Structure of human Bcl-2 in complex with fragment/ABT-263 hybrid

Experimental Data Snapshot

  • Resolution: 1.90 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 

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Establishing Drug Discovery and Identification of Hit Series for the Anti-apoptotic Proteins, Bcl-2 and Mcl-1.

Murray, J.B.Davidson, J.Chen, I.Davis, B.Dokurno, P.Graham, C.J.Harris, R.Jordan, A.Matassova, N.Pedder, C.Ray, S.Roughley, S.D.Smith, J.Walmsley, C.Wang, Y.Whitehead, N.Williamson, D.S.Casara, P.Le Diguarher, T.Hickman, J.Stark, J.Kotschy, A.Geneste, O.Hubbard, R.E.

(2019) ACS Omega 4: 8892-8906

  • DOI: https://doi.org/10.1021/acsomega.9b00611
  • Primary Citation of Related Structures:  
    6QFI, 6QFM, 6QFQ, 6QG8, 6QGD, 6QGG, 6QGH, 6QGJ, 6QGK

  • PubMed Abstract: 

    We describe our work to establish structure- and fragment-based drug discovery to identify small molecules that inhibit the anti-apoptotic activity of the proteins Mcl-1 and Bcl-2. This identified hit series of compounds, some of which were subsequently optimized to clinical candidates in trials for treating various cancers. Many protein constructs were designed to identify protein with suitable properties for different biophysical assays and structural methods. Fragment screening using ligand-observed NMR experiments identified several series of compounds for each protein. The series were assessed for their potential for subsequent optimization using 1 H and 15 N heteronuclear single-quantum correlation NMR, surface plasmon resonance, and isothermal titration calorimetry measurements to characterize and validate binding. Crystal structures could not be determined for the early hits, so NMR methods were developed to provide models of compound binding to guide compound optimization. For Mcl-1, a benzodioxane/benzoxazine series was optimized to a K d of 40 μM before a thienopyrimidine hit series was identified which subsequently led to the lead series from which the clinical candidate S 64315 (MIK 665) was identified. For Bcl-2, the fragment-derived series were difficult to progress, and a compound derived from a published tetrahydroquinone compound was taken forward as the hit from which the clinical candidate (S 55746) was obtained. For both the proteins, the work to establish a portfolio of assays gave confidence for identification of compounds suitable for optimization.

  • Organizational Affiliation

    Vernalis (R&D) Ltd., Granta Park, Abington, Cambridge CB21 6GB, U.K.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Apoptosis regulator Bcl-2,Bcl-2-like protein 1,Apoptosis regulator Bcl-2,Bcl-2-like protein 1177Homo sapiensMutation(s): 12 
UniProt & NIH Common Fund Data Resources
Find proteins for Q07817 (Homo sapiens)
Explore Q07817 
Go to UniProtKB:  Q07817
PHAROS:  Q07817
GTEx:  ENSG00000171552 
Find proteins for P10415 (Homo sapiens)
Explore P10415 
Go to UniProtKB:  P10415
PHAROS:  P10415
GTEx:  ENSG00000171791 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsQ07817P10415
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
J1T (Subject of Investigation/LOI)
Query on J1T

Download Ideal Coordinates CCD File 
B [auth A]4-[4-[(1~{R})-1-(6-methoxy-1,3-benzodioxol-5-yl)-2-pyrrolidin-1-yl-ethyl]phenyl]-~{N}-[4-[[(2~{R})-4-morpholin-4-yl-1-phenylsulfanyl-butan-2-yl]amino]-3-(trifluoromethylsulfonyl)phenyl]sulfonyl-benzamide
C48 H51 F3 N4 O9 S3
Experimental Data & Validation

Experimental Data

  • Resolution: 1.90 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.202 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.989α = 90
b = 56.173β = 90
c = 64.417γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
CrystalCleardata reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2019-06-12
    Type: Initial release
  • Version 1.1: 2019-09-11
    Changes: Data collection, Database references
  • Version 1.2: 2019-09-18
    Changes: Data collection, Refinement description
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Refinement description