9DC9

Mtb GuaB dCBS in complex with inhibitor compound 5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 

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: zhou.yuebiao@gene.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Inosine-5'-monophosphate dehydrogenase422Mycobacterium tuberculosisMutation(s): 0 
Gene Names: guaBguaB2Rv3411cMTCY78.17
EC: 1.1.1.205
UniProt
Find proteins for P9WKI7 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WKI7 
Go to UniProtKB:  P9WKI7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WKI7
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1A3K (Subject of Investigation/LOI)
Query on A1A3K

Download Ideal Coordinates CCD File 
C [auth A](3P)-3-(4-chloro-1H-imidazol-2-yl)-5-[(1R)-1-{[(3M)-3-(1H-pyrazol-5-yl)phenyl]oxy}ethyl]pyridine
C19 H16 Cl N5 O
FKQIJOHOBMULLA-GFCCVEGCSA-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
  • R-Value Free: 0.190 
  • R-Value Work: 0.166 
  • R-Value Observed: 0.167 
  • Space Group: I 4
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.749α = 90
b = 89.749β = 90
c = 85.963γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
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