5IF4

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.392 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.156 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Re-refinement Note

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

  • 5IEZ - determined by Zhao, B.  

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:  
  • Also Cited By: 5UJB

  • 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.,Department of Adult Oncology, The Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.,Department of Hematology and Medical Oncology and The Winship Cancer Institute, Emory University, Atlanta, GA, USA.,Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA.,Vanderbilt University Medical Center, Nashville, TN, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Induced myeloid leukemia cell differentiation protein Mcl-1
A, B
159Homo sapiensMutation(s): 0 
Gene Names: MCL1 (BCL2L3)
Find proteins for Q07820 (Homo sapiens)
Go to Gene View: MCL1
Go to UniProtKB:  Q07820
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
6AK
Query on 6AK

Download SDF File 
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 BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.392 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.156 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 39.748α = 90.00
b = 87.842β = 99.68
c = 54.072γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-2000data reduction
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



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 InstituteUnited States--

Revision History 

  • Version 1.0: 2017-01-18
    Type: Initial release
  • Version 1.1: 2017-01-25
    Type: Database references
  • Version 1.2: 2017-09-20
    Type: Author supporting evidence