2B7D

Factor VIIa Inhibitors: Chemical Optimization, Preclinical Pharmacokinetics, Pharmacodynamics, and Efficacy in a Baboon Thrombosis Model

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.250 

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Ligand Structure Quality Assessment 


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


Literature

Factor VIIa inhibitors: Chemical optimization, preclinical pharmacokinetics, pharmacodynamics, and efficacy in an arterial baboon thrombosis model.

Young, W.B., Mordenti, J., Torkelson, S., Shrader, W.D., Kolesnikov, A., Rai, R., Liu, L., Hu, H., Leahy, E.M., Green, M.J., Sprengeler, P.A., Katz, B.A., Yu, C., Janc, J.W., Elrod, K.C., Marzec, U.M., Hanson, S.R.

(2006) Bioorg Med Chem Lett 16: 2037-2041

  • DOI: 10.1016/j.bmcl.2005.12.059
  • Primary Citation of Related Structures:  
    2B7D

  • PubMed Abstract: 

    • Highly selective and potent factor VIIa-tissue factor (fVIIa.TF) complex inhibitors were generated through structure-based design. The pharmacokinetic properties of an optimized analog (9) were characterized in several preclinical species, demonstrating pharmacokinetic characteristics suitable for once-a-day dosing in humans ...

    Highly selective and potent factor VIIa-tissue factor (fVIIa.TF) complex inhibitors were generated through structure-based design. The pharmacokinetic properties of an optimized analog (9) were characterized in several preclinical species, demonstrating pharmacokinetic characteristics suitable for once-a-day dosing in humans. Analog 9 inhibited platelet and fibrin deposition in a dose-dependent manner after intravenous administration in a baboon thrombosis model, and a pharmacodynamic concentration-response model was developed to describe the platelet deposition data. Results for heparin and enoxaparin (Lovenox) in the baboon model are also presented.

    Organizational Affiliation: 

    Celera Genomics, 180 Kimball Way, South San Francisco, CA 94080, USA. wendy.young@yahoo.com



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Coagulation factor VIIA [auth L]152Homo sapiensMutation(s): 0 
Gene Names: F7
EC: 3.4.21.21
UniProt & NIH Common Fund Data Resources
Find proteins for P08709 (Homo sapiens)
Explore P08709 
Go to UniProtKB:  P08709
PHAROS:  P08709
GTEx:  ENSG00000057593
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Coagulation factor VIIB [auth H]254Homo sapiensMutation(s): 0 
Gene Names: F7
EC: 3.4.21.21
UniProt & NIH Common Fund Data Resources
Find proteins for P08709 (Homo sapiens)
Explore P08709 
Go to UniProtKB:  P08709
PHAROS:  P08709
GTEx:  ENSG00000057593
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
C1B (Subject of Investigation/LOI)
Query on C1B
Download Ideal Coordinates CCD File 
 D [auth H](2R)-2-[5-(5-CARBAMIMIDOYL-1H-BENZOIMIDAZOL-2-YL)-6,2'-DIHYDROXY-5'-UREIDOMETHYL-BIPHENYL-3-YL]-SUCCINIC ACID
C26 H24 N6 O7
JCBJULMYEXYZRC-CQSZACIVSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
C1B PDBBind:  2B7D Ki: 2 (nM) from 1 assay(s)
BindingDB:  2B7D Ki: min: 1, max: 2 (nM) from 2 assay(s)
Binding MOAD:  2B7D Ki: 2 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.250 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.7α = 90
b = 69.03β = 89.49
c = 78.19γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-sightmodel building
Accelrysmodel building
X-PLORrefinement
X-SIGHTphasing
ACCELRYSphasing

Structure Validation

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Ligand Structure Quality Assessment  


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-02-14
    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: Refinement description