2C97 | pdb_00002c97

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 (Depositor) 
  • R-Value Work: 
    0.146 (Depositor) 
  • R-Value Observed: 
    0.150 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.5 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: https://doi.org/10.1111/j.1742-4658.2006.05481.x
  • Primary Citation 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. 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

Macromolecule Content 

  • Total Structure Weight: 85.21 kDa 
  • Atom Count: 5,998 
  • Modeled Residue Count: 733 
  • Deposited Residue Count: 800 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE
A, B, C, D, E
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
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP9WHE9
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
JCL

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
DTD

Query on DTD



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

Query on MPD



Download:Ideal Coordinates CCD File
EA [auth D]
KA [auth E]
L [auth A]
M [auth A]
T [auth B]
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
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
K

Query on K



Download:Ideal Coordinates CCD File
BA [auth D]
CA [auth D]
G [auth A]
GA [auth E]
H [auth A]
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

Experimental Data & Validation

Experimental Data

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

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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, 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
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Derived calculations, Other, Refinement description
  • Version 1.5: 2025-10-01
    Changes: Advisory, Derived calculations, Structure summary