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: 2.90 Å
  • R-Value Work: 0.216 
  • R-Value Observed: 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: https://doi.org/10.1016/j.bmcl.2004.08.034
  • Primary Citation of Related Structures:  
    1X7A

  • 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 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: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Coagulation Factor IXaA [auth C]235Sus scrofaMutation(s): 0 
EC: 3.4.21.22
UniProt
Find proteins for P16293 (Sus scrofa)
Explore P16293 
Go to UniProtKB:  P16293
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16293
Sequence Annotations
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Coagulation Factor IX, light chainB [auth L]146Sus scrofaMutation(s): 0 
UniProt
Find proteins for P16293 (Sus scrofa)
Explore P16293 
Go to UniProtKB:  P16293
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16293
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
187
Query on 187
Download Ideal Coordinates 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
Binding Affinity Annotations 
IDSourceBinding Affinity
187 PDBBind:  1X7A Ki: 13 (nM) from 1 assay(s)
BindingDB:  1X7A Ki: 13 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Work: 0.216 
  • R-Value Observed: 0.216 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 129α = 90
b = 129β = 90
c = 71.3γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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