Crystal structure of human BRR2 in complex with T-1206548

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 

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Discovery of Allosteric Inhibitors Targeting the Spliceosomal RNA Helicase Brr2.

Iwatani-Yoshihara, M.Ito, M.Klein, M.G.Yamamoto, T.Yonemori, K.Tanaka, T.Miwa, M.Morishita, D.Endo, S.Tjhen, R.Qin, L.Nakanishi, A.Maezaki, H.Kawamoto, T.

(2017) J Med Chem 60: 5759-5771

  • DOI: https://doi.org/10.1021/acs.jmedchem.7b00461
  • Primary Citation of Related Structures:  
    5URJ, 5URK, 5URM

  • PubMed Abstract: 

    Brr2 is an RNA helicase belonging to the Ski2-like subfamily and an essential component of spliceosome. Brr2 catalyzes an ATP-dependent unwinding of the U4/U6 RNA duplex, which is a critical step for spliceosomal activation. An HTS campaign using an RNA-dependent ATPase assay and initial SAR study identified two different Brr2 inhibitors, 3 and 12. Cocrystal structures revealed 3 binds to an unexpected allosteric site between the C-terminal and the N-terminal helicase cassettes, while 12 binds an RNA-binding site inside the N-terminal cassette. Selectivity profiling indicated the allosteric inhibitor 3 is more Brr2-selective than the RNA site binder 12. Chemical optimization of 3 using SBDD culminated in the discovery of the potent and selective Brr2 inhibitor 9 with helicase inhibitory activity. Our findings demonstrate an effective strategy to explore selective inhibitors for helicases, and 9 could be a promising starting point for exploring molecular probes to elucidate biological functions and the therapeutic relevance of Brr2.

  • Organizational Affiliation

    Department of Structural Biology, Takeda California Inc. , 10410 Science Center Drive, San Diego, California 92121, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
U5 small nuclear ribonucleoprotein 200 kDa helicase
A, B
1,738Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O75643 (Homo sapiens)
Explore O75643 
Go to UniProtKB:  O75643
GTEx:  ENSG00000144028 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75643
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 8LV

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
3-(5-{[(2R)-5-amino-2-cyclohexyl-7-oxo-2,3-dihydro-7H-[1,3,4]thiadiazolo[3,2-a]pyrimidin-6-yl]methyl}furan-2-yl)benzoic acid
C23 H24 N4 O4 S
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.212 
  • R-Value Observed: 0.214 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.863α = 71.14
b = 105.874β = 70.48
c = 135.285γ = 89.83
Software Package:
Software NamePurpose
Aimlessdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-19
    Type: Initial release
  • Version 1.1: 2017-07-26
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Refinement description
  • Version 1.3: 2024-03-06
    Changes: Data collection, Database references