6QGK

Structure of human Bcl-2 in complex with THIQ-phenyl pyrazole compound


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.166 

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:  

  • 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 subsequen ...

    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.,YSBL, University of York, Heslington, York YO10 5DD, U.K.,Servier Research Institute of Medicinal Chemistry, Budapest 1031, Hungary.,Institut de Recherches Servier Oncology R&D Unit, Croissy Sur Seine 78290, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Apoptosis regulator Bcl-2,Bcl-2-like protein 1,Apoptosis regulator Bcl-2,Bcl-2-like protein 1
A
177Homo sapiensMutation(s): 15 
Gene Names: BCL2, BCL2L1 (BCL2L, BCLX)
Find proteins for P10415 (Homo sapiens)
Go to Gene View: BCL2
Go to UniProtKB:  P10415
Find proteins for Q07817 (Homo sapiens)
Go to Gene View: BCL2L1
Go to UniProtKB:  Q07817
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
J1Q
Query on J1Q

Download SDF File 
Download CCD File 
A
1-[2-[[(3~{S})-3-(aminomethyl)-3,4-dihydro-1~{H}-isoquinolin-2-yl]carbonyl]phenyl]-~{N},~{N}-dibutyl-5-methyl-pyrazole-3-carboxamide
C30 H39 N5 O2
CLINUOVVDXSAST-VWLOTQADSA-N
 Ligand Interaction
ACT
Query on ACT

Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.166 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 47.570α = 90.00
b = 50.104β = 90.00
c = 65.371γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
MOLREPphasing
REFMACrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

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