Experimental Data Snapshot

  • Resolution: 2.98 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.173 

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6-Substituted Hexamethylene Amiloride (HMA) Derivatives as Potent and Selective Inhibitors of the Human Urokinase Plasminogen Activator for Use in Cancer.

Buckley, B.J.Aboelela, A.Minaei, E.Jiang, L.X.Xu, Z.Ali, U.Fildes, K.Cheung, C.Y.Cook, S.M.Johnson, D.C.Bachovchin, D.A.Cook, G.M.Apte, M.Huang, M.Ranson, M.Kelso, M.J.

(2018) J Med Chem 61: 8299-8320

  • DOI: https://doi.org/10.1021/acs.jmedchem.8b00838
  • Primary Citation of Related Structures:  
    5ZA7, 5ZA8, 5ZA9, 5ZAE, 5ZAF, 5ZAG, 5ZAH, 5ZAJ, 5ZC5

  • PubMed Abstract: 

    Metastasis is the cause of death in the majority (∼90%) of malignant cancers. The oral potassium-sparing diuretic amiloride and its 5-substituted derivative 5 -N, N-(hexamethylene)amiloride (HMA) reportedly show robust antitumor/metastasis effects in multiple in vitro and animal models. These effects are likely due, at least in part, to inhibition of the urokinase plasminogen activator (uPA), a key protease determinant of cell invasiveness and metastasis. This study reports the discovery of 6-substituted HMA analogs that show nanomolar potency against uPA, high selectivity over related trypsin-like serine proteases, and minimal inhibitory effects against epithelial sodium channels (ENaC), the diuretic and antikaliuretic target of amiloride. Reductions in lung metastases were demonstrated for two analogs in a late-stage experimental mouse metastasis model, and one analog completely inhibited formation of liver metastases in an orthotopic xenograft mouse model of pancreatic cancer. The results support further evaluation of 6-substituted HMA derivatives as uPA-targeting anticancer drugs.

  • Organizational Affiliation

    Molecular Horizons and School of Chemistry & Molecular Bioscience , University of Wollongong , Wollongong , NSW 2522 , Australia.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Urokinase-type plasminogen activator chain BA [auth U]253Homo sapiensMutation(s): 2 
Gene Names: PLAU
UniProt & NIH Common Fund Data Resources
Find proteins for P00749 (Homo sapiens)
Explore P00749 
Go to UniProtKB:  P00749
PHAROS:  P00749
GTEx:  ENSG00000122861 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00749
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 30I

Download Ideal Coordinates CCD File 
B [auth U]3-azanyl-5-(azepan-1-yl)-N-carbamimidoyl-6-(2-methoxypyrimidin-5-yl)pyrazine-2-carboxamide
C17 H23 N9 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
30I BindingDB:  5ZAH Ki: 53 (nM) from 1 assay(s)
IC50: 39 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.98 Å
  • R-Value Free: 0.268 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.173 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 120.434α = 90
b = 120.434β = 90
c = 42.227γ = 120
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

Funding OrganizationLocationGrant Number
The National Health and Medical Research CouncilAustraliaAPP1100432

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-19
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description