1Z6J

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


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 

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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


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

  • 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' ...

    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.


    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

    Organizational Affiliation

    Department of Medicinal and Combinatorial Chemistry, Pfizer Corp., 800 N. Lindbergh Blvd., St. Louis, MO 63167, USA. barbara.a.schweitzer@pfizer.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Coagulation factor VIIA [auth L]142Homo sapiensMutation(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
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Coagulation factor VIIB [auth H]254Homo sapiensMutation(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
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Tissue factorC [auth T]211Homo sapiensMutation(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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PY3 (Subject of Investigation/LOI)
Query on PY3

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
D [auth L], F [auth H]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth L]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CGU
Query on CGU
A [auth L]L-PEPTIDE LINKINGC6 H9 N O6GLU
Binding Affinity Annotations 
IDSourceBinding 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 = 69.652α = 90
b = 81.137β = 90
c = 125.577γ = 90
Software Package:
Software NamePurpose
X-PLORrefinement
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
X-PLORphasing
DENZOdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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