9QC3 | pdb_00009qc3

CRYSTAL STRUCTURE OF LYSYL-TRNA SYNTHETASE FROM Mycobacterium tuberculosis COMPLEXED WITH L-LYSINE AND INHIBITOR DDD01993593


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free: 
    0.277 (Depositor), 0.277 (DCC) 
  • R-Value Work: 
    0.214 (Depositor), 0.217 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 9QC3

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Design and Development of Lysyl tRNA Synthetase Inhibitors, for the Treatment of Tuberculosis.

Davis, S.H.Mathieson, M.Buchanan, K.I.Dawson, A.Smith, A.Cocco, M.Tamaki, F.K.Post, J.M.Baragana, B.Jansen, C.Kiczun, M.Zuccotto, F.Wood, G.Scullion, P.Ray, P.C.Epemolu, O.Lopez-Roman, E.M.Lopez, L.G.Engelhart, C.A.Kim, J.Pino, P.A.Schnappinger, D.Read, K.D.Encinas, L.Bates, R.H.Wyatt, P.G.Green, S.R.Cleghorn, L.A.T.

(2025) J Med Chem 68: 16459-16482

  • DOI: https://doi.org/10.1021/acs.jmedchem.5c01331
  • Primary Citation Related Structures: 
    9QBR, 9QC3, 9QC4, 9QDJ, 9QEA, 9QEI

  • PubMed Abstract: 

    There is currently a public health crisis due to the rise of multidrug-resistant tuberculosis cases, as well as the rise in the number of deaths from tuberculosis. To achieve the United Nations Sustainable Development Goal of ending the tuberculosis epidemic by 2030, new treatments are urgently required. We previously reported the discovery of 49 , a preclinical candidate that acted through inhibition of the Mycobacterium tuberculosis lysyl tRNA synthetase (LysRS). In this report, the full medicinal chemistry program is reviewed from the original hit through to the optimized lead. The work was guided by the first crystal structures of M. tuberculosis LysRS. The physicochemical and pharmacokinetic properties were optimized to afford compounds suitable for evaluation in mouse efficacy models of tuberculosis and with the potential for clinical development.


  • Organizational Affiliation
    • Drug Discovery Unit, Division of Biological Chemistry and Drug Discovery, College of Life Sciences, University of Dundee, DD1 5EH Dundee, U.K.

Macromolecule Content 

  • Total Structure Weight: 58.63 kDa 
  • Atom Count: 3,704 
  • Modeled Residue Count: 462 
  • Deposited Residue Count: 526 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Lysine--tRNA ligase 1526Mycobacterium tuberculosisMutation(s): 0 
Gene Names: lysS1lysSRv3598cMTCY07H7B.24
EC: 6.1.1.6
UniProt
Find proteins for P9WFU9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WFU9 
Go to UniProtKB:  P9WFU9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WFU9
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1I50
(Subject of Investigation/LOI)

Query on A1I50



Download:Ideal Coordinates CCD File
C [auth A]2-azanyl-4-methoxy-6-[(1~{R},2~{S})-2-oxidanylcycloheptyl]-7~{H}-pyrrolo[3,4-d]pyrimidin-5-one
C14 H20 N4 O3
DXJAJOUDYQSXQN-YHMJZVADSA-N
LYS

Query on LYS



Download:Ideal Coordinates CCD File
B [auth A]LYSINE
C6 H15 N2 O2
KDXKERNSBIXSRK-YFKPBYRVSA-O

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.28 Å
  • R-Value Free:  0.277 (Depositor), 0.277 (DCC) 
  • R-Value Work:  0.214 (Depositor), 0.217 (DCC) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.669α = 90
b = 83.669β = 90
c = 147.261γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationUnited StatesOPP1066891
Bill & Melinda Gates FoundationUnited StatesOPP1191579
Wellcome TrustUnited Kingdom100195/Z/12/Z

Revision History  (Full details and data files)

  • Version 1.0: 2025-08-13
    Type: Initial release
  • Version 1.1: 2025-08-27
    Changes: Database references