8RG6

Arginase 2 in complex with inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.229 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 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 

  • DOI: https://doi.org/10.1021/acs.jmedchem.4c02309
  • Primary Citation of 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.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  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
A1H0B (Subject of Investigation/LOI)
Query on A1H0B

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
L [auth C]
(2~{S},3~{R})-3-[3-(dihydroxyboranyl)propyl]pyrrolidine-2-carboxylic acid
C8 H16 B N O4
AMHQFAXDSRWEOU-RQJHMYQMSA-N
MN
Query on MN

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
G [auth B]
H [auth B]
J [auth C]
D [auth A],
E [auth A],
G [auth B],
H [auth B],
J [auth C],
K [auth C]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.62 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.229 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.51α = 90
b = 134.29β = 90
c = 145.02γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling

Structure Validation

View Full Validation Report



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