3LC3

Benzothiophene Inhibitors of Factor IXa


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Studies of Benzothiophene Template as Potent Factor IXa (FIXa) Inhibitors in Thrombosis.

Wang, S.Beck, R.Blench, T.Burd, A.Buxton, S.Malic, M.Ayele, T.Shaikh, S.Chahwala, S.Chander, C.Holland, R.Merette, S.Zhao, L.Blackney, M.Watts, A.

(2010) J Med Chem 53: 1465-1472

  • DOI: 10.1021/jm901475e
  • Primary Citation of Related Structures:  
    3LC3

  • PubMed Abstract: 
  • FIXa is a serine protease enzyme involved in the intrinsic pathway of the coagulation cascade. The upstream intervention of the coagulation cascade in selectively inhibiting FIXa would leave hemostasis intact via the extrinsic pathway, leading to an ...

    FIXa is a serine protease enzyme involved in the intrinsic pathway of the coagulation cascade. The upstream intervention of the coagulation cascade in selectively inhibiting FIXa would leave hemostasis intact via the extrinsic pathway, leading to an optimum combination of efficacy and safety with low incidence of bleeding. We have identified 2-amindinobenzothiophene template as a lead scaffold for FIXa inhibiton based on its homology with urokinase plasminogen activator (uPA). Subsequent SAR work on the template revealed a number of highly potent FIXa inhibitors, though with moderate selectivity against FXa. X-ray study with one of the analogues demonstrated active site binding interaction with the induced opening of the S1 beta pocket and a secondary binding at the S2-S4 sites, which is in direct contrast with the previous finding.


    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Coagulation factor IXAC235Homo sapiensMutation(s): 0 
Gene Names: F9
EC: 3.4.21.22
Find proteins for P00740 (Homo sapiens)
Explore P00740 
Go to UniProtKB:  P00740
NIH Common Fund Data Resources
PHAROS  P00740
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Coagulation factor IXBD57Homo sapiensMutation(s): 0 
Gene Names: F9
EC: 3.4.21.22
Find proteins for P00740 (Homo sapiens)
Explore P00740 
Go to UniProtKB:  P00740
NIH Common Fund Data Resources
PHAROS  P00740
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IYX
Query on IYX

Download CCD File 
A, C
1-[5-(3,4-dimethoxyphenyl)-1-benzothiophen-2-yl]methanediamine
C17 H18 N2 O2 S
XZOIHOQTJVDJCE-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
IYXKi:  5900   nM  Binding MOAD
IYXKi :  5900   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 66.922α = 90
b = 96.035β = 89.93
c = 44.391γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



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
    Changes: Version format compliance