3LC5

Selective Benzothiophine Inhibitors of Factor IXa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure Based Drug Design: Development of Potent and Selective Factor IXa (FIXa) Inhibitors.

Wang, S.Beck, R.Burd, A.Blench, T.Marlin, F.Ayele, T.Buxton, S.Dagostin, C.Malic, M.Joshi, R.Barry, J.Sajad, M.Cheung, C.Shaikh, S.Chahwala, S.Chander, C.Baumgartner, C.Holthoff, H.P.Murray, E.Blackney, M.Giddings, A.

(2010) J.Med.Chem. 53: 1473-1482

  • DOI: 10.1021/jm901476x

  • PubMed Abstract: 
  • On the basis of our understanding on the binding interactions of the benzothiophene template within the FIXa active site by X-ray crystallography and molecular modeling studies, we developed our SAR strategy by targeting the 4-position of the templat ...

    On the basis of our understanding on the binding interactions of the benzothiophene template within the FIXa active site by X-ray crystallography and molecular modeling studies, we developed our SAR strategy by targeting the 4-position of the template to access the S1 beta and S2-S4 sites. A number of highly selective and potent factor Xa (FXa) and FIXa inhibitors were identified by simple switch of functional groups with conformational changes toward the S2-S4 sites.


    Organizational Affiliation

    Department of Medicinal Chemistry, Trigen Ltd., Emmanuel Kaye Building, 1B Manresa Road,London SW3 6LR, UK. shouming_wang@yahoo.co.uk




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Coagulation factor IX
A
235Homo sapiensMutation(s): 0 
Gene Names: F9
EC: 3.4.21.22
Find proteins for P00740 (Homo sapiens)
Go to Gene View: F9
Go to UniProtKB:  P00740
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Coagulation factor IX
B
57Homo sapiensMutation(s): 0 
Gene Names: F9
EC: 3.4.21.22
Find proteins for P00740 (Homo sapiens)
Go to Gene View: F9
Go to UniProtKB:  P00740
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
IZX
Query on IZX

Download SDF File 
Download CCD File 
A
1-{4-[(R)-phenyl(3-phenyl-1,2,4-oxadiazol-5-yl)methoxy]-1-benzothiophen-2-yl}methanediamine
C24 H20 N4 O2 S
VBSNODZWDZSFEZ-OAQYLSRUSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
IZXKi: 270 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.206 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 43.120α = 90.00
b = 65.738β = 90.00
c = 93.985γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
SCALAdata scaling
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2010-01-09 
  • Released Date: 2010-02-23 
  • Deposition Author(s): Wang, S., Beck, R.

Revision History 

  • Version 1.0: 2010-02-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance