Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - AB 

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

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 36273.19 
• Atom Count: 2443 
• Residue Count: 317 
• Unique protein chains: 2

1YGC

Short Factor VIIa with a small molecule inhibitor

• DOI: 10.2210/pdb1YGC/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda


• Deposited: 2005-01-04 Released: 2005-01-18 
• Deposition Author(s): Olivero, A.G., Eigenbrot, C., Goldsmith, R., Robarge, K., Artis, D.R., Flygare, J., Rawson, T., Refino, C., Bunting, S., Kirchhofer, D.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.205 
• R-Value Work: 0.188 

Literature

A selective, slow binding inhibitor of factor VIIa binds to a nonstandard active site conformation and attenuates thrombus formation in vivo.

Olivero, A.G., Eigenbrot, C., Goldsmith, R., Robarge, K., Artis, D.R., Flygare, J., Rawson, T., Sutherlin, D.P., Kadkhodayan, S., Beresini, M., Elliott, L.O., DeGuzman, G.G., Banner, D.W., Ultsch, M., Marzec, U., Hanson, S.R., Refino, C., Bunting, S., Kirchhofer, D.

(2005) J.Biol.Chem. 280: 9160-9169

• PubMed: 15632123 
• DOI: 10.1074/jbc.M409068200


• PubMed Abstract: 
  

The serine protease factor VIIa (FVIIa) in complex with its cellular cofactor tissue factor (TF) initiates the blood coagulation reactions. TF.FVIIa is also implicated in thrombosis-related disorders and constitutes an appealing therapeutic target for treatment of cardiovascular diseases. To this end, we generated the FVIIa active site inhibitor G17905, which displayed great potency toward TF.FVIIa (Ki = 0.35 +/- 0.11 nM). G17905 did not appreciably inhibit 12 of the 14 examined trypsin-like serine proteases, consistent with its TF.FVIIa-specific activity in clotting assays. The crystal structure of the FVIIa.G17905 complex provides insight into the molecular basis of the high selectivity. It shows that, compared with other serine proteases, FVIIa is uniquely equipped to accommodate conformational disturbances in the Gln217-Gly219 region caused by the ortho-hydroxy group of the inhibitor's aminobenzamidine moiety located in the S1 recognition pocket. Moreover, the structure revealed a novel, nonstandard conformation of FVIIa active site in the region of the oxyanion hole, a "flipped" Lys192-Gly193 peptide bond. Macromolecular substrate activation assays demonstrated that G17905 is a noncompetitive, slow-binding inhibitor. Nevertheless, G17905 effectively inhibited thrombus formation in a baboon arterio-venous shunt model, reducing platelet and fibrin deposition by approximately 70% at 0.4 mg/kg + 0.1 mg/kg/min infusion. Therefore, the in vitro potency of G17905, characterized by slow binding kinetics, correlated with efficacious antithrombotic activity in vivo.

---

Organizational Affiliation: 

Department of Medicinal Chemistry, Genentech, Inc., South San Francisco, California 94080, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Coagulation factor VII	H	254	Homo sapiens	Mutation(s): 0  Gene 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
Molecule	Chains	Sequence Length	Organism	Details
Coagulation factor VII	L	63	Homo sapiens	Mutation(s): 0  Gene Names: F7 EC: 3.4.21.21
Find proteins for P08709 (Homo sapiens) Go to Gene View: F7 Go to UniProtKB:  P08709

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	H, L	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
905	H	(R)-4-[2-(3-AMINO-BENZENESULFONYLAMINO)-1-(3,5-DIETHOXY-2-FLUOROPHENYL)-2-OXO-ETHYLAMINO]-2-HYDROXY-BENZAMIDINE C25 H28 F N5 O6 S MLPXCKVDBGAVRJ-HSZRJFAPSA-N
CA	H	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
905	Ki: 0.3 nM (100) BINDINGDB
905	Ki: 0.35 nM BINDINGMOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Free: 0.205 
• R-Value Work: 0.188 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length (Å)	Angle (°)
a = 95.220	α = 90.00
b = 95.220	β = 90.00
c = 116.320	γ = 90.00

Software Package:

Software Name	Purpose
DENZO	data reduction
CNX	refinement
AMoRE	phasing
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-01-04 
• Released Date: 2005-01-18 
• Deposition Author(s): Olivero, A.G., Eigenbrot, C., Goldsmith, R., Robarge, K., Artis, D.R., Flygare, J., Rawson, T., Refino, C., Bunting, S., Kirchhofer, D.

Revision History 

• Version 1.0: 2005-01-18
  Type: Initial release
• Version 1.1: 2008-04-30
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance