Crystal Structure of Bcl-xL bound to BM501

Experimental Data Snapshot

  • Resolution: 1.70 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 

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This is version 2.2 of the entry. See complete history


Design of Bcl-2 and Bcl-xL Inhibitors with Subnanomolar Binding Affinities Based upon a New Scaffold.

Zhou, H.Chen, J.Meagher, J.L.Yang, C.Y.Aguilar, A.Liu, L.Bai, L.Cong, X.Cai, Q.Fang, X.Stuckey, J.A.Wang, S.

(2012) J Med Chem 55: 4664-4682

  • DOI: https://doi.org/10.1021/jm300178u
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Employing a structure-based strategy, we have designed a new class of potent small-molecule inhibitors of the anti-apoptotic proteins Bcl-2 and Bcl-xL. An initial lead compound with a new scaffold was designed based upon the crystal structure of Bcl-xL and U.S. Food and Drug Administration (FDA) approved drugs and was found to have an affinity of 100 μM for both Bcl-2 and Bcl-xL. Linking this weak lead to another weak-affinity fragment derived from Abbott's ABT-737 led to an improvement of the binding affinity by a factor of >10 000. Further optimization ultimately yielded compounds with subnanomolar binding affinities for both Bcl-2 and Bcl-xL and potent cellular activity. The best compound (21) binds to Bcl-xL and Bcl-2 with K(i) < 1 nM, inhibits cell growth in the H146 and H1417 small-cell lung cancer cell lines with IC(50) values of 60-90 nM, and induces robust cell death in the H146 cancer cell line at 30-100 nM.

  • Organizational Affiliation

    Comprehensive Cancer Center and Department of Internal Medicine, University of Michigan , 1500 East Medical Center Drive, Ann Arbor, Michigan 48109-0934, United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bcl-2-like protein 1172Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q07817 (Homo sapiens)
Explore Q07817 
Go to UniProtKB:  Q07817
PHAROS:  Q07817
GTEx:  ENSG00000171552 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07817
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
B50 PDBBind:  3SPF Ki: 1.38e+5 (nM) from 1 assay(s)
Binding MOAD:  3SPF Ki: 1.38e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.70 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.185 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.748α = 90
b = 103.748β = 90
c = 35.32γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
MD2data collection
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-06-27
    Type: Initial release
  • Version 2.0: 2017-06-28
    Changes: Advisory, Database references, Polymer sequence, Source and taxonomy, Structure summary
  • Version 2.1: 2017-11-08
    Changes: Refinement description
  • Version 2.2: 2024-02-28
    Changes: Advisory, Data collection, Database references, Derived calculations