Human Arginase1 Complexed with Bicyclic Inhibitor Compound 12

Experimental Data Snapshot

  • Resolution: 1.99 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 

wwPDB Validation   3D Report Full Report

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Discovery and Optimization of Rationally Designed Bicyclic Inhibitors of Human Arginase to Enhance Cancer Immunotherapy.

Mitcheltree, M.J.Li, D.Achab, A.Beard, A.Chakravarthy, K.Cheng, M.Cho, H.Eangoor, P.Fan, P.Gathiaka, S.Kim, H.Y.Lesburg, C.A.Lyons, T.W.Martinot, T.A.Miller, J.R.McMinn, S.O'Neil, J.Palani, A.Palte, R.L.Sauri, J.Sloman, D.L.Zhang, H.Cumming, J.N.Fischer, C.

(2020) ACS Med Chem Lett 11: 582-588

  • DOI: https://doi.org/10.1021/acsmedchemlett.0c00058
  • Primary Citation of Related Structures:  
    6V7C, 6V7D, 6V7E, 6V7F

  • PubMed Abstract: 

    The action of arginase, a metalloenzyme responsible for the hydrolysis of arginine to urea and ornithine, is hypothesized to suppress immune-cell activity within the tumor microenvironment, and thus its inhibition may constitute a means by which to potentiate the efficacy of immunotherapeutics such as anti-PD-1 checkpoint inhibitors. Taking inspiration from reported enzyme-inhibitor cocrystal structures, we designed and synthesized novel inhibitors of human arginase possessing a fused 5,5-bicyclic ring system. The prototypical member of this class, 3 , when dosed orally, successfully demonstrated serum arginase inhibition and concomitant arginine elevation in a syngeneic mouse carcinoma model, despite modest oral bioavailability. Structure-based design strategies to improve the bioavailability of this class, including scaffold modification, fluorination, and installation of active-transport recognition motifs were explored.

  • Organizational Affiliation

    Discovery Chemistry; Quantitative Biosciences; Pharmacokinetics, Pharmacodynamics, and Drug Metabolism; Computational and Structural Chemistry; Analytical Research and Development; Process Research and Development; Oncology Discovery; and External Discovery Chemistry, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States.

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

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]
C12 H24 B N2 O5
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]
Binding Affinity Annotations 
IDSourceBinding Affinity
QRA Binding MOAD:  6V7E IC50: 2 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 1.99 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.214 
  • R-Value Observed: 0.216 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.72α = 90
b = 286.49β = 90.03
c = 67.12γ = 90
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
autoPROCdata scaling

Structure Validation

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Entry History 

Deposition Data

  • Released Date: 2020-05-06 
  • Deposition Author(s): Palte, R.L.

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-06
    Type: Initial release
  • Version 1.1: 2023-10-11
    Changes: Data collection, Database references, Derived calculations, Refinement description