 115.406	α = 90
b = 115.406	β = 90
c = 588.143	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2018-05-30 
Deposition Author(s): Nowak, R.P., DeAngelo, S.L., Buckley, D., Bradner, J.E., Fischer, E.S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	NCI R01CA214608
The Harvard University William F. Milton Fund	United States	--
the Friends of Dana Farber	United States	--
the Claudia Adams Barr Program for Innovative Cancer Research	United States	--
the Linde Family Foundation	United States	--

Revision History  

• Version 1.0: 2018-05-30
  Type: Initial release
  
• Version 1.1: 2018-08-01
  Changes: Data collection, Database references
• Version 1.2: 2018-11-07
  Changes: Data collection, Database references
• Version 1.3: 2019-02-20
  Changes: Author supporting evidence, Data collection
• Version 1.4: 2019-12-04
  Changes: Author supporting evidence