Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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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: 70294.04 
• Atom Count: 3904 
• Residue Count: 624 
• Unique protein chains: 3

2F9B

Discovery of Novel Heterocyclic Factor VIIa Inhibitors

• DOI: 10.2210/pdb2F9B/pdb

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


• Deposited: 2005-12-05 Released: 2006-02-28 
• Deposition Author(s): Rai, R., Kolesnikov, A., Sprengeler, P.A., Torkelson, S., Ton, T., Katz, B.A., Yu, C., Hendrix, J., Shrader, W.D., Stephens, R., Cabuslay, R., Sanford, E., Young, W.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.54 Å
• R-Value Free: 0.286 
• R-Value Work: 0.226 

Literature

Discovery of novel heterocyclic factor VIIa inhibitors.

Rai, R., Kolesnikov, A., Sprengeler, P.A., Torkelson, S., Ton, T., Katz, B.A., Yu, C., Hendrix, J., Shrader, W.D., Stephens, R., Cabuslay, R., Sanford, E., Young, W.B.

(2006) Bioorg.Med.Chem.Lett. 16: 2270-2273

• PubMed: 16460932 
• DOI: 10.1016/j.bmcl.2006.01.017


• PubMed Abstract: 
  

Structure-activity relationships and binding mode of novel heterocyclic factor VIIa inhibitors will be described. In these inhibitors, a highly basic 5-amidinoindole moiety has been successfully replaced with a less basic 5-aminopyrrolo[3,2-b]pyridine scaffold.

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Organizational Affiliation: 

Celera, 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
N1H	H	{5-(5-AMINO-1H-PYRROLO[3,2-B]PYRIDIN-2-YL)-6-HYDROXY-3'-NITRO-BIPHENYL-3-YL]-ACETIC ACID C21 H16 N4 O5 BVBGZXXLVHYBKI-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
N1H	Ki: 300 nM (100) BINDINGDB
N1H	Ki: 300 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.54 Å
• R-Value Free: 0.286 
• R-Value Work: 0.226 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 78.070	α = 90.00
b = 68.940	β = 90.17
c = 78.730	γ = 90.00

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	refinement
XTALVIEW	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-12-05 
• Released Date: 2006-02-28 
• Deposition Author(s): Rai, R., Kolesnikov, A., Sprengeler, P.A., Torkelson, S., Ton, T., Katz, B.A., Yu, C., Hendrix, J., Shrader, W.D., Stephens, R., Cabuslay, R., Sanford, E., Young, W.B.

Revision History 

• Version 1.0: 2006-02-28
  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: 2017-10-18
  Type: Refinement description