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 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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
  • Primary Citation of Related Structures:  
    3LC5

  • 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 template to access the S1 beta and S2-S4 sites ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Coagulation factor IXA235Homo sapiensMutation(s): 0 
Gene Names: F9
EC: 3.4.21.22
UniProt & NIH Common Fund Data Resources
Find proteins for P00740 (Homo sapiens)
Explore P00740 
Go to UniProtKB:  P00740
PHAROS:  P00740
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Coagulation factor IXB57Homo sapiensMutation(s): 0 
Gene Names: F9
EC: 3.4.21.22
UniProt & NIH Common Fund Data Resources
Find proteins for P00740 (Homo sapiens)
Explore P00740 
Go to UniProtKB:  P00740
PHAROS:  P00740
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IZX (Subject of Investigation/LOI)
Query on IZX

Download Ideal Coordinates CCD File 
D [auth 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
CA
Query on CA

Download Ideal Coordinates CCD File 
C [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
IZX PDBBind:  3LC5 Ki: 270 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.62 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.12α = 90
b = 65.738β = 90
c = 93.985γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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