Mycobacterium tuberculosis adenosine kinase bound to (2R,3S,4R,5R)-2-(hydroxymethyl)-5-(6-(thiophen-3-yl)-9H-purin-9-yl)tetrahydrofuran-3,4-diol

Experimental Data Snapshot

  • Resolution: 2.10 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report

Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


Structure-Guided Drug Design of 6-Substituted Adenosine Analogues as Potent Inhibitors of Mycobacterium tuberculosis Adenosine Kinase.

Crespo, R.A.Dang, Q.Zhou, N.E.Guthrie, L.M.Snavely, T.C.Dong, W.Loesch, K.A.Suzuki, T.You, L.Wang, W.O'Malley, T.Parish, T.Olsen, D.B.Sacchettini, J.C.

(2019) J Med Chem 62: 4483-4499

  • DOI: https://doi.org/10.1021/acs.jmedchem.9b00020
  • Primary Citation of Related Structures:  
    6C67, 6C9N, 6C9P, 6C9Q, 6C9R, 6C9S, 6C9V

  • PubMed Abstract: 

    Mycobacterium tuberculosis adenosine kinase (MtbAdoK) is an essential enzyme of Mtb and forms part of the purine salvage pathway within mycobacteria. Evidence suggests that the purine salvage pathway might play a crucial role in Mtb survival and persistence during its latent phase of infection. In these studies, we adopted a structural approach to the discovery, structure-guided design, and synthesis of a series of adenosine analogues that displayed inhibition constants ranging from 5 to 120 nM against the enzyme. Two of these compounds exhibited low micromolar activity against Mtb with half maximal effective inhibitory concentrations of 1.7 and 4.0 μM. Our selectivity and preliminary pharmacokinetic studies showed that the compounds possess a higher degree of specificity against MtbAdoK when compared with the human counterpart and are well tolerated in rodents, respectively. Finally, crystallographic studies showed the molecular basis of inhibition, potency, and selectivity and revealed the presence of a potentially therapeutically relevant cavity unique to the MtbAdoK homodimer.

  • Organizational Affiliation

    Department of Biochemistry and Biophysics , Texas A&M University , College Station , Texas 77843 , United States.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Adenosine kinase
A, B
337Mycobacterium tuberculosisMutation(s): 0 
Gene Names: adoKcbhKMRA_2218
Find proteins for P9WID5 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WID5 
Go to UniProtKB:  P9WID5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WID5
Sequence Annotations
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
ERJ BindingDB:  6C9R IC50: 197 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.10 Å
  • R-Value Free: 0.204 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.236α = 90
b = 81.984β = 90
c = 158.33γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Bill & Melinda Gates FoundationUnited StatesOPP1024055
Welch FoundationUnited StatesA-0015
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesP01A1095208

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-01
    Type: Initial release
  • Version 1.1: 2019-05-22
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.3: 2023-10-04
    Changes: Data collection, Database references, Refinement description