5BOC

Crystal structure of topoisomerase ParE inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.200 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Application of Fragment-based Drug Discovery against DNA GyraseB

Chen, G.Y.Ng, F.M.Tan, Y.W.Poulsen, A.Seetoh, W.Lin, G.Kang, C.Then, S.W.Ahmad, N.H.Wong, Y.L.Ng, H.Chia, B.C.S.Lau, Q.Y.Hill, J.Hung, A.W.Keller, T.H.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA topoisomerase 4 subunit BA226Streptococcus pneumoniae R6Mutation(s): 0 
Gene Names: parEspr0756
EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for Q8DQB5 (Streptococcus pneumoniae (strain ATCC BAA-255 / R6))
Explore Q8DQB5 
Go to UniProtKB:  Q8DQB5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8DQB5
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TSJ
Query on TSJ

Download Ideal Coordinates CCD File 
B [auth A]3-methyl-4-({3-[3-methyl-5-(trifluoromethyl)phenyl]-1H-pyrazol-5-yl}carbamoyl)benzoic acid
C20 H16 F3 N3 O3
MLGFDWKUOYDRDY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.200 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.782α = 90
b = 94.802β = 90
c = 60.817γ = 90
Software Package:
Software NamePurpose
SAINTdata scaling
PHASERdata processing
PHENIXrefinement
PDB_EXTRACTdata extraction
PHENIXdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Agency for Science, Technology and Research (A*STAR) Joint CouncilSingapore1231B105

Revision History  (Full details and data files)

  • Version 1.0: 2015-06-17
    Type: Initial release