2C9D

Lumazine Synthase from Mycobacterium tuberculosis Bound to 3-(1,3,7- TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL)HEXANE 1-PHOSPHATE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.326 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.262 

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Ligand Structure Quality Assessment 


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: 4790-4804

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

  • 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 SYNTHASE
A, B, C, D, E, F, G, H
A, B, C, D, E, F, G, H, I, J
160Mycobacterium 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PHR (Subject of Investigation/LOI)
Query on PHR

Download Ideal Coordinates CCD File 
AA [auth F] , CA [auth G] , EA [auth H] , GA [auth I] , IA [auth J] , K [auth A] , O [auth B] , S [auth C] , 
AA [auth F],  CA [auth G],  EA [auth H],  GA [auth I],  IA [auth J],  K [auth A],  O [auth B],  S [auth C],  V [auth D],  X [auth E]
3-(1,3,7-TRIHYDRO-9-D-RIBITYL-2,6,8-PURINETRIONE-7-YL ) HEXANE 1-PHOSPHATE
C16 H27 N4 O11 P
SLRQIPDGMUYATQ-FOGDFJRCSA-N
 Ligand Interaction
MPD
Query on MPD

Download Ideal Coordinates CCD File 
MA [auth J], N [auth A](4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
K
Query on K

Download Ideal Coordinates CCD File 
BA [auth F] , DA [auth G] , FA [auth H] , HA [auth I] , JA [auth J] , KA [auth J] , L [auth A] , LA [auth J] , 
BA [auth F],  DA [auth G],  FA [auth H],  HA [auth I],  JA [auth J],  KA [auth J],  L [auth A],  LA [auth J],  M [auth A],  P [auth B],  Q [auth B],  R [auth B],  T [auth C],  U [auth C],  W [auth D],  Y [auth E],  Z [auth E]
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
PHR PDBBind:  2C9D Kd: 480 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.326 
  • R-Value Work: 0.259 
  • R-Value Observed: 0.262 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 79.955α = 64.27
b = 79.959β = 64.39
c = 88.352γ = 62.81
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



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, Refinement description, Version format compliance
  • Version 1.2: 2018-06-20
    Changes: Data collection, Database references, Structure summary
  • Version 1.3: 2019-04-10
    Changes: Data collection, Source and taxonomy