5OU3

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å

wwPDB Validation   3D Report Full Report


This is version 1.4 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: https://doi.org/10.1021/acs.jmedchem.7b01622
  • Primary Citation of Related Structures:  
    5OU1, 5OU2, 5OU3

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase389Mycolicibacterium thermoresistibile ATCC 19527Mutation(s): 0 
Gene Names: guaBKEK_23061
EC: 1.1.1.205
UniProt
Find proteins for G7CNL4 (Mycolicibacterium thermoresistibile (strain ATCC 19527 / DSM 44167 / CIP 105390 / JCM 6362 / NCTC 10409 / 316))
Explore G7CNL4 
Go to UniProtKB:  G7CNL4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG7CNL4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AUN (Subject of Investigation/LOI)
Query on AUN

Download Ideal Coordinates CCD File 
C [auth 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
IMP
Query on IMP

Download Ideal Coordinates CCD File 
B [auth A]INOSINIC ACID
C10 H13 N4 O8 P
GRSZFWQUAKGDAV-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.28α = 90
b = 89.28β = 90
c = 85.09γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-03-28
    Type: Initial release
  • Version 1.1: 2018-04-04
    Changes: Data collection, Database references
  • Version 1.2: 2018-04-25
    Changes: Data collection, Database references
  • Version 1.3: 2019-10-16
    Changes: Data collection
  • Version 1.4: 2024-05-08
    Changes: Data collection, Database references