8RGF | pdb_00008rgf

Arginase 2 in complex with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 
    0.260 (Depositor), 0.252 (DCC) 
  • R-Value Work: 
    0.239 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 
    0.240 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8RGF

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Discovery of (2 R ,4 R )-4-(( S )-2-Amino-3-methylbutanamido)-2-(4-boronobutyl)pyrrolidine-2-carboxylic Acid (AZD0011), an Actively Transported Prodrug of a Potent Arginase Inhibitor to Treat Cancer.

Mlynarski, S.N.Aquila, B.M.Cantin, S.Cook, S.Doshi, A.Finlay, M.R.V.Gangl, E.T.Grebe, T.Gu, C.Kawatkar, S.P.Petersen, J.Pop-Damkov, P.Schuller, A.G.Shao, W.Shields, J.D.Simpson, I.Tavakoli, S.Tentarelli, S.Throner, S.Wang, H.Wang, J.Wu, D.Ye, Q.

(2024) J Med Chem 67: 20827-20841

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c02309
  • Primary Citation Related Structures: 
    8RFA, 8RG6, 8RGF, 8RGU

  • PubMed Abstract: 

    Arginase is a promising immuno-oncology target that can restore the innate immune response. However, it's highly polar active site often requires potent inhibitors to mimic amino acids, leading to poor passive permeability and low oral exposure. Using structure-based drug design, we discovered a novel proline-based arginase inhibitor ( 10 ) that was potent but had low oral bioavailability in rat. This issue was addressed by incorporating amino acids to target PepT1/2 active transport, followed by in vivo hydrolysis post absorption. The hydrolysis rate was highly tunable, and the valine prodrug ( 19 ) showed the best balance of stability and exposure of the potent payload. Dosing of 19 in mouse xenograft models significantly increased arginine in the tumor microenvironment, resulting in tumor growth inhibition as a monotherapy and in combination with an anti-PD-L1 antibody. Compound 19 (AZD0011) displays good pharmacokinetics and was selected as a clinical drug candidate for cancer.


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

Macromolecule Content 

  • Total Structure Weight: 110.39 kDa 
  • Atom Count: 7,644 
  • Modeled Residue Count: 960 
  • Deposited Residue Count: 1,005 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Arginase-2, mitochondrial
A, B, C
335Homo 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
A1H0A
(Subject of Investigation/LOI)

Query on A1H0A



Download:Ideal Coordinates CCD File
F [auth A],
K [auth C]
4-[(2~{R},4~{R})-4-azanyl-2-carboxy-pyrrolidin-2-yl]butyl-tris(oxidanyl)boranuide
C9 H20 B N2 O5
GEKJTUVCDKWVBP-VXNVDRBHSA-N
MN

Query on MN



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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free:  0.260 (Depositor), 0.252 (DCC) 
  • R-Value Work:  0.239 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 0.240 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.94α = 90
b = 135.16β = 90
c = 145.15γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data

  • Released Date: 2024-12-04 
  • Deposition Author(s): Petersen, J.

Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-12-04
    Type: Initial release
  • Version 1.1: 2024-12-25
    Changes: Database references