1X7A

Porcine Factor IXa Complexed to 1-{3-[amino(imino)methyl]phenyl}-N-[4-(1H-benzimidazol-1-yl)-2-fluorophenyl]-3-(trifluoromethyl)-1H-pyrazole-5-carboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Work: 0.216 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

SAR and factor IXa crystal structure of a dual inhibitor of factors IXa and Xa

Smallheer, J.M.Alexander, R.S.Wang, J.Wang, S.Nakajima, S.Rossi, K.A.Smallwood, A.Barbera, F.Burdick, D.Luettgen, J.M.Knabb, R.M.Wexler, R.R.Jadhav, P.K.

(2004) Bioorg.Med.Chem.Lett. 14: 5263-5267

  • DOI: 10.1016/j.bmcl.2004.08.034

  • PubMed Abstract: 
  • Modifications to the P4 moiety and pyrazole C3 substituent of factor Xa inhibitor SN-429 provided several new compounds, which are 5-10nM inhibitors of factor IXa. An X-ray crystal structure of one example complexed to factor IXa shows that these com ...

    Modifications to the P4 moiety and pyrazole C3 substituent of factor Xa inhibitor SN-429 provided several new compounds, which are 5-10nM inhibitors of factor IXa. An X-ray crystal structure of one example complexed to factor IXa shows that these compounds adopt a similar binding mode to that previously observed with pyrazole inhibitors in the factor Xa active site both with regard to how the inhibitor binds and the position of Tyr99.


    Organizational Affiliation

    Bristol-Myers Squibb Company, PO Box 5400, Princeton, NJ 08543-5400, USA. joanne.smallheer@bms.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Coagulation Factor IXa
C
235Sus scrofaGene Names: F9
EC: 3.4.21.22
Find proteins for P16293 (Sus scrofa)
Go to Gene View: F9
Go to UniProtKB:  P16293
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Coagulation Factor IX, light chain
L
146Sus scrofaGene Names: F9
EC: 3.4.21.22
Find proteins for P16293 (Sus scrofa)
Go to Gene View: F9
Go to UniProtKB:  P16293
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
187
Query on 187

Download SDF File 
Download CCD File 
C
1-{3-[AMINO(IMINO)METHYL]PHENYL}-N-[4-(1H-BENZIMIDAZOL-1-YL)-2-FLUOROPHENYL]-3-(TRIFLUOROMETHYL)-1H-PYRAZOLE-5-CARBOXAMIDE
C25 H17 F4 N7 O
TWBHVKYRNOGUJS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
187Ki: 13 nM (88) BINDINGDB
187Ki: 13 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Work: 0.216 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 129.000α = 90.00
b = 129.000β = 90.00
c = 71.300γ = 90.00
Software Package:
Software NamePurpose
X-PLORmodel building
SCALEPACKdata scaling
DENZOdata reduction
X-PLORrefinement
X-PLORphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-08-16
    Type: Initial release
  • Version 1.1: 2008-04-30
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance