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
  • Primary Citation of Related Structures:  
    2EI6

  • 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 synthesized, cyclohexane derivatives 3g and 3h and cycloheptane derivative 3j had potent anticoagulant activity as well as anti-fXa activity ...

    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:  (by identity cutoff)  |  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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Coagulation factor X, light chainB54Homo 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
D92 (Subject of Investigation/LOI)
Query on D92

Download Ideal Coordinates CCD File 
E [auth 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 Ideal Coordinates CCD File 
C [auth A], D [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
D92 BindingDB:  2EI6 IC50: min: 16, max: 41 (nM) from 2 assay(s)
Binding MOAD:  2EI6 IC50: 16 (nM) from 1 assay(s)
PDBBind:  2EI6 IC50: 41 (nM) from 1 assay(s)
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  (Full details and data files)

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