5OU3

M. thermoresistible IMPDH in complex with IMP and Compound 31 (AT080)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Fragment-Based Approach to Targeting Inosine-5'-monophosphate Dehydrogenase (IMPDH) from Mycobacterium tuberculosis.

Trapero, A.Pacitto, A.Singh, V.Sabbah, M.Coyne, A.G.Mizrahi, V.Blundell, T.L.Ascher, D.B.Abell, C.

(2018) J. Med. Chem. 61: 2806-2822

  • DOI: 10.1021/acs.jmedchem.7b01622
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Tuberculosis (TB) remains a major cause of mortality worldwide, and improved treatments are needed to combat emergence of drug resistance. Inosine 5'-monophosphate dehydrogenase (IMPDH), a crucial enzyme required for de novo synthesis of guanine nucl ...

    Tuberculosis (TB) remains a major cause of mortality worldwide, and improved treatments are needed to combat emergence of drug resistance. Inosine 5'-monophosphate dehydrogenase (IMPDH), a crucial enzyme required for de novo synthesis of guanine nucleotides, is an attractive TB drug target. Herein, we describe the identification of potent IMPDH inhibitors using fragment-based screening and structure-based design techniques. Screening of a fragment library for Mycobacterium thermoresistible ( Mth) IMPDH ΔCBS inhibitors identified a low affinity phenylimidazole derivative. X-ray crystallography of the Mth IMPDH ΔCBS-IMP-inhibitor complex revealed that two molecules of the fragment were bound in the NAD binding pocket of IMPDH. Linking the two molecules of the fragment afforded compounds with more than 1000-fold improvement in IMPDH affinity over the initial fragment hit.


    Organizational Affiliation

    Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase
A
389Mycobacterium thermoresistibile (strain ATCC 19527 / DSM 44167 / CIP 105390 / JCM 6362 / NCTC 10409 / 316)Mutation(s): 0 
Gene Names: guaB
EC: 1.1.1.205
Find proteins for G7CNL4 (Mycobacterium thermoresistibile (strain ATCC 19527 / DSM 44167 / CIP 105390 / JCM 6362 / NCTC 10409 / 316))
Go to UniProtKB:  G7CNL4
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IMP
Query on IMP

Download SDF File 
Download CCD File 
A
INOSINIC ACID
C10 H13 N4 O8 P
GRSZFWQUAKGDAV-KQYNXXCUSA-N
 Ligand Interaction
AUN
Query on AUN

Download SDF File 
Download CCD File 
A
(2~{S})-~{N}-[5-(4-bromophenyl)-1~{H}-imidazol-2-yl]-2-[4-(1-methylimidazol-4-yl)phenoxy]propanamide
C22 H20 Br N5 O2
NCECUTFKDWLGRR-AWEZNQCLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.6 Å
  • Space Group: I 4
Unit Cell:
Length (Å)Angle (°)
a = 89.280α = 90.00
b = 89.280β = 90.00
c = 85.090γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXphasing
PHENIXrefinement
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-03-28
    Type: Initial release
  • Version 1.1: 2018-04-04
    Type: Data collection, Database references
  • Version 1.2: 2018-04-25
    Type: Data collection, Database references