4ZBI

Mcl-1 complexed with small molecules


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 

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:4ZBF


Literature

Discovery of tricyclic indoles that potently inhibit mcl-1 using fragment-based methods and structure-based design.

Burke, J.P.Bian, Z.Shaw, S.Zhao, B.Goodwin, C.M.Belmar, J.Browning, C.F.Vigil, D.Friberg, A.Camper, D.V.Rossanese, O.W.Lee, T.Olejniczak, E.T.Fesik, S.W.

(2015) J Med Chem 58: 3794-3805

  • DOI: 10.1021/jm501984f
  • Primary Citation of Related Structures:  
    4ZBF, 4ZBI

  • PubMed Abstract: 
  • Myeloid cell leukemia-1 (Mcl-1) is an antiapoptotic member of the Bcl-2 family of proteins that is overexpressed and amplified in many cancers. Overexpression of Mcl-1 allows cancer cells to evade apoptosis and contributes to the resistance of cancer ...

    Myeloid cell leukemia-1 (Mcl-1) is an antiapoptotic member of the Bcl-2 family of proteins that is overexpressed and amplified in many cancers. Overexpression of Mcl-1 allows cancer cells to evade apoptosis and contributes to the resistance of cancer cells to be effectively treated with various chemotherapies. From an NMR-based screen of a large fragment library, several distinct chemical scaffolds that bind to Mcl-1 were discovered. Here, we describe the discovery of potent tricyclic 2-indole carboxylic acid inhibitors that exhibit single digit nanomolar binding affinity to Mcl-1 and greater than 1700-fold selectivity over Bcl-xL and greater than 100-fold selectivity over Bcl-2. X-ray structures of these compounds when complexed to Mcl-1 provide detailed information on how these small-molecules bind to the target, which was used to guide compound optimization.


    Organizational Affiliation

    Department of Biochemistry, Vanderbilt University School of Medicine, 2215 Garland Avenue, 607 Light Hall, Nashville, Tennessee 37232-0146, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Induced myeloid leukemia cell differentiation protein Mcl-1ABCDEFGHIJKL157Homo 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
4M6
Query on 4M6

Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L
1-[3-(naphthalen-1-yloxy)propyl]-5,6-dihydro-4H-pyrrolo[3,2,1-ij]quinoline-2-carboxylic acid
C25 H23 N O3
XOMAOOTVWOCYAD-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4M6Ki:  310   nM  Binding MOAD
4M6Ki:  310   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.183 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.256α = 90
b = 134.015β = 99.65
c = 135.931γ = 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: 2015-04-14 
  • Released Date: 2015-04-29 
  • Deposition Author(s): Zhao, B.

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

Revision History 

  • Version 1.0: 2015-04-29
    Type: Initial release
  • Version 1.1: 2015-05-27
    Changes: Database references
  • Version 1.2: 2017-09-27
    Changes: Author supporting evidence, Database references, Derived calculations, Source and taxonomy, Structure summary
  • Version 1.3: 2019-12-04
    Changes: Author supporting evidence