2D1J

Factor Xa in complex with the inhibitor 2-[[4-[(5-chloroindol-2-yl)sulfonyl]piperazin-1-yl] carbonyl]thieno[3,2-b]pyridine n-oxide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Design, synthesis, and biological activity of non-basic compounds as factor Xa inhibitors: SAR study of S1 and aryl binding sites.

Komoriya, S.Haginoya, N.Kobayashi, S.Nagata, T.Mochizuki, A.Suzuki, M.Yoshino, T.Horino, H.Nagahara, T.Suzuki, M.Isobe, Y.Furugoori, T.

(2005) Bioorg Med Chem 13: 3927-3954

  • DOI: 10.1016/j.bmc.2005.04.006
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Compound 7 was identified as the active metabolite of 6 by HPLC and mass spectral analysis. Modification of lead compound 7 by transformation of its N-oxide 6-6 biaryl ring system and fused aromatics produced a series of non-basic fXa inhibitors with ...

    Compound 7 was identified as the active metabolite of 6 by HPLC and mass spectral analysis. Modification of lead compound 7 by transformation of its N-oxide 6-6 biaryl ring system and fused aromatics produced a series of non-basic fXa inhibitors with excellent potency in anti-fXa and anticoagulant assays. The optimized compounds 73b and 75b showed sub to one digit micromolar anticoagulant activity (PTCT2). Particularly, anti-fXa activity was detected in plasma of rats orally administered with 1mg/kg of compound 75b.


    Related Citations: 
    • Design, synthesis, and biological activity of non-basic compounds as factor Xa inhibitors: SAR study of S1 and aryl binding sites
      Komoriya, S., Haginoya, N., Kobayashi, S., Nagata, T., Mochizuki, A., Suzuki, M., Yoshino, T., Horino, H., Nagahara, T., Suzuki, M., Isobe, Y., Furugoori, T.
      (2005) Bioorg Med Chem 13: 3927
    • Synthesis and conformational analysis of a non-amidine factor Xa inhibitor that incorporates 5-methyl-4,5,6,7-tetrahydrothiazolo[5,4-c]pyridine as S4 binding element
      Haginoya, N., Kobayashi, S., Komoriya, S., Yoshino, T., Suzuki, M., Shimada, T., Watanabe, K., Hirokawa, Y., Furugori, T., Nagahara, T.
      (2004) J Med Chem 47: 5167

    Organizational Affiliation

    Tokyo R&D Center, Daiichi Pharmaceutical Co. Ltd, 16-13 Kita-Kasai 1-Chome, Edogawa-ku, Tokyo 134-8630, Japan. komor0ni@daiichipharm.co.jp



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Coagulation factor X, heavy chain
A
233Homo sapiensMutation(s): 0 
Gene Names: F10
EC: 3.4.21.6
Find proteins for P00742 (Homo sapiens)
Go to UniProtKB:  P00742
NIH Common Fund Data Resources
PHAROS  P00742

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Coagulation factor X, light chain
B
54Homo sapiensMutation(s): 0 
Gene Names: F10
EC: 3.4.21.6
Find proteins for P00742 (Homo sapiens)
Go to UniProtKB:  P00742
NIH Common Fund Data Resources
PHAROS  P00742
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D01
Query on D01

Download CCD File 
A
2-({4-[(5-CHLORO-1H-INDOL-2-YL)SULFONYL]PIPERAZIN-1-YL}CARBONYL)THIENO[3,2-B]PYRIDINE 4-OXIDE
C20 H17 Cl N4 O4 S2
DHDQMXPAANQKDC-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.188 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.078α = 90
b = 73.122β = 90
c = 79.949γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
d*TREKdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2005-08-24 
  • Released Date: 2006-08-24 
  • Deposition Author(s): Suzuki, M.

Revision History 

  • Version 1.0: 2006-08-24
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance