2EI6

FACTOR XA IN COMPLEX WITH THE INHIBITOR (-)-cis-N1-[(5-Chloroindol-2-yl)carbonyl]-N2-[(5-methyl-4,5,6,7-tetrahydrothiazolo[5,4-c]pyridin-2-yl)carbonyl]-1,2-cyclohexanediamine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cycloalkanediamine derivatives as novel blood coagulation factor Xa inhibitors.

Nagata, T.Yoshino, T.Haginoya, N.Yoshikawa, K.Isobe, Y.Furugohri, T.Kanno, H.

(2007) Bioorg Med Chem Lett 17: 4683-4688

  • DOI: 10.1016/j.bmcl.2007.05.068
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • This paper describes the synthesis of orally available potent fXa inhibitors 2 and 3 by modification of the piperazine part of lead compound 1. Carbonyl derivative 3 showed potent fXa activity but not sulfonyl derivative 2. Among the compounds synthe ...

    This paper describes the synthesis of orally available potent fXa inhibitors 2 and 3 by modification of the piperazine part of lead compound 1. Carbonyl derivative 3 showed potent fXa activity but not sulfonyl derivative 2. Among the compounds synthesized, cyclohexane derivatives 3g and 3h and cycloheptane derivative 3j had potent anticoagulant activity as well as anti-fXa activity. Synthetic study of the optical isomers of 3g demonstrated that (-)-3g had more potent activity.


    Organizational Affiliation

    Medicinal Chemistry Research Laboratory, Daiichi Pharmaceutical Co., Ltd, 1-16-13, Kita-Kasai, Edogawa-ku, Tokyo 134-8630, Japan. nagatso1@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 UniProtKB:  P00742
NIH Common Fund Data Resources
PHAROS  P00742
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

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 UniProtKB:  P00742
NIH Common Fund Data Resources
PHAROS  P00742
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D92
Query on D92

Download CCD File 
A
N-((1R,2S)-2-(5-CHLORO-1H-INDOLE-2-CARBOXAMIDO)CYCLOHEXYL)-5-METHYL-4,5,6,7-TETRAHYDROTHIAZOLO[5,4-C]PYRIDINE-2-CARBOXAMIDE
C23 H26 Cl N5 O2 S
ARPFWVKYXJZULB-DLBZAZTESA-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 %)
D92IC50:  753   nM  Binding MOAD
D92IC50:  41   nM  BindingDB
D92IC50:  16   nM  BindingDB
D92IC50 :  41   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.805α = 90
b = 72.971β = 90
c = 79.552γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2007-03-12 
  • Released Date: 2008-03-18 
  • Deposition Author(s): Suzuki, M.

Revision History 

  • Version 1.0: 2008-03-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance