9FRV | pdb_00009frv

Arginase 2 in complex with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 
    0.315 (Depositor), 0.336 (DCC) 
  • R-Value Work: 
    0.279 (Depositor), 0.293 (DCC) 
  • R-Value Observed: 
    0.280 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9FRV

Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history

Literature

Design and Synthesis of Acyclic Boronic Acid Arginase Inhibitors.

Shields, J.D.Aquila, B.M.Emmons, D.Finlay, M.R.V.Gangl, E.T.Gu, C.Mlynarski, S.N.Petersen, J.Pop-Damkov, P.Sha, L.Simpson, I.Tavakoli, S.Tentarelli, S.Wang, H.Ye, Q.Zheng, X.

(2024) J Med Chem 67: 20799-20826

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c02295
  • Primary Citation Related Structures: 
    8RIM, 9FRV

  • PubMed Abstract: 

    Arginase has long been a target of interest in immuno-oncology, but discovering an orally bioavailable inhibitor is severely constrained by the requisite boronic acid pharmacophore. We began our drug discovery campaign by building off the β-position of the literature inhibitor ABH ( 1 ). A divergent synthesis with an Ireland-Claisen rearrangement as the key step allowed access to numerous compounds, some of which we crystallized in the active site of arginase 2. We subsequently used structure-based drug design to further improve the potency of this series, ultimately achieving an inhibitor with an IC 50 value of 12 nM. Many compounds in this series were designed to behave as prodrugs, releasing their payload with up to 4-fold improved oral exposure relative to the parent. Subtle stereochemical differences between these various inhibitors and prodrugs had substantial effects on potency and pharmacokinetics.


  • Organizational Affiliation
    • Early Oncology R&D, AstraZeneca, 35 Gatehouse Drive, Waltham, Massachusetts 02451, United States.

Macromolecule Content 

  • Total Structure Weight: 110.51 kDa 
  • Atom Count: 7,423 
  • Modeled Residue Count: 960 
  • Deposited Residue Count: 1,008 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Arginase-2, mitochondrial
A, B, C
336Homo 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
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1IFX
(Subject of Investigation/LOI)

Query on A1IFX



Download:Ideal Coordinates CCD File
J [auth C][(4~{S},5~{S})-4-(aminomethyl)-5-azanyl-6-oxidanyl-6-oxidanylidene-hexyl]-$l^{3}-oxidanyl-bis(oxidanyl)boron
C7 H18 B N2 O5
YMMHYLNSFFXXCS-WDSKDSINSA-N
MN

Query on MN



Download:Ideal Coordinates CCD File
D [auth A]
E [auth A]
F [auth B]
G [auth B]
H [auth C]
D [auth A],
E [auth A],
F [auth B],
G [auth B],
H [auth C],
I [auth C]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free:  0.315 (Depositor), 0.336 (DCC) 
  • R-Value Work:  0.279 (Depositor), 0.293 (DCC) 
  • R-Value Observed: 0.280 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.749α = 90
b = 134.59β = 90
c = 145.081γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
xia2data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data

  • Released Date: 2024-11-27 
  • Deposition Author(s): Petersen, j.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-27
    Type: Initial release
  • Version 2.0: 2024-12-04
    Changes: Non-polymer description
  • Version 2.1: 2024-12-25
    Changes: Database references