Crystal structure of human Arginase-1 complexed with inhibitor 1h

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.127 
  • R-Value Work: 0.106 
  • R-Value Observed: 0.108 

Starting Model: experimental
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2-Substituted-2-amino-6-boronohexanoic acids as arginase inhibitors.

Golebiowski, A.Paul Beckett, R.Van Zandt, M.Ji, M.K.Whitehouse, D.Ryder, T.R.Jagdmann, E.Andreoli, M.Mazur, A.Padmanilayam, M.Cousido-Siah, A.Mitschler, A.Ruiz, F.X.Podjarny, A.Schroeter, H.

(2013) Bioorg Med Chem Lett 23: 2027-2030

  • DOI: https://doi.org/10.1016/j.bmcl.2013.02.024
  • Primary Citation of Related Structures:  
    4IE1, 4IE2, 4IE3

  • PubMed Abstract: 

    Substitution at the alpha center of the known human arginase inhibitor 2-amino-6-boronohexanoic acid (ABH) is acceptable in the active site pockets of both human arginase I and arginase II. In particular, substituents with a tertiary amine linked via a two carbon chain show improved inhibitory potency for both enzyme isoforms. This potency improvement can be rationalized by X-ray crystallography, which shows a water-mediated contact between the basic nitrogen and the carboxylic acid side chain of Asp200, which is situated at the mouth of the active site pocket of arginase II (Asp181 in arginase I). We believe that this is the first literature report of compounds with improved arginase inhibitory activity, relative to ABH, and represents a promising starting point for further optimization of in vitro potency and the identification of better tool molecules for in vivo investigations of the potential pathophysiological roles of arginases.

  • Organizational Affiliation

    Institutes for Pharmaceutical Discovery, 23 Business Park Drive, Branford, CT, USA. golebiowski.a@gmail.com

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
GTEx:  ENSG00000118520 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05089
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.127 
  • R-Value Work: 0.106 
  • R-Value Observed: 0.108 
  • Space Group: P 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 90.074α = 90
b = 90.074β = 90
c = 69.272γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling

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: 2013-04-03
    Changes: Database references
  • Version 1.2: 2013-12-18
    Changes: Structure summary
  • Version 1.3: 2017-11-15
    Changes: Refinement description
  • Version 1.4: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description