5IF4

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.162 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Re-refinement Note

This entry reflects an alternative modeling of the original data in:5IEZ


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: 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 knock ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Induced myeloid leukemia cell differentiation protein Mcl-1AB159Homo sapiensMutation(s): 0 
Gene Names: MCL1BCL2L3
Find proteins for Q07820 (Homo sapiens)
Explore Q07820 
Go to UniProtKB:  Q07820
NIH Common Fund Data Resources
PHAROS  Q07820
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6AK
Query on 6AK

Download CCD File 
A, B
4-{8-chloro-11-[3-(4-chloro-3,5-dimethylphenoxy)propyl]-1-oxo-7-(1,3,5-trimethyl-1H-pyrazol-4-yl)-4,5-dihydro-1H-[1,4]diazepino[1,2-a]indol-2(3H)-yl}-1-methyl-1H-indole-6-carboxylic acid
C39 H39 Cl2 N5 O4
BDINUPBROUJUMH-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
6AKKi:  1   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.162 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 39.748α = 90
b = 87.842β = 99.68
c = 54.072γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-02-25 
  • 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 

  • 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