Crystal structure of human Arginase-1 complexed with inhibitor 9

Experimental Data Snapshot

  • Resolution: 1.30 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.159 

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This is version 1.4 of the entry. See complete history


Discovery of (R)-2-Amino-6-borono-2-(2-(piperidin-1-yl)ethyl)hexanoic Acid and Congeners As Highly Potent Inhibitors of Human Arginases I and II for Treatment of Myocardial Reperfusion Injury.

Van Zandt, M.C.Whitehouse, D.L.Golebiowski, A.Ji, M.K.Zhang, M.Beckett, R.P.Jagdmann, G.E.Ryder, T.R.Sheeler, R.Andreoli, M.Conway, B.Mahboubi, K.D'Angelo, G.Mitschler, A.Cousido-Siah, A.Ruiz, F.X.Howard, E.I.Podjarny, A.D.Schroeter, H.

(2013) J Med Chem 56: 2568-2580

  • DOI: https://doi.org/10.1021/jm400014c
  • Primary Citation of Related Structures:  
    4HWW, 4HXQ, 4HZE, 4I06

  • PubMed Abstract: 

    Recent efforts to identify treatments for myocardial ischemia reperfusion injury have resulted in the discovery of a novel series of highly potent α,α-disubstituted amino acid-based arginase inhibitors. The lead candidate, (R)-2-amino-6-borono-2-(2-(piperidin-1-yl)ethyl)hexanoic acid, compound 9, inhibits human arginases I and II with IC50s of 223 and 509 nM, respectively, and is active in a recombinant cellular assay overexpressing human arginase I (CHO cells). It is 28% orally bioavailable and significantly reduces the infarct size in a rat model of myocardial ischemia/reperfusion injury. Herein, we report the design, synthesis, and structure-activity relationships (SAR) for this novel series of inhibitors along with pharmacokinetic and in vivo efficacy data for compound 9 and X-ray crystallography data for selected lead compounds cocrystallized with arginases I and II.

  • Organizational Affiliation

    Institutes for Pharmaceutical Discovery , LLC, 23 Business Park Drive, Branford, Connecticut 06405, USA. mvzandt@snet.net

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
314Homo sapiensMutation(s): 0 
Gene Names: ARG1
UniProt & NIH Common Fund Data Resources
Find proteins for P05089 (Homo sapiens)
Explore P05089 
Go to UniProtKB:  P05089
PHAROS:  P05089
GTEx:  ENSG00000118520 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05089
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.30 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.159 
  • Space Group: P 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.143α = 90
b = 90.143β = 90
c = 69.328γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction

Structure Validation

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Ligand Structure Quality Assessment 

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2013-03-20
    Type: Initial release
  • Version 1.1: 2013-04-10
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description
  • Version 1.3: 2018-01-24
    Changes: Structure summary
  • Version 1.4: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description