6BDR

Schistosoma mansoni (Blood Fluke) Sulfotransferase/CIDD-0000206 (Compound 9f) Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.150 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Design, Synthesis, and Characterization of Novel Small Molecules as Broad Range Antischistosomal Agents.

Rugel, A.Tarpley, R.S.Lopez, A.Menard, T.Guzman, M.A.Taylor, A.B.Cao, X.Kovalskyy, D.Chevalier, F.D.Anderson, T.J.C.Hart, P.J.LoVerde, P.T.McHardy, S.F.

(2018) ACS Med Chem Lett 9: 967-973

  • DOI: https://doi.org/10.1021/acsmedchemlett.8b00257
  • Primary Citation of Related Structures:  
    6BDP, 6BDQ, 6BDR, 6BDS, 6MFE

  • PubMed Abstract: 

    Schistosomiasis is a major human parasitic disease afflicting more than 250 million people, historically treated with chemotherapies praziquantel or oxamniquine. Since oxamniquine is species-specific, killing Schistosoma mansoni but not other schistosome species ( S. haematobium or S. japonicum ) and evidence for drug resistant strains is growing, research efforts have focused on identifying novel approaches. Guided by data from X-ray crystallographic studies and Schistosoma worm killing assays on oxamniquine, our structure-based drug design approach produced a robust structure-activity relationship (SAR) program that identified several new lead compounds with effective worm killing. These studies culminated in the discovery of compound 12a , which demonstrated broad-species activity in killing S. mansoni (75%), S. haematobium (40%), and S. japonicum (83%).


  • Organizational Affiliation

    Department of Pathology and Laboratory Medicine, Department of Biochemistry and Structural Biology, and Greehey Children's Cancer Research Institute, UT Health San Antonio, 7703 Floyd Curl Drive, San Antonio, Texas 78229, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Sulfotransferase oxamniquine resistance protein259Schistosoma mansoniMutation(s): 0 
Gene Names: SULT-ORSmp_089320
UniProt
Find proteins for G4VLE5 (Schistosoma mansoni)
Explore G4VLE5 
Go to UniProtKB:  G4VLE5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG4VLE5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A3P
Query on A3P

Download Ideal Coordinates CCD File 
B [auth A]ADENOSINE-3'-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
WHTCPDAXWFLDIH-KQYNXXCUSA-N
DF7 (Subject of Investigation/LOI)
Query on DF7

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]
[4-({(3R)-1-[(1H-indol-3-yl)methyl]pyrrolidin-3-yl}amino)-2-nitrophenyl]methanol
C20 H22 N4 O3
LQBYYBOHEOEPPN-QGZVFWFLSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CAS
Query on CAS
A
L-PEPTIDE LINKINGC5 H12 As N O2 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.66 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.147 
  • R-Value Observed: 0.150 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 141.271α = 90
b = 39.364β = 90
c = 53.627γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2018-10-03 
  • Deposition Author(s): Taylor, A.B.

Revision History  (Full details and data files)

  • Version 1.0: 2018-10-03
    Type: Initial release
  • Version 1.1: 2018-11-07
    Changes: Data collection, Database references, Source and taxonomy
  • Version 1.2: 2023-10-04
    Changes: Data collection, Database references, Refinement description
  • Version 2.0: 2024-05-01
    Changes: Data collection, Derived calculations, Non-polymer description, Structure summary