4IE2

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.170 

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:  
    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 t ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Arginase-2, mitochondrial ABC306Homo sapiensMutation(s): 0 
Gene Names: ARG2
EC: 3.5.3.1
Find proteins for P78540 (Homo sapiens)
Explore P78540 
Go to UniProtKB:  P78540
NIH Common Fund Data Resources
PHAROS:  P78540
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1EC
Query on 1EC

Download Ideal Coordinates 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
BEN
Query on BEN

Download Ideal Coordinates CCD File 
A, B, C
BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N
 Ligand Interaction
BME
Query on BME

Download Ideal Coordinates CCD File 
A, B, C
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
 Ligand Interaction
MN
Query on MN

Download Ideal Coordinates CCD File 
A, B, C
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1ECIC50:  4500   nM  Binding MOAD
1ECIC50 :  4500   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.170 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.094α = 90
b = 128.094β = 90
c = 159.085γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • 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