1PM7 | pdb_00001pm7

RmlC (dTDP-6-DEOXY-D-XYLO-4-HEXULOSE 3,5-EPIMERASE)STRUCTURE FROM MYCOBACTERIUM TUBERCULOSIS AND INHIBITOR DESIGN. THE APO STRUCTURE.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 
    0.283 (Depositor), 0.293 (DCC) 
  • R-Value Work: 
    0.207 (Depositor) 
  • R-Value Observed: 
    0.211 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1PM7

This is version 1.3 of the entry. See complete history

Literature

Novel inhibitors of an emerging target in Mycobacterium tuberculosis; substituted thiazolidinones as inhibitors of dTDP-rhamnose synthesis.

Babaoglu, K.Page, M.A.Jones, V.C.McNeil, M.R.Dong, C.Naismith, J.H.Lee, R.E.

(2003) Bioorg Med Chem Lett 13: 3227-3230

  • DOI: https://doi.org/10.1016/s0960-894x(03)00673-5
  • Primary Citation Related Structures: 
    1PM7

  • PubMed Abstract: 

    The emergence of multi-drug resistant tuberculosis, coupled with the increasing overlap of the AIDS and tuberculosis pandemics has brought tuberculosis to the forefront as a major worldwide health concern. In an attempt to find new inhibitors of the enzymes in the essential rhamnose biosynthetic pathway, a virtual library of 2,3,5 trisubstituted-4-thiazolidinones was created. These compounds were then docked into the active site cavity of 6'hydroxyl; dTDP-6-deoxy-D-xylo-4-hexulose 3,5-epimerase (RmlC) from Mycobacterium tuberculosis. The resulting docked conformations were consensus scored and the top 5% were slated for synthesis. Thus far, 94 compounds have been successfully synthesized and initially tested. Of those, 30 (32%) have > or =50% inhibitory activity (at 20 microM) in the coupled rhamnose synthetic assay with seven of the 30 also having modest activity against whole-cell M. tuberculosis.


  • Organizational Affiliation
    • Department of Pharmaceutical Sciences, University of Tennessee Health Science Center, Memphis, TN 38163, USA.

Macromolecule Content 

  • Total Structure Weight: 44.98 kDa 
  • Atom Count: 3,275 
  • Modeled Residue Count: 398 
  • Deposited Residue Count: 404 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
RFBC
A, B
202Mycobacterium tuberculosisMutation(s): 0 
Gene Names: rmlc (rfbc)
EC: 5.1.3.13
UniProt
Find proteins for P9WH11 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WH11 
Go to UniProtKB:  P9WH11
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WH11
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free:  0.283 (Depositor), 0.293 (DCC) 
  • R-Value Work:  0.207 (Depositor) 
  • R-Value Observed: 0.211 (Depositor) 
Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.066α = 90
b = 66.066β = 90
c = 87.62γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-12-09
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations