4IXH

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


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 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


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

  • 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 streaml ...

    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.


    Organizational Affiliation

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



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Inosine-5'-monophosphate dehydrogenase ABCD361Cryptosporidium parvumMutation(s): 0 
Gene Names: 56k.02cgd6_20
EC: 1.1.1.205
Find proteins for Q8T6T2 (Cryptosporidium parvum)
Explore Q8T6T2 
Go to UniProtKB:  Q8T6T2
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
Q21IC50:  6.099999904632568   nM  Binding MOAD
Q21IC50:  6.099999904632568   nM  BindingDB
Q21IC50:  9   nM  BindingDB
Q21IC50 :  6.099999904632568   nM  PDBBind
Q21Ki:  13   nM  BindingDB
Q21IC50:  8   nM  BindingDB
Q21Ki:  64   nM  BindingDB
Q21IC50:  14   nM  BindingDB
Experimental Data & Validation

Experimental Data

Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.185α = 90
b = 92.016β = 103.85
c = 92.139γ = 90
Software Package:
Software NamePurpose
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
MOLREPphasing
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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