2FLB

Discovery of a Novel Hydroxy Pyrazole Based Factor IXa Inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.250 

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This is version 1.3 of the entry. See complete history. 


Literature

Discovery of novel hydroxy pyrazole based factor IXa inhibitor.

Vijaykumar, D., Sprengeler, P.A., Shaghafi, M., Spencer, J.R., Katz, B.A., Yu, C., Rai, R., Young, W.B., Schultz, B., Janc, J.

(2006) Bioorg Med Chem Lett 16: 2796-2799

  • DOI: https://doi.org/10.1016/j.bmcl.2006.01.123
  • Primary Citation of Related Structures:  
    2FLB

  • PubMed Abstract: 

    Synthesis and biological data of a novel selective and efficacious factor IXa inhibitor are described along with its crystal structure in factor VIIa.

    • Organizational Affiliation: 

    Celera, 180 Kimball Way, South San Francisco, CA 94080, USA. dvijayku@hotmail.com


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Coagulation factor VIIA [auth L]152Homo sapiensMutation(s): 0 
Gene Names: F7
UniProt & NIH Common Fund Data Resources
Find proteins for P08709 (Homo sapiens)
Explore P08709 
Go to UniProtKB:  P08709
PHAROS:  P08709
GTEx:  ENSG00000057593 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08709
Sequence Annotations
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  • Reference Sequence
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Coagulation factor VIIB [auth H]254Homo sapiensMutation(s): 0 
Gene Names: F7
UniProt & NIH Common Fund Data Resources
Find proteins for P08709 (Homo sapiens)
Explore P08709 
Go to UniProtKB:  P08709
PHAROS:  P08709
GTEx:  ENSG00000057593 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08709
Sequence Annotations
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Tissue factorC [auth T]218Homo sapiensMutation(s): 0 
Gene Names: F3
UniProt & NIH Common Fund Data Resources
Find proteins for P13726 (Homo sapiens)
Explore P13726 
Go to UniProtKB:  P13726
PHAROS:  P13726
GTEx:  ENSG00000117525 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13726
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
6NH
Query on 6NH
Download Ideal Coordinates CCD File 
D [auth H]2-(4-HYDROXY-5-PHENYL-1H-PYRAZOL-3-YL)-1H-BENZOIMIDAZOLE-5-CARBOXAMIDINE
C17 H14 N6 O
CKSIVONWCYACAP-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
6NH PDBBind:  2FLB Ki: 1800 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.280 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.250 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.45α = 90
b = 69.03β = 90.21
c = 78.76γ = 90
Software Package:
Software NamePurpose
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Released Date: 2006-04-04 
    • Deposition Author(s): Katz, B.A.

Revision History  (Full details and data files)

  • Version 1.0: 2006-04-04
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Data collection, Refinement description