1WU1

Factor Xa in complex with the inhibitor 4-[(5-chloroindol-2-yl)sulfonyl]-2-(2-methylpropyl)-1-[[5-(pyridin-4-yl) pyrimidin-2-yl]carbonyl]piperazine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 
    • Structural basis for chemical inhibition of human blood coagulation factor Xa
      Kamata, K.,Kawamoto, H.,Honma, T.,Iwama, T.,Kim, S.H.
      (1998) Proc.Natl.Acad.Sci.Usa 95: 6630
    • 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
    • Structure of human des(1-45) factor Xa at 2.2 A resolution
      Padmanabhan, K.,Padmanabhan, K.P.,Tulinsky, A.,Park, C.H.,Bode, W.,Huber, R.,Blankenship, D.T.,Cardin, A.D.,Kisiel, W.
      (1993) J.Mol.Biol. 232: 947
    • X-ray structure of active site-inhibited clotting factor Xa. Implications for drug design and substrate recognition
      Brandstetter, H.,Kuhne, A.,Bode, W.,Huber, R.,von der Saal, W.,Wirthensohn, K.,Engh, R.A.
      (1996) J.Biol.Chem. 271: 29988


    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
95Homo 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
D91
Query on D91

Download SDF File 
Download CCD File 
A
5-CHLORO-2-({3-ISOBUTYL-4-[(5-PYRIDIN-4-YLPYRIMIDIN-2-YL)CARBONYL]PIPERAZIN-1-YL}SULFONYL)-1H-INDOLE
4-[(5-CHLOROINDOL-2-YL)SULFONYL]-2-(2-METHYLPROPYL)-1-[[5-(PYRIDIN-4-YL)PYRIMIDIN-2-YL]CARBONYL]PIPERAZINE
C26 H27 Cl N6 O3 S
JUUFKVAFKAKWRV-JOCHJYFZSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
BHD
Query on BHD
B
L-PEPTIDE LINKINGC4 H7 N O5ASP
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
D91IC50: 18 nM BINDINGMOAD
D91IC50: 18 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 56.569α = 90.00
b = 72.487β = 90.00
c = 79.020γ = 90.00
Software Package:
Software NamePurpose
d*TREKdata reduction
REFMACrefinement
d*TREKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2004-11-29 
  • Released Date: 2005-11-29 
  • Deposition Author(s): Suzuki, M.

Revision History 

  • Version 1.0: 2005-11-29
    Type: Initial release
  • Version 1.1: 2008-04-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2012-06-20
    Type: Non-polymer description