Biological Assembly 1  

 3D View: Structure | Electron Density | 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: 70.40 kDa 
• Atom Count: 4812 
• Modelled Residue Count: 591 
• Deposited Residue Count: 617 
• Unique protein chains: 3

2AEI

Crystal structure of a ternary complex of factor VIIa/tissue factor and 2-[[6-[3-(aminoiminomethyl)phenoxy]-3,5-difluro-4-[(1-methyl-3-phenylpropyl)amino]-2-pyridinyl]oxy]-benzoic acid

• DOI: 10.2210/pdb2AEI/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus, Saccharomyces cerevisiae
• Mutation(s): Yes 


• Deposited: 2005-07-22 Released: 2006-08-01 
• Deposition Author(s): Adler, M., Whitlow, M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.52 Å
• R-Value Free: 0.297 
• R-Value Work: 0.199 
• R-Value Observed: 0.204 

Literature

The discovery of fluoropyridine-based inhibitors of the Factor VIIa/TF complex.

Kohrt, J.T., Filipski, K.J., Cody, W.L., Cai, C., Dudley, D.A., Van Huis, C.A., Willardsen, J.A., Rapundalo, S.T., Saiya-Cork, K., Leadley, R.J., Narasimhan, L., Zhang, E., Whitlow, M., Adler, M., McLean, K., Chou, Y.L., McKnight, C., Arnaiz, D.O., Shaw, K.J., Light, D.R., Edmunds, J.J.

(2005) Bioorg Med Chem Lett 15: 4752-4756

• PubMed: 16125385 
• DOI: 10.1016/j.bmcl.2005.07.059
• Primary Citation of Related Structures:  
  2AEI


• PubMed Abstract: 
  

The activated Factor VII/tissue factor complex (FVIIa/TF) plays a key role in the formation of blood clots. Inhibition of this complex may lead to new antithrombotic drugs. An X-ray crystal structure of a fluoropyridine-based FVIIa/TF inhibitor bound in the active site of the enzyme complex suggested that incorporation of substitution at the 5-position of the hydroxybenzoic acid side chain could lead to the formation of more potent inhibitors through interactions with the S1'/S2' pocket.

---

Organizational Affiliation: 

Pfizer Global Research and Development, Michigan Laboratories, 2800 Plymouth Road, Ann Arbor, MI 48105, 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): 10  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]	211	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
03R (Subject of Investigation/LOI)	M [auth H]	2-({6-{3-[AMINO(IMINO)METHYL]PHENOXY}-3,5-DIFLUORO-4-[(1-METHYL-3-PHENYLPROPYL)AMINO]-2-PYRIDINYL}OXY)BENZOIC ACID C29 H26 F2 N4 O4 BUZNVJZUYOBGFM-KRWDZBQOSA-N
CAC	L [auth H]	CACODYLATE ION C2 H6 As O2 OGGXGZAMXPVRFZ-UHFFFAOYSA-M
CA	D [auth L], E [auth L], F [auth L], G [auth L], H [auth L], I [auth L], J [auth L], K [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
03R	PDBBind:  2AEI	IC50: 86 (nM) from 1 assay(s)
	BindingDB:  2AEI	IC50: 86 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.52 Å
• R-Value Free: 0.297 
• R-Value Work: 0.199 
• R-Value Observed: 0.204 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.215	α = 90
b = 80.496	β = 90
c = 125.936	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MERLOT	phasing
X-PLOR	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2005-07-22 
• Released Date: 2006-08-01 
Deposition Author(s): Adler, M., Whitlow, M.

Revision History  

• Version 1.0: 2006-08-01
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance