1Z6E

Factor XA in complex with the inhibitor 1-(3'-amino-1,2-benzisoxazol-5'-yl)-n-(4-(2'-((dimethylamino)methyl)-1h-imidazol-1-yl)-2-fluorophenyl)-3-(trifluoromethyl)-1h-pyrazole-5-carboxamide (razaxaban; DPC906; BMS-561389)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Discovery of 1-(3'-aminobenzisoxazol-5'-yl)-3-trifluoromethyl-N-[2-fluoro-4-[(2'-dimethylaminomethyl)imidazol-1-yl]phenyl]-1H-pyrazole-5-carboxyamide hydrochloride (razaxaban), a highly potent, selective, and orally bioavailable factor Xa inhibitor.

Quan, M.L.Lam, P.Y.S.Han, Q.Pinto, D.J.P.He, M.Y.Li, R.Ellis, C.D.Clark, C.G.Teleha, C.A.Sun, J.-H.Alexander, R.S.Bai, S.Luettgen, J.M.Knabb, R.M.Wong, P.C.Wexler, R.R.

(2005) J Med Chem 48: 1729-1744

  • DOI: 10.1021/jm0497949
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Modification of a series of pyrazole factor Xa inhibitors to incorporate an aminobenzisoxazole as the P(1) ligand resulted in compounds with improved selectivity for factor Xa relative to trypsin and plasma kallikrein. Further optimization of the P(4 ...

    Modification of a series of pyrazole factor Xa inhibitors to incorporate an aminobenzisoxazole as the P(1) ligand resulted in compounds with improved selectivity for factor Xa relative to trypsin and plasma kallikrein. Further optimization of the P(4) moiety led to compounds with enhanced permeability and reduced protein binding. The SAR and pharmacokinetic profile of this series of compounds is described herein. These efforts culminated in 1-(3'-aminobenzisoxazol-5'-yl)-3-trifluoromethyl-N-[2-fluoro-4-[(2'-dimethylaminomethyl)imidazol-1-yl]phenyl]-1H-pyrazole-5-carboxyamide (11d), a potent, selective, and orally bioavailable inhibitor of factor Xa. On the basis of its excellent in vitro potency and selectivity profile, high free fraction in human plasma, good oral bioavailability, and in vivo efficacy in antithrombotic models, the HCl salt of this compound was selected for clinical development as razaxaban (DPC 906, BMS-561389).


    Organizational Affiliation

    Discovery Chemistry, Pharmaceutical Research Institute, Bristol-Myers Squibb Co., P.O. Box 5400, Princeton, New Jersey 08543-5400, USA. mimi.quan@bms.com



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Coagulation factor X
A
234Homo 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Coagulation factor X
L
52Homo 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
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IK8
Query on IK8

Download CCD File 
A
1-(3-AMINO-1,2-BENZISOXAZOL-5-YL)-N-(4-{2-[(DIMETHYLAMINO)METHYL]-1H-IMIDAZOL-1-YL}-2-FLUOROPHENYL)-3-(TRIFLUOROMETHYL) -1H-PYRAZOLE-5-CARBOXAMIDE
C24 H20 F4 N8 O2
OFJRNBWSFXEHSA-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
IK8Ki:  0.1899999976158142   nM  Binding MOAD
IK8Ki :  0.1899999976158142   nM  PDBBind
IK8Ki:  1.600000023841858   nM  BindingDB
IK8Ki:  0.1899999976158142   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.221 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.1α = 90
b = 71.7β = 90
c = 78.3γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
EPMRphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
CNXrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2005-03-22 
  • Released Date: 2006-03-28 
  • Deposition Author(s): Alexander, R.S.

Revision History 

  • Version 1.0: 2006-03-28
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance