4ZBI

Mcl-1 complexed with small molecules


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.182 

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: 

  • 4ZBF - determined by Zhao, B.  

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:  

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Induced myeloid leukemia cell differentiation protein Mcl-1
A, B, C, D, E, F, G, H, I, J, K, L
157Homo 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
4M6
Query on 4M6

Download SDF File 
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 (100) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.182 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 62.256α = 90.00
b = 134.015β = 99.65
c = 135.931γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
HKL-2000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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 InstituteUnited States--

Revision History 

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