4I06 | pdb_00004i06

Crystal structure of human Arginase-2 complexed with inhibitor 14

• PDB DOI: https://doi.org/10.2210/pdb4I06/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-11-16 Released: 2013-03-20 
• Deposition Author(s): Cousido-Siah, A., Mitschler, A., Ruiz, F.X., Whitehouse, D.L., Golebiowski, A., Ji, M., Zhang, M., Beckett, P., Sheeler, R., Andreoli, M., Conway, B., Mahboubi, K., Schroeter, H., Van Zandt, M.C., Podjarny, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.195 (Depositor), 0.191 (DCC) 
• R-Value Work: 
  0.164 (Depositor) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

Literature

Discovery of (R)-2-Amino-6-borono-2-(2-(piperidin-1-yl)ethyl)hexanoic Acid and Congeners As Highly Potent Inhibitors of Human Arginases I and II for Treatment of Myocardial Reperfusion Injury.

Van Zandt, M.C., Whitehouse, D.L., Golebiowski, A., Ji, M.K., Zhang, M., Beckett, R.P., Jagdmann, G.E., Ryder, T.R., Sheeler, R., Andreoli, M., Conway, B., Mahboubi, K., D'Angelo, G., Mitschler, A., Cousido-Siah, A., Ruiz, F.X., Howard, E.I., Podjarny, A.D., Schroeter, H.

(2013) J Med Chem 56: 2568-2580

• PubMed: 23472952 
• DOI: https://doi.org/10.1021/jm400014c
• Primary Citation Related Structures: 
  4HWW, 4HXQ, 4HZE, 4I06


• PubMed Abstract: 
  

  Recent efforts to identify treatments for myocardial ischemia reperfusion injury have resulted in the discovery of a novel series of highly potent α,α-disubstituted amino acid-based arginase inhibitors. The lead candidate, (R)-2-amino-6-borono-2-(2-(piperidin-1-yl)ethyl)hexanoic acid, compound 9, inhibits human arginases I and II with IC50s of 223 and 509 nM, respectively, and is active in a recombinant cellular assay overexpressing human arginase I (CHO cells). It is 28% orally bioavailable and significantly reduces the infarct size in a rat model of myocardial ischemia/reperfusion injury. Herein, we report the design, synthesis, and structure-activity relationships (SAR) for this novel series of inhibitors along with pharmacokinetic and in vivo efficacy data for compound 9 and X-ray crystallography data for selected lead compounds cocrystallized with arginases I and II.

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Organizational Affiliation: 
• Institutes for Pharmaceutical Discovery , LLC, 23 Business Park Drive, Branford, Connecticut 06405, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C3  (Explore in 3D)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 generated by PISA (software)

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 generated by PISA (software)

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 101.81 kDa 
• Atom Count: 8,335 
• Modeled Residue Count: 918 
• Deposited Residue Count: 918 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Arginase-2, mitochondrial	A, B, C	306	Homo sapiens	Mutation(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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
X8A	I [auth A], O [auth B], U [auth C]	[(5R)-5-carboxy-5-(methylamino)-7-(piperidin-1-yl)heptyl](trihydroxy)borate(1-) C14 H30 B N2 O5 XUSDRKPOXSYXRQ-CQSZACIVSA-N
BEN	F [auth A], L [auth B], R [auth C]	BENZAMIDINE C7 H8 N2 PXXJHWLDUBFPOL-UHFFFAOYSA-N
BME	G [auth A], H [auth A], M [auth B], N [auth B], S [auth C], T [auth C]	BETA-MERCAPTOETHANOL C2 H6 O S DGVVWUTYPXICAM-UHFFFAOYSA-N
MN	D [auth A], E [auth A], J [auth B], K [auth B], P [auth C], Q [auth C]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.195 (Depositor), 0.191 (DCC) 
• R-Value Work:  0.164 (Depositor) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.805	α = 90
b = 127.805	β = 90
c = 159.094	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-20 
Deposition Author(s): Cousido-Siah, A., Mitschler, A., Ruiz, F.X., Whitehouse, D.L., Golebiowski, A., Ji, M., Zhang, M., Beckett, P., Sheeler, R., Andreoli, M., Conway, B., Mahboubi, K., Schroeter, H., Van Zandt, M.C., Podjarny, A.

Revision History  

• Version 1.0: 2013-03-20
  Type: Initial release
  
• Version 1.1: 2013-04-10
  Changes: Database references
• Version 1.2: 2018-01-24
  Changes: Structure summary
• Version 1.3: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description