4HWW

Crystal structure of human Arginase-1 complexed with inhibitor 9


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 
    0.169 (Depositor), 0.170 (DCC) 
  • R-Value Work: 
    0.151 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 
    0.159 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted X7AClick on this verticalbar to view details

This is version 1.4 of the entry. See complete history


Literature

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Arginase-1
A, B
314Homo sapiensMutation(s): 0 
Gene Names: ARG1
EC: 3.5.3.1
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
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free:  0.169 (Depositor), 0.170 (DCC) 
  • R-Value Work:  0.151 (Depositor), 0.150 (DCC) 
  • R-Value Observed: 0.159 (Depositor) 
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
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted X7AClick on this verticalbar to view details

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