6Q37

Complex of Arginase 2 with Example 23

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.150 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Discovery ofN-Substituted 3-Amino-4-(3-boronopropyl)pyrrolidine-3-carboxylic Acids as Highly Potent Third-Generation Inhibitors of Human Arginase I and II.

Van Zandt, M.C., Jagdmann, G.E., Whitehouse, D.L., Ji, M., Savoy, J., Potapova, O., Cousido-Siah, A., Mitschler, A., Howard, E.I., Pyle, A.M., Podjarny, A.D.

(2019) J Med Chem 62: 8164-8177

  • DOI: 10.1021/acs.jmedchem.9b00931
  • Primary Citation of Related Structures:  
    6Q37, 6Q39

  • PubMed Abstract: 

    • Recent efforts to identify new highly potent arginase inhibitors have resulted in the discovery of a novel family of (3 R ,4 S )-3-amino-4-(3-boronopropyl)pyrrolidine-3-carboxylic acid analogues with up to a 1000-fold increase in potency re ...

    Recent efforts to identify new highly potent arginase inhibitors have resulted in the discovery of a novel family of (3 R ,4 S )-3-amino-4-(3-boronopropyl)pyrrolidine-3-carboxylic acid analogues with up to a 1000-fold increase in potency relative to the current standards, 2-amino-6-boronohexanoic acid (ABH) and N -hydroxy-nor-l-arginine (nor-NOHA). The lead candidate, with an N -2-amino-3-phenylpropyl substituent (NED-3238), example 43 , inhibits arginase I and II with IC 50 values of 1.3 and 8.1 nM, respectively. Herein, we report the design, synthesis, and structure-activity relationships for this novel series of inhibitors, along with X-ray crystallographic data for selected examples bound to human arginase II.

    Organizational Affiliation: 

    Department of Integrative Biology, IGBMC, CNRS, INSERM , Université de Strasbourg , 1 rue Laurent Fries , 67404 Illkirch , France.



Macromolecules
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(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
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HE8
Query on HE8
Download Ideal Coordinates CCD File 
A, B, C
3-[(3~{S},4~{R})-4-azanyl-4-carboxy-pyrrolidin-3-yl]propyl-tris(oxidanyl)boranuide
C8 H18 B N2 O5
JNNZQSJBRFVUJB-XPUUQOCRSA-N		 Ligand Interaction
BAM
Query on BAM
Download Ideal Coordinates CCD File 
A, B, C
BENZAMIDINE
C7 H9 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-O		 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
EDO
Query on EDO
Download Ideal Coordinates CCD File 
C
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-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 %)
HE8IC50:  440   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.21 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.148 
  • R-Value Observed: 0.150 
  • Space Group: P 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 128.162α = 90
b = 128.162β = 90
c = 158.985γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2019-08-28
    Type: Initial release
  • Version 1.1: 2019-09-25
    Changes: Data collection, Database references
  • Version 1.2: 2019-10-16
    Changes: Data collection