2RA0

X-ray Structure of FXa in complex with 7-fluoroindazole


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.246 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

7-fluoroindazoles as potent and selective inhibitors of factor xa.

Lee, Y.K.Parks, D.J.Lu, T.Thieu, T.V.Markotan, T.Pan, W.McComsey, D.F.Milkiewicz, K.L.Crysler, C.S.Ninan, N.Abad, M.C.Giardino, E.C.Maryanoff, B.E.Damiano, B.P.Player, M.R.

(2008) J.Med.Chem. 51: 282-297

  • DOI: 10.1021/jm701217r

  • PubMed Abstract: 
  • We have developed a novel series of potent and selective factor Xa inhibitors that employ a key 7-fluoroindazolyl moiety. The 7-fluoro group on the indazole scaffold replaces the carbonyl group of an amide that is found in previously reported factor ...

    We have developed a novel series of potent and selective factor Xa inhibitors that employ a key 7-fluoroindazolyl moiety. The 7-fluoro group on the indazole scaffold replaces the carbonyl group of an amide that is found in previously reported factor Xa inhibitors. The structure of a factor Xa cocrystal containing 7-fluoroindazole 51a showed the 7-fluoro atom hydrogen-bonding with the N-H of Gly216 (2.9 A) in the peptide backbone. Thus, the 7-fluoroindazolyl moiety not only occupied the same space as the carbonyl group of an amide found in prior factor Xa inhibitors but also maintained a hydrogen bond interaction with the protein's beta-sheet domain. The structure-activity relationship for this series was consistent with this finding, as the factor Xa inhibitory potencies were about 60-fold greater (DeltaDelta G approximately 2.4 kcal/mol) for the 7-fluoroindazoles 25a and 25c versus the corresponding indazoles 25b and 25d. Highly convergent synthesis of these factor Xa inhibitors is also described.


    Organizational Affiliation

    Johnson & Johnson Pharmaceutical Research and Development, Welsh and McKean Roads, Spring House, Pennsylvania 19477-0776, USA.




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 Gene View: F10
Go to UniProtKB:  P00742
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Coagulation factor X
L
51Homo sapiensMutation(s): 1 
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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JNJ
Query on JNJ

Download SDF File 
Download CCD File 
A
1-(3-amino-1,2-benzisoxazol-5-yl)-6-(4-{2-[(dimethylamino)methyl]-1H-imidazol-1-yl}-2-fluorophenyl)-7-fluoro-1H-indazole-3-carboxamide
1-(3-Aminobenzo[d]isoxazol-5-yl)-6-[4-(2-dimethylaminomethylimidazol-1-yl)-2-fluorophenyl]-7-fluoro-1H-indazole-3-carboxylic Acid Amide
C27 H22 F2 N8 O2
MGUDDBRJHXFTEY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
JNJKi: 15.9 nM (98) BINDINGDB
JNJKi: 15.9 nM BINDINGMOAD
JNJKi: 15.9 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Free: 0.314 
  • R-Value Work: 0.246 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 48.871α = 90.00
b = 74.984β = 90.00
c = 75.089γ = 90.00
Software Package:
Software NamePurpose
PROTEUM PLUSdata collection
CNSrefinement
SAINTdata scaling
SAINTdata reduction
CNSphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2007-09-14 
  • Released Date: 2008-01-29 
  • Deposition Author(s): Abad, M.C.

Revision History 

  • Version 1.0: 2008-01-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance