2RA0

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 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
  • Primary Citation of Related Structures:  
    2RA0

  • 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 Xa inhibitors ...

    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: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Coagulation factor X A234Homo sapiensMutation(s): 0 
Gene Names: F10
EC: 3.4.21.6
Find proteins for P00742 (Homo sapiens)
Explore P00742 
Go to UniProtKB:  P00742
NIH Common Fund Data Resources
PHAROS:  P00742
GTEx:  ENSG00000126218
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Coagulation factor X L51Homo sapiensMutation(s): 1 
Gene Names: F10
EC: 3.4.21.6
Find proteins for P00742 (Homo sapiens)
Explore P00742 
Go to UniProtKB:  P00742
NIH Common Fund Data Resources
PHAROS:  P00742
GTEx:  ENSG00000126218
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JNJ
Query on JNJ
Download Ideal Coordinates 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
C27 H22 F2 N8 O2
MGUDDBRJHXFTEY-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
JNJKi:  15.899999618530273   nM  Binding MOAD
JNJKi :  15.899999618530273   nM  PDBBind
JNJKi:  15.899999618530273   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 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
b = 74.984β = 90
c = 75.089γ = 90
Software Package:
Software NamePurpose
SAINTdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
PROTEUM PLUSdata collection
SAINTdata reduction
CNSphasing

Structure Validation

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Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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