6U67

Mcl-1 bound to compound 24


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery and Characterization of 2,5-Substituted Benzoic Acid Dual Inhibitors of the Anti-apoptotic Mcl-1 and Bfl-1 Proteins.

Kump, K.J.Miao, L.Mady, A.S.A.Ansari, N.H.Shrestha, U.K.Yang, Y.Pal, M.Liao, C.Perdih, A.Abulwerdi, F.A.Chinnaswamy, K.Meagher, J.L.Carlson, J.M.Khanna, M.Stuckey, J.A.Nikolovska-Coleska, Z.

(2020) J Med Chem 63: 2489-2510

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b01442
  • Primary Citation of Related Structures:  
    6U63, 6U64, 6U65, 6U67, 6U6F

  • PubMed Abstract: 

    Anti-apoptotic Bcl-2 family proteins are overexpressed in a wide spectrum of cancers and have become well validated therapeutic targets. Cancer cells display survival dependence on individual or subsets of anti-apoptotic proteins that could be effectively targeted by multimodal inhibitors. We designed a 2,5-substituted benzoic acid scaffold that displayed equipotent binding to Mcl-1 and Bfl-1. Structure-based design was guided by several solved cocrystal structures with Mcl-1, leading to the development of compound 24 , which binds both Mcl-1 and Bfl-1 with K i values of 100 nM and shows appreciable selectivity over Bcl-2/Bcl-xL. The selective binding profile of 24 was translated to on-target cellular activity in model lymphoma cell lines. These studies lay a foundation for developing more advanced dual Mcl-1/Bfl-1 inhibitors that have potential to provide greater single agent efficacy and broader coverage to combat resistance in several types of cancer than selective Mcl-1 inhibitors alone.


  • Organizational Affiliation

    National Institute of Chemistry, Ljubljana 1000, Slovenia.


Macromolecules
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
156Homo 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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Q01 (Subject of Investigation/LOI)
Query on Q01

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
G [auth B]
H [auth B]
C [auth A],
D [auth A],
E [auth A],
G [auth B],
H [auth B],
I [auth B]
2-({[4-(4-tert-butylphenyl)piperazin-1-yl]sulfonyl}amino)-5-{[3-oxo-3-(phenylamino)propyl]sulfanyl}benzoic acid
C30 H36 N4 O5 S2
STJXGZZMVAELRV-UHFFFAOYSA-N
BNL
Query on BNL

Download Ideal Coordinates CCD File 
F [auth A],
J [auth B]
BIPHENYL
C12 H10
ZUOUZKKEUPVFJK-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
Q01 BindingDB:  6U67 Ki: 950 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.192 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 67.514α = 90
b = 134.376β = 90
c = 70.794γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
BUSTERrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01-CA-217141-01

Revision History  (Full details and data files)

  • Version 1.0: 2020-03-04
    Type: Initial release
  • Version 1.1: 2020-03-25
    Changes: Database references
  • Version 1.2: 2024-03-13
    Changes: Data collection, Database references