2AQ7

Structure-activity relationships at the 5-posiiton of thiolactomycin: an intact 5(R)-isoprene unit is required for activity against the condensing enzymes from Mycobacterium tuberculosis and Escherichia coli


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure-Activity Relationships at the 5-Position of Thiolactomycin: An Intact (5R)-Isoprene Unit Is Required for Activity against the Condensing Enzymes from Mycobacterium tuberculosis and Escherichia coli

Kim, P.Zhang, Y.M.Shenoy, G.Nguyen, Q.A.Boshoff, H.I.Manjunatha, U.H.Goodwin, M.B.Lonsdale, J.Price, A.C.Miller, D.J.Duncan, K.White, S.W.Rock, C.O.Barry III, C.E.Dowd, C.S.

(2006) J Med Chem 49: 159-171

  • DOI: 10.1021/jm050825p
  • Primary Citation of Related Structures:  
    2AQ7, 2AQB

  • PubMed Abstract: 
  • Thiolactomycin inhibits bacterial cell growth through inhibition of the beta-ketoacyl-ACP synthase activity of type II fatty acid synthases. The effect of modifications of the 5-position isoprenoid side chain on both IC(50) and MIC were determined. Synthesis and screening of a structurally diverse set of 5-position analogues revealed very little tolerance for substitution in purified enzyme assays, but a few analogues retained MIC, presumably through another target ...

    Thiolactomycin inhibits bacterial cell growth through inhibition of the beta-ketoacyl-ACP synthase activity of type II fatty acid synthases. The effect of modifications of the 5-position isoprenoid side chain on both IC(50) and MIC were determined. Synthesis and screening of a structurally diverse set of 5-position analogues revealed very little tolerance for substitution in purified enzyme assays, but a few analogues retained MIC, presumably through another target. Even subtle modifications such as reducing one or both double bonds of the diene were not tolerated. The only permissible structural modifications were removal of the isoprene methyl group or addition of a methyl group to the terminus. Cocrystallization of these two inhibitors with the condensing enzyme from Escherichia coli revealed that they retained the TLM binding mode at the active site with reduced affinity. These results suggest a strict requirement for a conjugated, planar side chain inserting within the condensing enzyme active site.


    Organizational Affiliation

    Tuberculosis Research Section, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Maryland 20852, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3-oxoacyl-[acyl-carrier-protein] synthase IA, B, C, D406Escherichia coliMutation(s): 0 
Gene Names: fabBfabC
EC: 2.3.1.41
UniProt
Find proteins for P0A953 (Escherichia coli (strain K12))
Explore P0A953 
Go to UniProtKB:  P0A953
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A953
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TL5
Query on TL5

Download Ideal Coordinates CCD File 
E [auth A],
F [auth B],
G [auth D]
(5R)-4-HYDROXY-3,5-DIMETHYL-5-[(1E,3E)-2-METHYLPENTA-1,3-DIENYL]THIOPHEN-2(5H)-ONE
C12 H16 O2 S
FVTQYHVYLPKMOX-SJFBBLFCSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
TL5 PDBBind:  2AQ7 IC50: 5.00e+5 (nM) from 1 assay(s)
Binding MOAD:  2AQ7 IC50: 5.00e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.118α = 90
b = 138.997β = 90
c = 212.458γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-01-17
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance