Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - ABC 

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

Macromolecule Content

• Total Structure Weight: 70422.17 
• Atom Count: 3927 
• Residue Count: 624 
• Unique protein chains: 3

2B7D

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

• DOI: 10.2210/pdb2B7D/pdb

• Classification: BLOOD CLOTTING
• Organism(s): Homo sapiens
• Expression System: Escherichia coli, Homo sapiens


• Deposited: 2005-10-04 Released: 2006-02-14 
• Deposition Author(s): 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.

---

Experimental Data Snapshot

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

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

• PubMed: 16412633 
• DOI: 10.1016/j.bmcl.2005.12.059


• 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. 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. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Coagulation factor VII	L	152	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	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: 3
Molecule	Chains	Sequence Length	Organism	Details
Tissue factor	T	218	Homo sapiens	Mutation(s): 0  Gene Names: F3
Find proteins for P13726 (Homo sapiens) Go to Gene View: F3 Go to UniProtKB:  P13726

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
C1B	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

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
C1B	Ki: 1 - 2 nM (100) BINDINGDB
C1B	Ki: 2 nM BINDINGMOAD
C1B	Ki: 2 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free: 0.289 
• R-Value Work: 0.247 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 78.700	α = 90.00
b = 69.030	β = 89.49
c = 78.190	γ = 90.00

Software Package:

Software Name	Purpose
X-sight	model building
Accelrys	model building
ACCELRYS	phasing
X-PLOR	refinement
SCALEPACK	data scaling
X-SIGHT	phasing
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-10-04 
• Released Date: 2006-02-14 
• Deposition Author(s): 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.

Revision History 

• Version 1.0: 2006-02-14
  Type: Initial release
• Version 1.1: 2008-05-01
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2017-10-11
  Type: Refinement description