6QFQ

Structure of human Mcl-1 in complex with indole acid inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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: 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Induced myeloid leukemia cell differentiation protein Mcl-1170Homo sapiensMutation(s): 0 
Gene Names: MCL1BCL2L3
UniProt & NIH Common Fund Data Resources
Find proteins for Q07820 (Homo sapiens)
Explore Q07820 
Go to UniProtKB:  Q07820
PHAROS:  Q07820
GTEx:  ENSG00000143384 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ07820
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
J3E (Subject of Investigation/LOI)
Query on J3E

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
7-(3,5-dimethyl-1~{H}-pyrazol-4-yl)-3-(3-naphthalen-1-yloxypropyl)-1~{H}-indole-2-carboxylic acid
C27 H25 N3 O3
MXUJPYKOCHOAAY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
J3E BindingDB:  6QFQ IC50: 100 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.064α = 90
b = 48.064β = 90
c = 148.47γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



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