Biological Assembly 1  

 3D View: Structure | 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: 69.04 kDa 
• Atom Count: 5207 
• Modelled Residue Count: 603 
• Deposited Residue Count: 607 
• Unique protein chains: 3

1Z6J

Crystal Structure of a ternary complex of Factor VIIa/Tissue Factor/Pyrazinone Inhibitor

• DOI: 10.2210/pdb1Z6J/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Cricetinae, Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-03-22 Released: 2005-05-03 
• Deposition Author(s): Schweitzer, B.A., Neumann, W.L., Rahman, H.K., Kusturin, C.L., Sample, K.R., Poda, G.I., Kurumbail, R.G., Stevens, A.M., Stegeman, R.A., Stallings, W.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.258 
• R-Value Work: 0.209 
• R-Value Observed: 0.220 

Literature

Structure-based design and synthesis of pyrazinones containing novel P1 'side pocket' moieties as inhibitors of TF/VIIa.

Schweitzer, B.A., Neumann, W.L., Rahman, H.K., Kusturin, C.L., Sample, K.R., Poda, G.I., Kurumbail, R.G., Stevens, A.M., Stegeman, R.A., Stallings, W.C., South, M.S.

(2005) Bioorg Med Chem Lett 15: 3006-3011

• PubMed: 15913999 
• DOI: 10.1016/j.bmcl.2005.04.037
• Primary Citation of Related Structures:  
  1Z6J


• PubMed Abstract: 
  

We describe the structure-based design, synthesis, and enzymatic activity of a series of substituted pyrazinones as inhibitors of the TF/VIIa complex. These inhibitors contain substituents meta to the P(1) amidine designed to explore additional interactions with the VIIa residues in the so-called 'S(1) side pocket'. A crystal structure of the designed inhibitors demonstrates the ability of the P(1) side pocket moiety to engage Lys192 and main chain of Gly216 via hydrogen bond interactions, thus, providing additional possibility for chemical modification to improve selectivity and/or physical properties of inhibitors.

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Related Citations: 

• Structure-based design of pyrazinone antithrombotics as selective inhibitors of the tissue factor VIIa complex
  South, M.S., Case, B.L., Wood, R.S., Jones, D.E., Hayes, M.J., Girard, T.J., LaChance, R.M., Nicholson, N.S., Clare, M., Stevens, A.M., Stegeman, R.A., Stallings, W.C., Kurumbail, R.G., Parlow, J.J.
  (2003) Bioorg Med Chem Lett 13: 2319

• Polymer-assisted solution-phase library synthesis and crystal structure of alpha-ketothiazoles as tissue factor VIIa inhibitors
  Parlow, J.J., Dice, T.A., LaChance, R.M., Girard, T.J., Stevens, A.M., Stegeman, R.A., Stallings, W.C., Kurumbail, R.G., South, M.S.
  (2003) J Med Chem 46: 4043

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Organizational Affiliation: 

Department of Medicinal and Combinatorial Chemistry, Pfizer Corp., 800 N. Lindbergh Blvd., St. Louis, MO 63167, USA. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor VII	A [auth L]	142	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
PY3 (Subject of Investigation/LOI)	G [auth H]	5-[AMINO(IMINO)METHYL]-2-[({[6-[3-AMINO-5-({[(1R)-1-METHYLPROPYL]AMINO}CARBONYL)PHENYL]-3-(ISOPROPYLAMINO)-2-OXOPYRAZIN-1(2H)-YL]ACETYL}AMINO)METHYL]-N-PYRIDIN-4-YLBENZAMIDE C34 H40 N10 O4 HLQIVSDFLBJBKY-HXUWFJFHSA-N
CA	D [auth L], F [auth H]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
MG	E [auth L]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-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
PY3	PDBBind:  1Z6J	IC50: 9.4 (nM) from 1 assay(s)
	BindingDB:  1Z6J	IC50: 9.4 (nM) from 1 assay(s)
	Binding MOAD:  1Z6J	IC50: 9.4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.258 
• R-Value Work: 0.209 
• R-Value Observed: 0.220 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.652	α = 90
b = 81.137	β = 90
c = 125.577	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	refinement
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
X-PLOR	phasing
DENZO	data reduction

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2005-03-22 
• Released Date: 2005-05-03 
Deposition Author(s): Schweitzer, B.A., Neumann, W.L., Rahman, H.K., Kusturin, C.L., Sample, K.R., Poda, G.I., Kurumbail, R.G., Stevens, A.M., Stegeman, R.A., Stallings, W.C.

Revision History  

• Version 1.0: 2005-05-03
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description