7KLM

Human Arginase1 Complexed with Inhibitor Compound 24a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.27 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Structure-Based Discovery of Proline-Derived Arginase Inhibitors with Improved Oral Bioavailability for Immuno-Oncology.

Lu, M.Zhang, H.Li, D.Childers, M.Pu, Q.Palte, R.L.Gathiaka, S.Lyons, T.W.Palani, A.Fan, P.W.Spacciapoli, P.Miller, J.R.Cho, H.Cheng, M.Chakravarthy, K.O'Neil, J.Eangoor, P.Beard, A.Kim, H.Y.Sauri, J.Gunaydin, H.Sloman, D.L.Siliphaivanh, P.Cumming, J.Fischer, C.

(2021) ACS Med Chem Lett 12: 1380-1388

  • DOI: https://doi.org/10.1021/acsmedchemlett.1c00195
  • Primary Citation of Related Structures:  
    7KLK, 7KLL, 7KLM

  • PubMed Abstract: 

    Recent data suggest that the inhibition of arginase (ARG) has therapeutic potential for the treatment of a number of indications ranging from pulmonary and vascular disease to cancer. Thus, high demand exists for selective small molecule ARG inhibitors with favorable druglike properties and good oral bioavailability. In light of the significant challenges associated with the unique physicochemical properties of previously disclosed ARG inhibitors, we use structure-based drug design combined with a focused optimization strategy to discover a class of boronic acids featuring a privileged proline scaffold with superior potency and oral bioavailability. These compounds, exemplified by inhibitors 4a , 18 , and 27 , demonstrated a favorable overall profile, and 4a was well tolerated following multiple days of dosing at concentrations that exceed those required for serum arginase inhibition and concomitant arginine elevation in a syngeneic mouse carcinoma model.


  • Organizational Affiliation

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


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
PHAROS:  P05089
GTEx:  ENSG00000118520 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP05089
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
0IZ (Subject of Investigation/LOI)
Query on 0IZ

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]
3-[(2~{S},3~{R},4~{R})-4-[[(2~{S})-2-azanyl-3-methyl-butanoyl]amino]-2-carboxy-pyrrolidin-3-yl]propyl-$l^{3}-oxidanyl-bis(oxidanyl)boron
C13 H27 B N3 O6
BIHQJUDSCKNIPN-RCWTZXSCSA-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: 2.27 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.68α = 90
b = 289.27β = 90.58
c = 67.43γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
autoBUSTERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2021-09-29 
  • Deposition Author(s): Palte, R.L.

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-29
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Refinement description