Mcl-1 complexed with small molecule inhibitor

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.227 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.4 of the entry. See complete history


Discovery of 2-Indole-acylsulfonamide Myeloid Cell Leukemia 1 (Mcl-1) Inhibitors Using Fragment-Based Methods.

Pelz, N.F.Bian, Z.Zhao, B.Shaw, S.Tarr, J.C.Belmar, J.Gregg, C.Camper, D.V.Goodwin, C.M.Arnold, A.L.Sensintaffar, J.L.Friberg, A.Rossanese, O.W.Lee, T.Olejniczak, E.T.Fesik, S.W.

(2016) J Med Chem 59: 2054-2066

  • DOI: https://doi.org/10.1021/acs.jmedchem.5b01660
  • Primary Citation of Related Structures:  
    5FC4, 5FDO, 5FDR

  • PubMed Abstract: 

    Myeloid cell leukemia-1 (Mcl-1) is a member of the Bcl-2 family of proteins responsible for the regulation of programmed cell death. Amplification of Mcl-1 is a common genetic aberration in human cancer whose overexpression contributes to the evasion of apoptosis and is one of the major resistance mechanisms for many chemotherapies. Mcl-1 mediates its effects primarily through interactions with pro-apoptotic BH3 containing proteins that achieve high affinity for the target by utilizing four hydrophobic pockets in its binding groove. Here we describe the discovery of Mcl-1 inhibitors using fragment-based methods and structure-based design. These novel inhibitors exhibit low nanomolar binding affinities to Mcl-1 and >500-fold selectivity over Bcl-xL. X-ray structures of lead Mcl-1 inhibitors when complexed to Mcl-1 provided detailed information on how these small-molecules bind to the target and were used extensively 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.

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
158Homo 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
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 5X3

Download Ideal Coordinates CCD File 
E [auth A],
F [auth B],
G [auth C],
H [auth D]
5-[[6-chloranyl-3-[3-(4-chloranyl-3,5-dimethyl-phenoxy)propyl]-7-(3,5-dimethyl-1~{H}-pyrazol-4-yl)-1~{H}-indol-2-yl]carbonylsulfamoyl]furan-2-carboxylic acid
C30 H28 Cl2 N4 O7 S
Binding Affinity Annotations 
IDSourceBinding Affinity
5X3 BindingDB:  5FDR Ki: 0.36 (nM) from 1 assay(s)
IC50: 0.94 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.283 
  • R-Value Work: 0.224 
  • R-Value Observed: 0.227 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 35.04α = 90
b = 115.005β = 91.17
c = 95.327γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

  • Released Date: 2016-03-02 
  • 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: 2016-03-02
    Type: Initial release
  • Version 1.1: 2016-03-23
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence, Database references, Derived calculations
  • Version 1.3: 2019-12-04
    Changes: Author supporting evidence
  • Version 1.4: 2023-09-27
    Changes: Data collection, Database references, Refinement description