3KHJ

C. parvum inosine monophosphate dehydrogenase bound by inhibitor C64


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.224 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

The structural basis of Cryptosporidium -specific IMP dehydrogenase inhibitor selectivity.

Macpherson, I.S.Kirubakaran, S.Gorla, S.K.Riera, T.V.D'Aquino, J.A.Zhang, M.Cuny, G.D.Hedstrom, L.

(2010) J.Am.Chem.Soc. 132: 1230-1231

  • DOI: 10.1021/ja909947a
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Cryptosporidium parvum is a potential biowarfare agent, an important AIDS pathogen, and a major cause of diarrhea and malnutrition. No vaccines or effective drug treatment exist to combat Cryptosporidium infection. This parasite relies on inosine 5'- ...

    Cryptosporidium parvum is a potential biowarfare agent, an important AIDS pathogen, and a major cause of diarrhea and malnutrition. No vaccines or effective drug treatment exist to combat Cryptosporidium infection. This parasite relies on inosine 5'-monophosphate dehydrogenase (IMPDH) to obtain guanine nucleotides, and inhibition of this enzyme blocks parasite proliferation. Here, we report the first crystal structures of CpIMPDH. These structures reveal the structural basis of inhibitor selectivity and suggest a strategy for further optimization. Using this information, we have synthesized low-nanomolar inhibitors that display 10(3) selectivity for the parasite enzyme over human IMPDH2.


    Organizational Affiliation

    Departments of Biology, Brandeis University, MS009, 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, E, F, G, H
361Cryptosporidium parvum (strain Iowa II)Mutation(s): 0 
EC: 1.1.1.205
Find proteins for Q5CPK7 (Cryptosporidium parvum (strain Iowa II))
Go to UniProtKB:  Q5CPK7
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, E, F, G, H
INOSINIC ACID
C10 H13 N4 O8 P
GRSZFWQUAKGDAV-KQYNXXCUSA-N
 Ligand Interaction
ACT
Query on ACT

Download SDF File 
Download CCD File 
D
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
C64
Query on C64

Download SDF File 
Download CCD File 
B, D, H
N-(4-bromophenyl)-2-[2-(1,3-thiazol-2-yl)-1H-benzimidazol-1-yl]acetamide
C18 H13 Br N4 O S
GUHIASUSWSGRHY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
C64IC50: 27 - 28 nM (89) BINDINGDB
C64IC50: 28 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.224 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 83.481α = 90.00
b = 166.141β = 105.14
c = 101.289γ = 90.00
Software Package:
Software NamePurpose
ADSCdata collection
REFMACrefinement
HKL-2000data reduction
MOLREPphasing
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-02-02
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-07-02
    Type: Structure summary
  • Version 1.3: 2017-08-02
    Type: Refinement description, Source and taxonomy