4IXH

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.105 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.162 

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

  • 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 str ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Inosine-5'-monophosphate dehydrogenase
A, B, C, D
361Cryptosporidium parvumMutation(s): 0 
EC: 1.1.1.205
Find proteins for Q8T6T2 (Cryptosporidium parvum)
Go to UniProtKB:  Q8T6T2
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IMP
Query on IMP

Download SDF File 
Download CCD File 
A, B, C, D
INOSINIC ACID
C10 H13 N4 O8 P
GRSZFWQUAKGDAV-KQYNXXCUSA-N
 Ligand Interaction
EDO
Query on EDO

Download SDF File 
Download CCD File 
A, C
1,2-ETHANEDIOL
ETHYLENE GLYCOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
 Ligand Interaction
Q21
Query on Q21

Download SDF File 
Download CCD File 
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
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
Q21IC50: 6.1 - 14 nM (89) BINDINGDB
Q21Ki: 13 - 64 nM (89) BINDINGDB
Q21IC50: 6.1 nM BINDINGMOAD
Q21IC50: 6.1 nM PDBBIND
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 89.185α = 90.00
b = 92.016β = 103.85
c = 92.139γ = 90.00
Software Package:
Software NamePurpose
HKL-3000data scaling
HKL-3000data collection
PHENIXrefinement
HKL-3000data reduction
MOLREPphasing
HKL-3000phasing
SBC-Collectdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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