5IEZ

Discovery of Potent Myeloid Cell Leukemia-1 (Mcl-1) inhibitors using Structure-Based Design


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.277 (Depositor), 0.280 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 
    0.198 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 6ALClick on this verticalbar to view details

This is version 1.4 of the entry. See complete history

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 5IF4


Literature

Discovery and biological characterization of potent myeloid cell leukemia-1 inhibitors.

Lee, T.Bian, Z.Zhao, B.Hogdal, L.J.Sensintaffar, J.L.Goodwin, C.M.Belmar, J.Shaw, S.Tarr, J.C.Veerasamy, N.Matulis, S.M.Koss, B.Fischer, M.A.Arnold, A.L.Camper, D.V.Browning, C.F.Rossanese, O.W.Budhraja, A.Opferman, J.Boise, L.H.Savona, M.R.Letai, A.Olejniczak, E.T.Fesik, S.W.

(2017) FEBS Lett 591: 240-251

  • DOI: https://doi.org/10.1002/1873-3468.12497
  • Primary Citation of Related Structures:  
    5IEZ, 5IF4

  • PubMed Abstract: 

    Myeloid cell leukemia 1 (Mcl-1) is an antiapoptotic member of the Bcl-2 family of proteins that when overexpressed is associated with high tumor grade, poor survival, and resistance to chemotherapy. Mcl-1 is amplified in many human cancers, and knockdown of Mcl-1 using RNAi can lead to apoptosis. Thus, Mcl-1 is a promising cancer target. Here, we describe the discovery of picomolar Mcl-1 inhibitors that cause caspase activation, mitochondrial depolarization, and selective growth inhibition. These compounds represent valuable tools to study the role of Mcl-1 in cancer and serve as useful starting points for the discovery of clinically useful Mcl-1 inhibitors. Comp. 2: 5IEZ; Comp. 5: 5IF4.


  • Organizational Affiliation

    Department of Biochemistry, Vanderbilt University School of Medicine, Nashville, TN, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Induced myeloid leukemia cell differentiation protein Mcl-1
A, B, C, D
159Homo 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
Binding Affinity Annotations 
IDSourceBinding Affinity
6AL BindingDB:  5IEZ Ki: min: 7.2, max: 108 (nM) from 4 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.277 (Depositor), 0.280 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.200 (DCC) 
  • R-Value Observed: 0.198 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.914α = 90
b = 136.046β = 101.62
c = 63.499γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 6ALClick on this verticalbar to view details

Entry History & Funding Information

Deposition Data

  • Released Date: 2017-01-18 
  • Deposition Author(s): Zhao, B.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2017-01-18
    Type: Initial release
  • Version 1.1: 2017-01-25
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence
  • Version 1.3: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.4: 2024-03-06
    Changes: Data collection, Database references