9AV0

Crystal structure of S. aureus GuaB dCBS with inhibitor GNE2011


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.226 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Discovery of potent dihydro-oxazinoquinolinone inhibitors of GuaB for the treatment of tuberculosis.

Zhou, Y.Aliagas, I.Wang, S.Li, C.S.Liu, Z.Bowman, C.M.Burdick, D.J.Clark, K.R.Dening, T.J.Flygare, J.Ganti, A.Girgis, H.S.Hanan, E.J.Harris, S.F.Hu, C.Kapadia, S.B.Koehler, M.F.T.Lai, T.Liang, J.Liu, X.Ma, F.Mao, J.Nicolai, J.Sims, J.Unhayaker, S.Wai, J.Wang, X.Wu, P.Xu, Y.Yen, C.W.Zhang, R.Elfert, T.F.Tan, M.W.Kofoed, E.M.Crawford, T.D.

(2024) Bioorg Med Chem Lett : 130026-130026

  • DOI: https://doi.org/10.1016/j.bmcl.2024.130026
  • Primary Citation of Related Structures:  
    9AV0, 9DC8, 9DC9

  • PubMed Abstract: 

    Tuberculosis is the leading cause of death from an infectious disease, and is caused by Mycobacterium tuberculosis (M.tb). More than 1 billion people worldwide are thought to harbor an M.tb infection. The multidrug therapy that represents the current standard of care requires a minimum of four months of dosing and drug resistant Mycobacterium tuberculosis treatment regimens are significantly longer. Inosine-5'-monophosphate dehydrogenase (GuaB) is the enzyme that performs the rate-limiting step in de novo guanine nucleotide biosynthesis that is critical for growth and viability of bacteria including M.tb. The development of a novel antibiotic that inhibits GuaB could combine with existing therapies in novel ways and thereby contribute to effective therapeutic regimens for the treatment of tuberculosis. Here we describe the discovery of structurally distinct small molecule GuaB inhibitors that are potent against M.tb H37Ra and H37Rv strains and have desirable safety and AMDE profiles.


  • Organizational Affiliation

    Genentech Inc., 1 DNA Way, South San Francisco, CA 94080, United States. Electronic address: [email protected].


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Inosine-5'-monophosphate dehydrogenase380Staphylococcus aureusMutation(s): 0 
Gene Names: guaBSAUSA300_0388
EC: 1.1.1.205
UniProt
Find proteins for Q2G0Y7 (Staphylococcus aureus (strain NCTC 8325 / PS 47))
Explore Q2G0Y7 
Go to UniProtKB:  Q2G0Y7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ2G0Y7
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1AG0 (Subject of Investigation/LOI)
Query on A1AG0

Download Ideal Coordinates CCD File 
C [auth A]9-{(1R)-1-[(5P)-5-(4-chloro-1H-imidazol-2-yl)pyridin-3-yl]ethoxy}-1,4-dihydro-2H-pyrano[3,4-c]quinoline
C22 H19 Cl N4 O2
ZZTIEDAGFODKQY-CYBMUJFWSA-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: 2.20 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.225 
  • R-Value Observed: 0.226 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.442α = 90
b = 104.442β = 90
c = 64.413γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-27
    Type: Initial release