2EC9

Crystal structure analysis of human Factor VIIa , Souluble tissue factor complexed with BCX-3607

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.242 

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


Literature

Probing the S2 site of factor VIIa to generate potent and selective inhibitors: the structure of BCX-3607 in complex with tissue factor-factor VIIa.

Krishnan, R., Kotian, P.L., Chand, P., Bantia, S., Rowland, S., Babu, Y.S.

(2007) Acta Crystallogr D Biol Crystallogr 63: 689-697

  • DOI: 10.1107/S0907444907014187
  • Primary Citation of Related Structures:  
    2EC9

  • PubMed Abstract: 

    • Factor VIIa (FVIIa) is a trypsin-like serine protease in the coagulation cascade. Its complex with tissue factor (TF) triggers the extrinsic pathway of the coagulation cascade, generating a blood clot. Research programs at several centers now recognize t ...

    Factor VIIa (FVIIa) is a trypsin-like serine protease in the coagulation cascade. Its complex with tissue factor (TF) triggers the extrinsic pathway of the coagulation cascade, generating a blood clot. Research programs at several centers now recognize the important roles played by TF and FVIIa in both the thrombotic and inflammatory processes associated with cardiovascular diseases. Therefore, inhibition of the TF-FVIIa complex is seen as a promising target that is key to the development of clinical candidates for various cardiovascular applications. The crystal structure of the TF-FVIIa enzyme complex has been analyzed in order to design and synthesize small-molecule inhibitors. Using structure-based drug design (SBDD), a new series of inhibitors have been discovered that demonstrate high potency against the TF-FVIIa complex while maintaining substantial selectivity versus other closely related serine proteases such as trypsin, thrombin, factor Xa and plasmin.

    Organizational Affiliation: 

    BioCryst Pharmaceuticals, 2190 Parkway Lake Drive, Birmingham, AL 35216, USA. rkrishnan@biocryst.com



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Coagulation factor VII L142Homo sapiensMutation(s): 0 
Gene Names: F7
EC: 3.4.21.21
Find proteins for P08709 (Homo sapiens)
Explore P08709 
Go to UniProtKB:  P08709
NIH Common Fund Data Resources
PHAROS:  P08709
GTEx:  ENSG00000057593
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Coagulation factor VII H254Homo sapiensMutation(s): 0 
Gene Names: F7
EC: 3.4.21.21
Find proteins for P08709 (Homo sapiens)
Explore P08709 
Go to UniProtKB:  P08709
NIH Common Fund Data Resources
PHAROS:  P08709
GTEx:  ENSG00000057593
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Tissue factor T75Homo sapiensMutation(s): 0 
Gene Names: F3
Find proteins for P13726 (Homo sapiens)
Explore P13726 
Go to UniProtKB:  P13726
NIH Common Fund Data Resources
PHAROS:  P13726
GTEx:  ENSG00000117525
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Tissue factor U120Homo sapiensMutation(s): 0 
Gene Names: F3
Find proteins for P13726 (Homo sapiens)
Explore P13726 
Go to UniProtKB:  P13726
NIH Common Fund Data Resources
PHAROS:  P13726
GTEx:  ENSG00000117525
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CGU
Query on CGU		LL-PEPTIDE LINKINGC6 H9 N O6GLU
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
24XIC50:  4.300000190734863   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.242 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.78α = 90
b = 81.41β = 90
c = 125.35γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
CNXrefinement
d*TREKdata reduction
CrystalCleardata scaling
CNXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-02-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.2: 2012-09-05
    Changes: Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Data collection, Derived calculations, Structure summary