3Q3K

Factor Xa in complex with a phenylenediamine derivative

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Design, synthesis and SAR of novel ethylenediamine and phenylenediamine derivatives as factor Xa inhibitors.

Yoshikawa, K., Yoshino, T., Yokomizo, Y., Uoto, K., Naito, H., Kawakami, K., Mochizuki, A., Nagata, T., Suzuki, M., Kanno, H., Takemura, M., Ohta, T.

(2011) Bioorg Med Chem Lett 21: 2133-2140

  • DOI: 10.1016/j.bmcl.2011.01.132
  • Primary Citation of Related Structures:  
    3Q3K

  • PubMed Abstract: 

    • We previously reported on a series of cyclohexanediamine derivatives as highly potent factor Xa inhibitors. Herein, we describe the modification of the spacer moiety to discover an alternative scaffold. Ethylenediamine derivatives possessing a substituent at the C1 position in S configuration and phenylenediamine derivatives possessing a substituent at the C5 position demonstrated moderate to strong anti-fXa activity ...

    We previously reported on a series of cyclohexanediamine derivatives as highly potent factor Xa inhibitors. Herein, we describe the modification of the spacer moiety to discover an alternative scaffold. Ethylenediamine derivatives possessing a substituent at the C1 position in S configuration and phenylenediamine derivatives possessing a substituent at the C5 position demonstrated moderate to strong anti-fXa activity. Further SAR studies led to the identification of compound 30 h which showed both good in vitro activity (fXa IC(50) = 2.2 nM, PTCT2 = 3.9 μM) and in vivo antithrombotic efficacy.

    Organizational Affiliation: 

    R&D Division, Daiichi Sankyo Co, Ltd, 1-16-13, Kita-Kasai, Edogawa-ku, Tokyo 134-8630, Japan. yoshikawa.kenji.t6@daiichisankyo.co.jp



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Activated factor Xa heavy chainA233Homo sapiensMutation(s): 0 
Gene Names: F10
EC: 3.4.21.6
Find proteins for P00742 (Homo sapiens)
Explore P00742 
Go to UniProtKB:  P00742
NIH Common Fund Data Resources
PHAROS  P00742
GTEx  ENSG00000126218
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Factor X light chainB54Homo sapiensMutation(s): 0 
Gene Names: F10
EC: 3.4.21.6
Find proteins for P00742 (Homo sapiens)
Explore P00742 
Go to UniProtKB:  P00742
NIH Common Fund Data Resources
PHAROS  P00742
GTEx  ENSG00000126218
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D90
Query on D90
Download CCD File 
A
N-(2-{[(5-chloro-1H-indol-2-yl)carbonyl]amino}phenyl)-5-methyl-4,5,6,7-tetrahydro[1,3]thiazolo[5,4-c]pyridine-2-carboxamide
C23 H20 Cl N5 O2 S
HLZHKMHNSZRIOD-UHFFFAOYSA-N		 Ligand Interaction
CA
Query on CA
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
D90IC50:  7.400000095367432   nM  Binding MOAD
D90IC50 :  7.400000095367432   nM  PDBBind
D90IC50:  7.400000095367432   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 57.073α = 90
b = 73.202β = 90
c = 79.52γ = 90
Software Package:
Software NamePurpose
specificarydata collection
REFMACrefinement
PROCESSdata reduction
PROCESSdata scaling
REFMACphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2010-12-22 
  • Released Date: 2011-12-28 
    • Deposition Author(s): Suzuki, M., Imai, E.

Revision History 

  • Version 1.0: 2011-12-28
    Type: Initial release
  • Version 1.1: 2012-06-20
    Changes: Structure summary