4IXV

Crystal structure of human Arginase-2 complexed with inhibitor 2d: {(5R)-5-amino-5-carboxy-5-[1-(4-chlorobenzyl)piperidin-4-yl]pentyl}(trihydroxy)borate(1-)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Synthesis of quaternary alpha-amino acid-based arginase inhibitors via the Ugi reaction.

Golebiowski, A.Whitehouse, D.Beckett, R.P.Van Zandt, M.Ji, M.K.Ryder, T.R.Jagdmann, E.Andreoli, M.Lee, Y.Sheeler, R.Conway, B.Olczak, J.Mazur, M.Czestkowski, W.Piotrowska, W.Cousido-Siah, A.Ruiz, F.X.Mitschler, A.Podjarny, A.Schroeter, H.

(2013) Bioorg.Med.Chem.Lett. 23: 4837-4841

  • DOI: 10.1016/j.bmcl.2013.06.092
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The Ugi reaction has been successfully applied to the synthesis of novel arginase inhibitors. In an effort to decrease conformational flexibility of the previously reported series of 2-amino-6-boronohexanoic acid (ABH) analogs 1, we designed and synt ...

    The Ugi reaction has been successfully applied to the synthesis of novel arginase inhibitors. In an effort to decrease conformational flexibility of the previously reported series of 2-amino-6-boronohexanoic acid (ABH) analogs 1, we designed and synthesized a series of compounds, 2, in which a piperidine ring is linked directly to a quaternary amino acid center. Further improvement of in vitro activity was achieved by adding two carbon bridge in the piperidine ring, that is, tropane analogs 11. These improvements in activity are rationalized by X-ray crystallography analysis, which show that the tropane ring nitrogen atom moves into direct contact with Asp202 (arginase II numbering). The synthetic routes described here enabled the design of novel arginase inhibitors with improved potency and markedly different physico-chemical properties compared to ABH. Compound 11c represents the most in vitro active arginase inhibitor reported to date.


    Organizational Affiliation

    Institutes for Pharmaceutical Discovery, 23 Business Park Drive, Branford, CT, United States. 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
MN
Query on MN

Download SDF File 
Download CCD File 
A, B, C
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
 Ligand Interaction
XA1
Query on XA1

Download SDF File 
Download CCD File 
A, B, C
{(5R)-5-amino-5-carboxy-5-[1-(4-chlorobenzyl)piperidin-4-yl]pentyl}(trihydroxy)borate(1-)
C18 H29 B Cl N2 O5
ZRLSZURFUKVIRB-GOSISDBHSA-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 %)
XA1IC50: 240 nM BINDINGMOAD
XA1IC50: 240 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.180 
  • Space Group: P 42 21 2
Unit Cell:
Length (Å)Angle (°)
a = 128.123α = 90.00
b = 128.123β = 90.00
c = 159.362γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
SCALEPACKdata scaling
AMoREphasing
HKL-2000data collection
PDB_EXTRACTdata extraction
DENZOdata reduction
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2013-12-11
    Type: Initial release
  • Version 1.1: 2017-11-15
    Type: Refinement description