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 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 2.1 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: https://doi.org/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 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

    New England Discovery Partners , 23 Business Park Drive , Branford , Connecticut 06405 , United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Arginase-2, mitochondrial
A, B, C
306Homo sapiensMutation(s): 0 
Gene Names: ARG2
EC: 3.5.3.1
UniProt & NIH Common Fund Data Resources
Find proteins for P78540 (Homo sapiens)
Explore P78540 
Go to UniProtKB:  P78540
PHAROS:  P78540
GTEx:  ENSG00000081181 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP78540
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HE8 (Subject of Investigation/LOI)
Query on HE8

Download Ideal Coordinates CCD File 
H [auth A],
M [auth B],
S [auth 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
BEN
Query on BEN

Download Ideal Coordinates CCD File 
F [auth A],
K [auth B],
P [auth C]
BENZAMIDINE
C7 H8 N2
PXXJHWLDUBFPOL-UHFFFAOYSA-N
BME
Query on BME

Download Ideal Coordinates CCD File 
G [auth A],
L [auth B],
Q [auth C]
BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
R [auth C]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
I [auth B]
J [auth B]
N [auth C]
D [auth A],
E [auth A],
I [auth B],
J [auth B],
N [auth C],
O [auth C]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
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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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 2.0: 2021-08-04
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description