4IXU

Crystal structure of human Arginase-2 complexed with inhibitor 11d: {(5R)-5-amino-5-carboxy-5-[(3-endo)-8-(3,4-dichlorobenzyl)-8-azabicyclo[3.2.1]oct-3-yl]pentyl}(trihydroxy)borate(1-)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 

wwPDB Validation   3D Report Full Report



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:  
    4IXU, 4IXV

  • 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 synthesi ...

    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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Arginase-2, mitochondrial A, B, C306Homo 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
GTEx:  ENSG00000081181
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
38I
Query on 38I
Download Ideal Coordinates CCD File 
A, B, C
{(5R)-5-amino-5-carboxy-5-[(3-endo)-8-(3,4-dichlorobenzyl)-8-azabicyclo[3.2.1]oct-3-yl]pentyl}(trihydroxy)borate(1-)
C20 H30 B Cl2 N2 O5
KCKQBVVBSIZAMB-UIVXKWKOSA-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 %)
38IIC50:  290   nM  Binding MOAD
38IIC50 :  23   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.193 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.169 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 127.4α = 90
b = 127.4β = 90
c = 159.249γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-12-11
    Type: Initial release