4ZQP

Crystal Structure of the Catalytic Domain of the Inosine Monophosphate Dehydrogenase from Mycobacterium tuberculosis in the complex with IMP and the inhibitor MAD1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.145 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

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: 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 ...

    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; Structural Biology Center, Biosciences, Argonne National Laboratory, 9700 S Cass Ave. Argonne, IL, United States of America.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenaseA407Mycobacterium tuberculosis H37RvMutation(s): 0 
Gene Names: guaBguaB2Rv3411cMTCY78.17
EC: 1.1.1.205
Find proteins for P9WKI7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WKI7 
Go to UniProtKB:  P9WKI7
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KP3
Query on KP3

Download CCD File 
A
5'-O-({1-[(2E)-4-(4-hydroxy-6-methoxy-7-methyl-3-oxo-1,3-dihydro-2-benzofuran-5-yl)-2-methylbut-2-en-1-yl]-1H-1,2,3-triazol-4-yl}methyl)adenosine
C28 H32 N8 O8
KHAINKCXZBTBIV-WDLZNNHFSA-N
 Ligand Interaction
IMP
Query on IMP

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A
INOSINIC ACID
C10 H13 N4 O8 P
GRSZFWQUAKGDAV-KQYNXXCUSA-N
 Ligand Interaction
PO4
Query on PO4

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A
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

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A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
PGO
Query on PGO

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A
S-1,2-PROPANEDIOL
C3 H8 O2
DNIAPMSPPWPWGF-VKHMYHEASA-N
 Ligand Interaction
K
Query on K

Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
KP3Ki:  1580   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.189 
  • R-Value Work: 0.143 
  • R-Value Observed: 0.145 
  • Space Group: I 4
  • Diffraction Data DOI: 10.18430/M34ZQP Protein Diffraction
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.225α = 90
b = 88.225β = 90
c = 84.63γ = 90
Software Package:
Software NamePurpose
SBC-Collectdata collection
HKL-3000data collection
HKL-3000phasing
HKL-3000data scaling
MOLREPphasing
PHENIXrefinement

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of HealthUnited States--

Revision History 

  • 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