Crystal structure of Bcl2 in complex with S-10r

Experimental Data Snapshot

  • Resolution: 1.25 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 

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Discovery of the Clinical Candidate Sonrotoclax (BGB-11417), a Highly Potent and Selective Inhibitor for Both WT and G101V Mutant Bcl-2.

Guo, Y.Xue, H.Hu, N.Liu, Y.Sun, H.Yu, D.Qin, L.Shi, G.Wang, F.Xin, L.Sun, W.Zhang, F.Song, X.Li, S.Wei, Q.Guo, Y.Li, Y.Liu, X.Chen, S.Zhang, T.Wu, Y.Su, D.Zhu, Y.Xu, A.Xu, H.Yang, S.Zheng, Z.Liu, J.Yang, X.Yuan, X.Hong, Y.Sun, X.Guo, Y.Zhou, C.Liu, X.Wang, L.Wang, Z.

(2024) J Med Chem 

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c00027
  • Primary Citation of Related Structures:  
    8HTR, 8HTS

  • PubMed Abstract: 

    The approval of venetoclax, a B-cell lymphoma-2 (Bcl-2) selective inhibitor, for the treatment of chronic lymphocytic leukemia demonstrated that the antiapoptotic protein Bcl-2 is a druggable target for B-cell malignancies. However, venetoclax's limited potency cannot produce a strong, durable clinical benefit in other Bcl-2-mediated malignancies (e.g., diffuse large B-cell lymphomas) and multiple recurrent Bcl-2 mutations (e.g., G101V) have been reported to mediate resistance to venetoclax after long-term treatment. Herein, we described novel Bcl-2 inhibitors with increased potency for both wild-type (WT) and mutant Bcl-2. Comprehensive structure optimization led to the clinical candidate BGB-11417 (compound 12e , sonrotoclax), which exhibits strong in vitro and in vivo inhibitory activity against both WT Bcl-2 and the G101V mutant, as well as excellent selectivity over Bcl-x L without obvious cytochrome P450 inhibition. Currently, BGB-11417 is undergoing phase II/III clinical assessments as monotherapy and combination treatment.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Apoptosis regulator Bcl-2171Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
N2L (Subject of Investigation/LOI)
Query on N2L

Download Ideal Coordinates CCD File 
B [auth A]4-[2-[(2~{S})-2-(2-cyclopropylphenyl)pyrrolidin-1-yl]-7-azaspiro[3.5]nonan-7-yl]-~{N}-[3-nitro-4-(oxan-4-ylmethylamino)phenyl]sulfonyl-2-(1~{H}-pyrrolo[2,3-b]pyridin-5-yloxy)benzamide
C47 H53 N7 O7 S
Experimental Data & Validation

Experimental Data

  • Resolution: 1.25 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.304α = 90
b = 55.151β = 90
c = 61.488γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-05-15
    Type: Initial release