4IE2

Crystal structure of human Arginase-2 complexed with inhibitor 1h

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2082 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history. 

Literature

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: 10.1016/j.bmcl.2013.02.024
  • Primary Citation of Related Structures:  

  • 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 ...

    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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Arginase-2, mitochondrial
A, B, C
306Homo sapiensMutation(s): 0 
Gene Names: ARG2
EC: 3.5.3.1
Find proteins for P78540 (Homo sapiens)
Go to Gene View: ARG2
Go to UniProtKB:  P78540
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1EC
Query on 1EC
Download SDF File 
Download CCD File 
A, B, C
[(5R)-5-amino-5-carboxy-8-hydroxyoctyl](trihydroxy)borate(1-)
C9 H21 B N O6
NLSMSWJRKXBPCL-SECBINFHSA-N
 Ligand Interaction
MN
Query on MN
Download SDF File 
Download CCD File 
A, B, C
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
BME
Query on BME
Download SDF File 
Download CCD File 
A, B, C
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
BEN
Query on BEN
Download SDF File 
Download CCD File 
A, B, C
BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1ECIC50: 4500 nM BINDINGMOAD
1ECIC50: 4500 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2082 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.167 
  • Space Group: P 42 21 2
Unit Cell:
Length (Å)Angle (°)
a = 128.094α = 90.00
b = 128.094β = 90.00
c = 159.085γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
HKL-2000data collection
PHENIXrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-03-20
    Type: Initial release
  • Version 1.1: 2013-04-03
    Type: Database references
  • Version 1.2: 2013-12-18
    Type: Structure summary
  • Version 1.3: 2017-11-15
    Type: Refinement description