2EC9

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.2 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.,Sect.D 63: 689-697

  • DOI: 10.1107/S0907444907014187

  • 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 recogni ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Coagulation factor VII
L
142Homo sapiensGene Names: F7
EC: 3.4.21.21
Find proteins for P08709 (Homo sapiens)
Go to Gene View: F7
Go to UniProtKB:  P08709
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Coagulation factor VII
H
254Homo sapiensGene Names: F7
EC: 3.4.21.21
Find proteins for P08709 (Homo sapiens)
Go to Gene View: F7
Go to UniProtKB:  P08709
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Tissue factor
T
75Homo sapiensGene Names: F3
Find proteins for P13726 (Homo sapiens)
Go to Gene View: F3
Go to UniProtKB:  P13726
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
Tissue factor
U
120Homo sapiensGene Names: F3
Find proteins for P13726 (Homo sapiens)
Go to Gene View: F3
Go to UniProtKB:  P13726
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
H, L
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
FUC
Query on FUC

Download SDF File 
Download CCD File 
L
ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
ASO
Query on ASO

Download SDF File 
Download CCD File 
L
1,5-ANHYDROSORBITOL
C6 H12 O5
MPCAJMNYNOGXPB-SLPGGIOYSA-N
 Ligand Interaction
24X
Query on 24X

Download SDF File 
Download CCD File 
H
2'-((5-CARBAMIMIDOYLPYRIDIN-2-YLAMINO)METHYL)-4-(ISOBUTYLCARBAMOYL)-4'-VINYLBIPHENYL-2-CARBOXYLIC ACID
C27 H29 N5 O3
HHFWQMFTPDFWLM-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CGU
Query on CGU
L
L-PEPTIDE LINKINGC6 H9 N O6GLU
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
24XIC50: 4.3 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.242 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 69.780α = 90.00
b = 81.410β = 90.00
c = 125.350γ = 90.00
Software Package:
Software NamePurpose
CNXphasing
CrystalCleardata scaling
CrystalCleardata collection
CNXrefinement
d*TREKdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-02-19
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Derived calculations, Version format compliance
  • Version 1.2: 2012-09-05
    Type: Database references