Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C4  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 157.37 kDa 
• Atom Count: 10776 
• Residue Count: 1340 
• Unique protein chains: 1

4IXH

Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Cryptosporidium parvum

• DOI: 10.2210/pdb4IXH/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Cryptosporidium parvum
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2013-01-25 Released: 2013-04-03 
• Deposition Author(s): Kim, Y., Makowska-Grzyska, M., Gu, M., Kavitha, M., Hedstrom, L., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.210 
• R-Value Work: 0.162 
• R-Value Observed: 0.164 

Literature

Optimization of Benzoxazole-Based Inhibitors of Cryptosporidium parvum Inosine 5'-Monophosphate Dehydrogenase.

Gorla, S.K., Kavitha, M., Zhang, M., Chin, J.E., Liu, X., Striepen, B., Makowska-Grzyska, M., Kim, Y., Joachimiak, A., Hedstrom, L., Cuny, G.D.

(2013) J Med Chem 56: 4028-4043

• PubMed: 23668331 
• DOI: 10.1021/jm400241j
• Primary Citation of Related Structures:  
  4IXH


• PubMed Abstract: 
  

Cryptosporidium parvum is an enteric protozoan parasite that has emerged as a major cause of diarrhea, malnutrition, and gastroenteritis and poses a potential bioterrorism threat. C. parvum synthesizes guanine nucleotides from host adenosine in a streamlined pathway that relies on inosine 5'-monophosphate dehydrogenase (IMPDH). We have previously identified several parasite-selective C. parvum IMPDH (CpIMPDH) inhibitors by high-throughput screening. In this paper, we report the structure-activity relationship (SAR) for a series of benzoxazole derivatives with many compounds demonstrating CpIMPDH IC50 values in the nanomolar range and >500-fold selectivity over human IMPDH (hIMPDH). Unlike previously reported CpIMPDH inhibitors, these compounds are competitive inhibitors versus NAD(+). The SAR study reveals that pyridine and other small heteroaromatic substituents are required at the 2-position of the benzoxazole for potent inhibitory activity. In addition, several other SAR conclusions are highlighted with regard to the benzoxazole and the amide portion of the inhibitor, including preferred stereochemistry. An X-ray crystal structure of a representative E·IMP·inhibitor complex is also presented. Overall, the secondary amine derivative 15a demonstrated excellent CpIMPDH inhibitory activity (IC50 = 0.5 ± 0.1 nM) and moderate stability (t1/2 = 44 min) in mouse liver microsomes. Compound 73, the racemic version of 15a, also displayed superb antiparasitic activity in a Toxoplasma gondii strain that relies on CpIMPDH (EC50 = 20 ± 20 nM), and selectivity versus a wild-type T. gondii strain (200-fold). No toxicity was observed (LD50 > 50 μM) against a panel of four mammalian cells lines.

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Organizational Affiliation: 

Department of Biology, Brandeis University , 415 South Street, Waltham, Massachusetts 02454, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Inosine-5'-monophosphate dehydrogenase	A, B, C, D	361	Cryptosporidium parvum	Mutation(s): 0  Gene Names: 56k.02, cgd6_20 EC: 1.1.1.205
Find proteins for Q8T6T2 (Cryptosporidium parvum) Explore Q8T6T2  Go to UniProtKB:  Q8T6T2

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
Q21	A, B, C	(2S)-2-(naphthalen-1-yloxy)-N-[2-(pyridin-4-yl)-1,3-benzoxazol-5-yl]propanamide C25 H19 N3 O3 QCNXGTHMVPSAAC-INIZCTEOSA-N
IMP	A, B, C, D	INOSINIC ACID C10 H13 N4 O8 P GRSZFWQUAKGDAV-KQYNXXCUSA-N
EDO	A, C	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
Q21	IC50:  6.099999904632568   nM  Binding MOAD
Q21	IC50:  6.099999904632568   nM  BindingDB
Q21	IC50:  9   nM  BindingDB
Q21	IC50 :  6.099999904632568   nM  PDBBind
Q21	Ki:  13   nM  BindingDB
Q21	IC50:  8   nM  BindingDB
Q21	Ki:  64   nM  BindingDB
Q21	IC50:  14   nM  BindingDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.210 
• R-Value Work: 0.162 
• R-Value Observed: 0.164 
• Space Group: P 1 2₁ 1
• Diffraction Data DOI: 10.18430/M34IXH Protein Diffraction

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.185	α = 90
b = 92.016	β = 103.85
c = 92.139	γ = 90

Software Package:

Software Name	Purpose
SBC-Collect	data collection
HKL-3000	data collection
HKL-3000	phasing
MOLREP	phasing
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-01-25 
• Released Date: 2013-04-03 
Deposition Author(s): Kim, Y., Makowska-Grzyska, M., Gu, M., Kavitha, M., Hedstrom, L., Anderson, W.F., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History 

• Version 1.0: 2013-04-03
  Type: Initial release
  
• Version 1.1: 2013-06-19
  Changes: Database references
• Version 1.2: 2013-07-17
  Changes: Structure summary
• Version 1.3: 2017-08-02
  Changes: Refinement description, Source and taxonomy