Crystal structure of BRDT bromodomain 2 in complex with CDD-1102

Experimental Data Snapshot

  • Resolution: 2.27 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.236 

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Discovery and characterization of bromodomain 2-specific inhibitors of BRDT.

Yu, Z.Ku, A.F.Anglin, J.L.Sharma, R.Ucisik, M.N.Faver, J.C.Li, F.Nyshadham, P.Simmons, N.Sharma, K.L.Nagarajan, S.Riehle, K.Kaur, G.Sankaran, B.Storl-Desmond, M.Palmer, S.S.Young, D.W.Kim, C.Matzuk, M.M.

(2021) Proc Natl Acad Sci U S A 118

  • DOI: https://doi.org/10.1073/pnas.2021102118
  • Primary Citation of Related Structures:  
    7L99, 7L9A

  • PubMed Abstract: 

    Bromodomain testis (BRDT), a member of the bromodomain and extraterminal (BET) subfamily that includes the cancer targets BRD2, BRD3, and BRD4, is a validated contraceptive target. All BET subfamily members have two tandem bromodomains (BD1 and BD2). Knockout mice lacking BRDT-BD1 or both bromodomains are infertile. Treatment of mice with JQ1, a BET BD1/BD2 nonselective inhibitor with the highest affinity for BRD4, disrupts spermatogenesis and reduces sperm number and motility. To assess the contribution of each BRDT bromodomain, we screened our collection of DNA-encoded chemical libraries for BRDT-BD1 and BRDT-BD2 binders. High-enrichment hits were identified and resynthesized off-DNA and examined for their ability to compete with JQ1 in BRDT and BRD4 bromodomain AlphaScreen assays. These studies identified CDD-1102 as a selective BRDT-BD2 inhibitor with low nanomolar potency and >1,000-fold selectivity over BRDT-BD1. Structure-activity relationship studies of CDD-1102 produced a series of additional BRDT-BD2/BRD4-BD2 selective inhibitors, including CDD-1302, a truncated analog of CDD-1102 with similar activity, and CDD-1349, an analog with sixfold selectivity for BRDT-BD2 versus BRD4-BD2. BROMOscan bromodomain profiling confirmed the great affinity and selectivity of CDD-1102 and CDD-1302 on all BET BD2 versus BD1 with the highest affinity for BRDT-BD2. Cocrystals of BRDT-BD2 with CDD-1102 and CDD-1302 were determined at 2.27 and 1.90 Å resolution, respectively, and revealed BRDT-BD2 specific contacts that explain the high affinity and selectivity of these compounds. These BD2-specific compounds and their binding to BRDT-BD2 are unique compared with recent reports and enable further evaluation of their nonhormonal contraceptive potential in vitro and in vivo.

  • Organizational Affiliation

    Center for Drug Discovery, Department of Pathology & Immunology, Baylor College of Medicine, Houston, TX 77030.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain testis-specific protein
A, B
135Homo sapiensMutation(s): 0 
Gene Names: BRDT
UniProt & NIH Common Fund Data Resources
Find proteins for Q58F21 (Homo sapiens)
Explore Q58F21 
Go to UniProtKB:  Q58F21
GTEx:  ENSG00000137948 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ58F21
Sequence Annotations
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Resolution: 2.27 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.236 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.47α = 90
b = 56.47β = 90
c = 191.901γ = 120
Software Package:
Software NamePurpose
iMOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)United StatesP01HD087157

Revision History  (Full details and data files)

  • Version 1.0: 2021-06-30
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description