Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Mycobacterium tuberculosis in the complex with XMP and NAD

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 

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Mycobacterium tuberculosis IMPDH in Complexes with Substrates, Products and Antitubercular Compounds.

Makowska-Grzyska, M.Kim, Y.Gorla, S.K.Wei, Y.Mandapati, K.Zhang, M.Maltseva, N.Modi, G.Boshoff, H.I.Gu, M.Aldrich, C.Cuny, G.D.Hedstrom, L.Joachimiak, A.

(2015) PLoS One 10: e0138976-e0138976

  • DOI: https://doi.org/10.1371/journal.pone.0138976
  • Primary Citation of Related Structures:  
    4ZQM, 4ZQN, 4ZQO, 4ZQP, 4ZQR

  • PubMed Abstract: 

    Tuberculosis (TB) remains a worldwide problem and the need for new drugs is increasingly more urgent with the emergence of multidrug- and extensively-drug resistant TB. Inosine 5'-monophosphate dehydrogenase 2 (IMPDH2) from Mycobacterium tuberculosis (Mtb) is an attractive drug target. The enzyme catalyzes the conversion of inosine 5'-monophosphate into xanthosine 5'-monophosphate with the concomitant reduction of NAD+ to NADH. This reaction controls flux into the guanine nucleotide pool. We report seventeen selective IMPDH inhibitors with antitubercular activity. The crystal structures of a deletion mutant of MtbIMPDH2 in the apo form and in complex with the product XMP and substrate NAD+ are determined. We also report the structures of complexes with IMP and three structurally distinct inhibitors, including two with antitubercular activity. These structures will greatly facilitate the development of MtbIMPDH2-targeted antibiotics.

  • Organizational Affiliation

    Center for Structural Genomics of Infectious Diseases, University of Chicago, Chicago, IL, United States of America.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase407Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: guaBguaB2Rv3411cMTCY78.17
Find proteins for P9WKI7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WKI7 
Go to UniProtKB:  P9WKI7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WKI7
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on NAD

Download Ideal Coordinates CCD File 
C21 H27 N7 O14 P2
Query on XMP

Download Ideal Coordinates CCD File 
C10 H14 N4 O9 P
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.191 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.162 
  • Space Group: I 4
  • Diffraction Data: https://doi.org/10.18430/M34ZQM
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.154α = 90
b = 88.154β = 90
c = 85.512γ = 90
Software Package:
Software NamePurpose
HKL-3000data reduction
SBC-Collectdata collection
HKL-3000data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-17
    Type: Initial release
  • Version 1.1: 2015-12-16
    Changes: Database references
  • Version 1.2: 2017-02-08
    Changes: Structure summary
  • Version 1.3: 2017-11-22
    Changes: Refinement description
  • Version 1.4: 2022-03-30
    Changes: Author supporting evidence, Database references
  • Version 1.5: 2024-05-22
    Changes: Data collection