3Q3K

Factor Xa in complex with a phenylenediamine derivative

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.198 

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

  • 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 substi ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Activated factor Xa 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
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
D90
Query on D90
Download SDF File 
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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
D90IC50: 7.4 nM (100) BINDINGDB
D90IC50: 7.4 nM BINDINGMOAD
D90IC50: 7.4 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.198 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 57.073α = 90.00
b = 73.202β = 90.00
c = 79.520γ = 90.00
Software Package:
Software NamePurpose
PROCESSdata scaling
REFMACphasing
specificarydata collection
REFMACrefinement
PROCESSdata reduction

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
    Type: Structure summary