6B2Q

Dual Inhibition of the Essential Protein Kinases A and B in Mycobacterium tuberculosis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.232 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Mtb PKNA/PKNB Dual Inhibition Provides Selectivity Advantages for Inhibitor Design To Minimize Host Kinase Interactions.

Wang, T.Bemis, G.Hanzelka, B.Zuccola, H.Wynn, M.Moody, C.S.Green, J.Locher, C.Liu, A.Gao, H.Xu, Y.Wang, S.Wang, J.Bennani, Y.L.Thomson, J.A.Muh, U.

(2017) ACS Med Chem Lett 8: 1224-1229

  • DOI: 10.1021/acsmedchemlett.7b00239
  • Primary Citation of Related Structures:  
    6B2P, 6B2Q

  • PubMed Abstract: 
  • Drug resistant tuberculosis (TB) infections are on the rise and antibiotics that inhibit Mycobacterium tuberculosis through a novel mechanism could be an important component of evolving TB therapy. Protein kinase A (PknA) and protein kinase B (PknB) are both essential serine-threonine kinases in M ...

    Drug resistant tuberculosis (TB) infections are on the rise and antibiotics that inhibit Mycobacterium tuberculosis through a novel mechanism could be an important component of evolving TB therapy. Protein kinase A (PknA) and protein kinase B (PknB) are both essential serine-threonine kinases in M. tuberculosis . Given the extensive knowledge base in kinase inhibition, these enzymes present an interesting opportunity for antimycobacterial drug discovery. This study focused on targeting both PknA and PknB while improving the selectivity window over related mammalian kinases. Compounds achieved potent inhibition ( K i ≈ 5 nM) of both PknA and PknB. A binding pocket unique to mycobacterial kinases was identified. Substitutions that filled this pocket resulted in a 100-fold differential against a broad selection of mammalian kinases. Reducing lipophilicity improved antimycobacterial activity with the most potent compounds achieving minimum inhibitory concentrations ranging from 3 to 5 μM (1-2 μg/mL) against the H37Ra isolate of M. tuberculosis .


    Organizational Affiliation

    Vertex Pharmaceuticals Incorporated, 50 Northern Avenue, Boston, Massachusetts 02210, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein kinase PknAA, B, C, D317Mycobacterium tuberculosisMutation(s): 0 
Gene Names: pknA
EC: 2.7.11.1
UniProt
Find proteins for P9WI83 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WI83 
Go to UniProtKB:  P9WI83
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WI83
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0BD
Query on 0BD

Download Ideal Coordinates CCD File 
F [auth A]3-methyl-1-(2-methylpropyl)butyl 4-O-beta-L-gulopyranosyl-beta-D-glucopyranoside
C21 H40 O11
RCXNRCWFTSDLDY-RDEKNSNJSA-N
 Ligand Interaction
CJJ
Query on CJJ

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
H [auth C],
I [auth D]
5-{5-chloro-4-[(5-cyclopropyl-1H-pyrazol-3-yl)amino]pyrimidin-2-yl}thiophene-2-sulfonamide
C14 H13 Cl N6 O2 S2
KRMDPWLIHGQVGZ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
A, B, C, D L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Binding Affinity Annotations 
IDSourceBinding Affinity
CJJ BindingDB:  6B2Q Ki: 9 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.88 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.230 
  • R-Value Observed: 0.232 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.065α = 90
b = 227.432β = 90
c = 158.606γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PROCESSdata reduction
PROCESSdata scaling
BUSTERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 



Entry History 

Deposition Data

  • Deposited Date: 2017-09-20 
  • Released Date: 2018-02-14 
  • Deposition Author(s): Zuccola, H.J.

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-14
    Type: Initial release