Human Arginase 1 in complex with compound 01.

Experimental Data Snapshot

  • Resolution: 1.80 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.229 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 2.1 of the entry. See complete history


Comprehensive Strategies to Bicyclic Prolines: Applications in the Synthesis of Potent Arginase Inhibitors.

Li, D.Zhang, H.Lyons, T.W.Lu, M.Achab, A.Pu, Q.Childers, M.Mitcheltree, M.J.Wang, J.Martinot, T.A.McMinn, S.E.Sloman, D.L.Palani, A.Beard, A.Nogle, L.Gathiaka, S.Sauri, J.Kim, H.Y.Adpressa, D.Spacciapoli, P.Miller, J.R.Palte, R.L.Lesburg, C.A.Cumming, J.Fischer, C.

(2021) ACS Med Chem Lett 12: 1678-1688

  • DOI: https://doi.org/10.1021/acsmedchemlett.1c00258
  • Primary Citation of Related Structures:  
    7K4G, 7K4H, 7K4I, 7K4J, 7K4K

  • PubMed Abstract: 

    Comprehensive synthetic strategies afforded a diverse set of structurally unique bicyclic proline-containing arginase inhibitors with a high degree of three-dimensionality. The analogs that favored the Cγ-exo conformation of the proline improved the arginase potency over the initial lead. The novel synthetic strategies reported here not only enable access to previously unknown stereochemically complex proline derivatives but also provide a foundation for the future synthesis of bicyclic proline analogs, which incorporate inherent three-dimensional character into building blocks, medicine, and catalysts and could have a profound impact on the conformation of proline-containing peptides and macrocycles.

  • Organizational Affiliation

    Department of Discovery Chemistry, Department of Discovery Process Chemistry, Department of In Vitro Pharmacology, Department of Computational and Structural Chemistry, and Department of Analytical Research and Development, 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
VUV (Subject of Investigation/LOI)
Query on VUV

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]
C8 H17 B N 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]
Experimental Data & Validation

Experimental Data

  • Resolution: 1.80 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.229 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 53.14α = 90
b = 280.6β = 90.02
c = 67.09γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

  • Released Date: 2021-12-01 
  • Deposition Author(s): Palte, R.L.

Revision History  (Full details and data files)

  • Version 1.0: 2021-12-01
    Type: Initial release
  • Version 2.0: 2021-12-08
    Changes: Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2023-10-18
    Changes: Data collection, Refinement description