Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 

Biological assembly 1 assigned by authors and generated by PISA,PQS (software)

Macromolecule Content

• Total Structure Weight: 68.08 kDa 
• Atom Count: 4952 
• Modelled Residue Count: 587 
• Deposited Residue Count: 591 
• Unique protein chains: 4

2EC9

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

• PDB DOI: 10.2210/pdb2EC9/pdb

• Classification: BLOOD CLOTTING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2007-02-13 Released: 2008-02-19 
• Deposition Author(s): Raman, K., Yarlagadda, B.

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Experimental Data Snapshot

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

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

• PubMed: 17505107 
• 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 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.

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Organizational Affiliation: 

BioCryst Pharmaceuticals, 2190 Parkway Lake Drive, Birmingham, AL 35216, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor VII	A [auth L]	142	Homo sapiens	Mutation(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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor VII	B [auth H]	254	Homo sapiens	Mutation(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

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Tissue factor	C [auth T]	75	Homo sapiens	Mutation(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 ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Tissue factor	D [auth U]	120	Homo sapiens	Mutation(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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
24X	P [auth H]	2'-((5-CARBAMIMIDOYLPYRIDIN-2-YLAMINO)METHYL)-4-(ISOBUTYLCARBAMOYL)-4'-VINYLBIPHENYL-2-CARBOXYLIC ACID C27 H29 N5 O3 HHFWQMFTPDFWLM-UHFFFAOYSA-N
FUC	F [auth L]	alpha-L-fucopyranose C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N
ASO	E [auth L]	1,5-anhydro-D-glucitol C6 H12 O5 MPCAJMNYNOGXPB-SLPGGIOYSA-N
CA	G [auth L], H [auth L], I [auth L], J [auth L], K [auth L], L, M [auth L], N [auth L], O [auth H]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CGU	A [auth L]	L-PEPTIDE LINKING	C6 H9 N O6		GLU

Binding Affinity Annotations
ID	Source	Binding Affinity
24X	Binding MOAD:  2EC9	IC50: 4.3 (nM) from 1 assay(s)

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 = 69.78	α = 90
b = 81.41	β = 90
c = 125.35	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
CNX	refinement
d*TREK	data reduction
CrystalClear	data scaling
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-02-13 
• Released Date: 2008-02-19 
Deposition Author(s): Raman, K., Yarlagadda, B.

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