Biological Assembly 1  

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

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Macromolecule Content

• Total Structure Weight: 70.42 kDa 
• Atom Count: 4233 
• Modelled Residue Count: 497 
• Deposited Residue Count: 624 
• Unique protein chains: 3

2B7D

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

• PDB DOI: 10.2210/pdb2B7D/pdb

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


• 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free: 0.289 
• R-Value Work: 0.247 
• R-Value Observed: 0.250 

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
• Primary Citation of Related Structures:  
  2B7D


• 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.

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Organizational Affiliation: 

Celera Genomics, 180 Kimball Way, South San Francisco, CA 94080, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor VII	A [auth L]	152	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]	218	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
C1B	D [auth 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

Binding Affinity Annotations
ID	Source	Binding Affinity
C1B	PDBBind:  2B7D	Ki: 2 (nM) from 1 assay(s)
	Binding MOAD:  2B7D	Ki: 2 (nM) from 1 assay(s)
	BindingDB:  2B7D	Ki: min: 1, max: 2 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free: 0.289 
• R-Value Work: 0.247 
• R-Value Observed: 0.250 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.7	α = 90
b = 69.03	β = 89.49
c = 78.19	γ = 90

Software Package:

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

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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description