8E5M

Structure of ARG1 complex with pyrrolidine-based non-boronic acid inhibitor 6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery of non-boronic acid Arginase 1 inhibitors through virtual screening and biophysical methods.

Gathiaka, S.Palte, R.L.So, S.S.Chai, X.Richard Miller, J.Kuvelkar, R.Wen, X.Cifelli, S.Kreamer, A.Liaw, A.McLaren, D.G.Fischer, C.

(2023) Bioorg Med Chem Lett 84: 129193-129193

  • DOI: https://doi.org/10.1016/j.bmcl.2023.129193
  • Primary Citation of Related Structures:  
    8E5M, 8E5N

  • PubMed Abstract: 

    Inhibiting Arginase 1 (ARG1), a metalloenzyme that hydrolyzes l-arginine in the urea cycle, has been demonstrated as a promising therapeutic avenue in immuno-oncology through the restoration of suppressed immune response in several types of cancers. Most of the currently reported small molecule inhibitors are boronic acid based. Herein, we report the discovery of non-boronic acid ARG1 inhibitors through virtual screening. Biophysical and biochemical methods were used to experimentally profile the hits while X-ray crystallography confirmed a class of trisubstituted pyrrolidine derivatives as optimizable alternatives for the development of novel classes of immuno-oncology agents targeting this enzyme.


  • Organizational Affiliation

    Computational & Structural Chemistry, Merck & Co., Inc., Boston, MA 02115, USA. Electronic address: symon.gathiaka@gmail.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Arginase-1
A, B, C, D, E
A, B, C, D, E, F
322Homo sapiensMutation(s): 0 
Gene Names: ARG1
EC: 3.5.3.1
UniProt & NIH Common Fund Data Resources
Find proteins for P05089 (Homo sapiens)
Explore P05089 
Go to UniProtKB:  P05089
GTEx:  ENSG00000118520 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05089
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
UKR (Subject of Investigation/LOI)
Query on UKR

Download Ideal Coordinates CCD File 
I [auth A]
L [auth B]
O [auth C]
R [auth D]
U [auth E]
I [auth A],
L [auth B],
O [auth C],
R [auth D],
U [auth E],
X [auth F]
1-{[(3S,4S)-3-({4-[2-(4-fluorobenzene-1-sulfonyl)ethyl]piperidin-1-yl}methyl)-4-(3-fluorophenyl)pyrrolidin-1-yl]methyl}cyclopentane-1-carboxylic acid
C31 H40 F2 N2 O4 S
JLKKIAYYHXNZIY-ABYGYWHVSA-N
MN
Query on MN

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.84 Å
  • R-Value Free: 0.231 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.47α = 90
b = 286.1β = 90.32
c = 67.35γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
autoBUSTERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-03-08
    Type: Initial release
  • Version 1.1: 2023-03-15
    Changes: Database references
  • Version 1.2: 2023-10-25
    Changes: Data collection, Refinement description