4IXH | pdb_00004ixh

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 (Depositor), 0.211 (DCC) 
  • R-Value Work: 
    0.162 (Depositor), 0.163 (DCC) 
  • R-Value Observed: 
    0.164 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.4 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: https://doi.org/10.1021/jm400241j
  • Primary Citation 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.


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

Macromolecule Content 

  • Total Structure Weight: 157.37 kDa 
  • Atom Count: 10,776 
  • Modeled Residue Count: 1,340 
  • Deposited Residue Count: 1,444 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Inosine-5'-monophosphate dehydrogenase
A, B, C, D
361Cryptosporidium parvumMutation(s): 0 
Gene Names: 56k.02cgd6_20
EC: 1.1.1.205
UniProt
Find proteins for Q8T6T2 (Cryptosporidium parvum)
Explore Q8T6T2 
Go to UniProtKB:  Q8T6T2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8T6T2
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Q21

Query on Q21



Download:Ideal Coordinates CCD File
H [auth A],
J [auth B],
L [auth B],
N [auth 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

Query on IMP



Download:Ideal Coordinates CCD File
E [auth A],
K [auth B],
M [auth C],
Q [auth D]
INOSINIC ACID
C10 H13 N4 O8 P
GRSZFWQUAKGDAV-KQYNXXCUSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
F [auth A],
G [auth A],
I [auth A],
O [auth C],
P [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.210 (Depositor), 0.211 (DCC) 
  • R-Value Work:  0.162 (Depositor), 0.163 (DCC) 
  • R-Value Observed: 0.164 (Depositor) 
Space Group: P 1 21 1
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

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Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • 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
  • Version 1.4: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description