6QG8

Structure of human Bcl-2 in complex with PUMA BH3 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

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: 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 ...

    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

    YSBL, University of York, Heslington, York YO10 5DD, U.K.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Apoptosis regulator Bcl-2,Bcl-2-like protein 1,Apoptosis regulator Bcl-2,Bcl-2-like protein 1A177Homo sapiensMutation(s): 12 
Gene Names: BCL2BCL2L1BCL2LBCLX
UniProt & NIH Common Fund Data Resources
Find proteins for Q07817 (Homo sapiens)
Explore Q07817 
Go to UniProtKB:  Q07817
PHAROS:  Q07817
Find proteins for P10415 (Homo sapiens)
Explore P10415 
Go to UniProtKB:  P10415
PHAROS:  P10415
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Bcl-2-binding component 3B23Homo sapiensMutation(s): 0 
Gene Names: BBC3PUMA
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BXH1 (Homo sapiens)
Explore Q9BXH1 
Go to UniProtKB:  Q9BXH1
PHAROS:  Q9BXH1
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.169 
  • R-Value Observed: 0.171 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.135α = 90
b = 54.95β = 90
c = 84.725γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report




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