5J5R | pdb_00005j5r

M. thermoresistible GuaB2 delta-CBS in complex with inhibitor VCC234718


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.189 (Depositor), 0.195 (DCC) 
  • R-Value Work: 
    0.168 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 
    0.169 (Depositor) 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history

Literature

The Inosine Monophosphate Dehydrogenase, GuaB2, Is a Vulnerable New Bactericidal Drug Target for Tuberculosis.

Singh, V.Donini, S.Pacitto, A.Sala, C.Hartkoorn, R.C.Dhar, N.Keri, G.Ascher, D.B.Mondesert, G.Vocat, A.Lupien, A.Sommer, R.Vermet, H.Lagrange, S.Buechler, J.Warner, D.F.McKinney, J.D.Pato, J.Cole, S.T.Blundell, T.L.Rizzi, M.Mizrahi, V.

(2017) ACS Infect Dis 3: 5-17

  • DOI: https://doi.org/10.1021/acsinfecdis.6b00102
  • Primary Citation Related Structures: 
    5J5R

  • PubMed Abstract: 

    VCC234718, a molecule with growth inhibitory activity against Mycobacterium tuberculosis (Mtb), was identified by phenotypic screening of a 15344-compound library. Sequencing of a VCC234718-resistant mutant identified a Y487C substitution in the inosine monophosphate dehydrogenase, GuaB2, which was subsequently validated to be the primary molecular target of VCC234718 in Mtb. VCC234718 inhibits Mtb GuaB2 with a K i of 100 nM and is uncompetitive with respect to IMP and NAD + . This compound binds at the NAD + site, after IMP has bound, and makes direct interactions with IMP; therefore, the inhibitor is by definition uncompetitive. VCC234718 forms strong pi interactions with the Y487 residue side chain from the adjacent protomer in the tetramer, explaining the resistance-conferring mutation. In addition to sensitizing Mtb to VCC234718, depletion of GuaB2 was bactericidal in Mtb in vitro and in macrophages. When supplied at a high concentration (≥125 μM), guanine alleviated the toxicity of VCC234718 treatment or GuaB2 depletion via purine salvage. However, transcriptional silencing of guaB2 prevented Mtb from establishing an infection in mice, confirming that Mtb has limited access to guanine in this animal model. Together, these data provide compelling validation of GuaB2 as a new tuberculosis drug target.


  • Organizational Affiliation
    • MRC/NHLS/UCT Molecular Mycobacteriology Research Unit & DST/NRF Centre of Excellence for Biomedical TB Research, Institute of Infectious Disease and Molecular Medicine & Department of Pathology, University of Cape Town , Anzio Road, Observatory 7925, South Africa.

Macromolecule Content 

  • Total Structure Weight: 40.59 kDa 
  • Atom Count: 2,672 
  • Modeled Residue Count: 332 
  • Deposited Residue Count: 389 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Inosine-5'-monophosphate dehydrogenase,Inosine-5'-monophosphate dehydrogenase389Mycolicibacterium thermoresistibile ATCC 19527Mutation(s): 0 
Gene Names: KEK_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
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6G1

Query on 6G1



Download:Ideal Coordinates CCD File
B [auth A]cyclohexyl{4-[(isoquinolin-5-yl)sulfonyl]piperazin-1-yl}methanone
C20 H25 N3 O3 S
RQGSIJUNMAAIRB-UHFFFAOYSA-N
IMP

Query on IMP



Download:Ideal Coordinates CCD File
C [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
  • R-Value Free:  0.189 (Depositor), 0.195 (DCC) 
  • R-Value Work:  0.168 (Depositor), 0.174 (DCC) 
  • R-Value Observed: 0.169 (Depositor) 
Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.36α = 90
b = 89.36β = 90
c = 84.92γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European UnionUnited Kingdom260872
Medical Research Council (United Kingdom)United KingdomMR/M026302/1
NHMRCAustraliaAPP1072476

Revision History  (Full details and data files)

  • Version 1.0: 2016-10-19
    Type: Initial release
  • Version 1.1: 2017-01-25
    Changes: Database references
  • Version 1.2: 2017-09-13
    Changes: Author supporting evidence
  • Version 1.3: 2019-10-16
    Changes: Data collection
  • Version 1.4: 2024-05-08
    Changes: Data collection, Database references