2C97

LUMAZINE SYNTHASE FROM MYCOBACTERIUM TUBERCULOSIS BOUND TO 4-(6- chloro-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-5-yl)butyl phosphate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.150 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural and Thermodynamic Insights Into the Binding Mode of Five Novel Inhibitors of Lumazine Synthase from Mycobacterium Tuberculosis.

Morgunova, E.Illarionov, B.Sambaiah, T.Haase, I.Bacher, A.Cushman, M.Fischer, M.Ladenstein, R.

(2006) FEBS J 273: 4790

  • DOI: 10.1111/j.1742-4658.2006.05481.x
  • Primary Citation of Related Structures:  
    2C92, 2C94, 2C97, 2C9B, 2C9D

  • PubMed Abstract: 
  • Recently published genomic investigations of the human pathogen Mycobacterium tuberculosis have revealed that genes coding the proteins involved in riboflavin biosynthesis are essential for the growth of the organism. Because the enzymes involved in cofactor biosynthesis pathways are not present in humans, they appear to be promising candidates for the development of therapeutic drugs ...

    Recently published genomic investigations of the human pathogen Mycobacterium tuberculosis have revealed that genes coding the proteins involved in riboflavin biosynthesis are essential for the growth of the organism. Because the enzymes involved in cofactor biosynthesis pathways are not present in humans, they appear to be promising candidates for the development of therapeutic drugs. The substituted purinetrione compounds have demonstrated high affinity and specificity to lumazine synthase, which catalyzes the penultimate step of riboflavin biosynthesis in bacteria and plants. The structure of M. tuberculosis lumazine synthase in complex with five different inhibitor compounds is presented, together with studies of the binding reactions by isothermal titration calorimetry. The inhibitors showed the association constants in the micromolar range. The analysis of the structures demonstrated the specific features of the binding of different inhibitors. The comparison of the structures and binding modes of five different inhibitors allows us to propose the ribitylpurinetrione compounds with C4-C5 alkylphosphate chains as most promising leads for further development of therapeutic drugs against M. tuberculosis.


    Organizational Affiliation

    Karolinska Institutet, NOVUM, Centre for Structural Biochemistry, Huddinge, Sweden. katja.morgunova@biosci.ki.se



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASEA, B, C, D, E160Mycobacterium tuberculosisMutation(s): 0 
EC: 2.5.1.9 (PDB Primary Data), 2.5.1.78 (UniProt)
UniProt
Find proteins for P9WHE9 (Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv))
Explore P9WHE9 
Go to UniProtKB:  P9WHE9
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JCL (Subject of Investigation/LOI)
Query on JCL

Download Ideal Coordinates CCD File 
AA [auth D], F [auth A], FA [auth E], O [auth B], U [auth C]4-(6-CHLORO-2,4-DIOXO-1,2,3,4-TETRAHYDROPYRIMIDIN-5-YL) BUTYL PHOSPHATE
C8 H12 Cl N2 O6 P
DAUATIBSDSXXHA-UHFFFAOYSA-N
 Ligand Interaction
DTD (Subject of Investigation/LOI)
Query on DTD

Download Ideal Coordinates CCD File 
LA [auth E]DITHIANE DIOL
C4 H8 O2 S2
YPGMOWHXEQDBBV-IMJSIDKUSA-N
 Ligand Interaction
MPD
Query on MPD

Download Ideal Coordinates CCD File 
EA [auth D], KA [auth E], L [auth A], M [auth A], T [auth B], Z [auth C](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
DA [auth D], JA [auth E], K [auth A], N [auth B], Y [auth C]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
BA [auth D] , CA [auth D] , G [auth A] , GA [auth E] , H [auth A] , HA [auth E] , I [auth A] , IA [auth E] , 
BA [auth D], CA [auth D], G [auth A], GA [auth E], H [auth A], HA [auth E], I [auth A], IA [auth E], J [auth A], P [auth B], Q [auth B], R [auth B], S [auth B], V [auth C], W [auth C], X [auth C]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
JCL PDBBind:  2C97 Kd: 720 (nM) from 1 assay(s)
Binding MOAD:  2C97 Ka: 1.38e+6 (M^-1) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.146 
  • R-Value Observed: 0.150 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.64α = 90
b = 82.244β = 120.53
c = 86.346γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-12-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2019-04-10
    Changes: Data collection, Derived calculations, Other, Source and taxonomy
  • Version 1.3: 2019-07-24
    Changes: Data collection