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: 2.30 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

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:  
    1WU1, 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 excellent potency in anti-fXa and anticoagulant assays ...

    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 U S A 95: 6630
    • 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
    • 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
    • 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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Coagulation factor X, heavy chainA233Homo sapiensMutation(s): 0 
Gene Names: F10
EC: 3.4.21.6
UniProt & NIH Common Fund Data Resources
Find proteins for P00742 (Homo sapiens)
Explore P00742 
Go to UniProtKB:  P00742
PHAROS:  P00742
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00742
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Coagulation factor X, light chainB95Homo sapiensMutation(s): 0 
Gene Names: F10
EC: 3.4.21.6
UniProt & NIH Common Fund Data Resources
Find proteins for P00742 (Homo sapiens)
Explore P00742 
Go to UniProtKB:  P00742
PHAROS:  P00742
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00742
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D91
Query on D91
Download Ideal Coordinates CCD File 
E [auth A]5-CHLORO-2-({3-ISOBUTYL-4-[(5-PYRIDIN-4-YLPYRIMIDIN-2-YL)CARBONYL]PIPERAZIN-1-YL}SULFONYL)-1H-INDOLE
C26 H27 Cl N6 O3 S
JUUFKVAFKAKWRV-JOCHJYFZSA-N		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
C [auth A],
D [auth A]		CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
BHD
Query on BHD		B L-PEPTIDE LINKINGC4 H7 N O5ASP
Binding Affinity Annotations 
IDSourceBinding Affinity
D91 PDBBind:  1WU1 IC50: 18 (nM) from 1 assay(s)
Binding MOAD:  1WU1 IC50: 18 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.569α = 90
b = 72.487β = 90
c = 79.02γ = 90
Software Package:
Software NamePurpose
d*TREKdata scaling
d*TREKdata reduction
REFMACrefinement

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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