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: 2.2 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.186 

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
  • Primary Citation of Related Structures:  
  • Also Cited By: 2D1J

  • 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: 
    • 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
    • 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


    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 Gene View: F10
Go to UniProtKB:  P00742
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 Gene View: F10
Go to UniProtKB:  P00742
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
D01
Query on D01

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.186 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 57.078α = 90.00
b = 73.122β = 90.00
c = 79.949γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



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
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance