4JYV

Structure of factor VIIA in complex with the inhibitor (2R)-2-[3-ETHOXY-4-(PROPAN-2-YLOXY)PHENYL]-2-(ISOQUINOLIN-6-YLAMINO)-N-[(3-SULFAMOYLPHENYL)SULFONYL]ETHANAMIDE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history. 


Literature

Nonbenzamidine acylsulfonamide tissue factor-factor VIIa inhibitors.

Glunz, P.W., Zhang, X., Zou, Y., Delucca, I., Nirschl, A.H., Cheng, X., Weigelt, C.A., Cheney, D.L., Wei, A., Anumula, R., Luettgen, J.M., Rendina, A.R., Harpel, M., Luo, G., Knabb, R., Wong, P.C., Wexler, R.R., Priestley, E.S.

(2013) Bioorg Med Chem Lett 23: 5244-5248

  • DOI: 10.1016/j.bmcl.2013.06.027
  • Primary Citation of Related Structures:  
    4JYU, 4JYV

  • PubMed Abstract: 

    • Aminoisoquinoline and isoquinoline groups have successfully replaced the more basic P1 benzamidine group of an acylsulfonamide factor VIIa inhibitor. Inhibitory activity was optimized by the identification of additional hydrophobic and hydrophilic P' binding interactions ...

    Aminoisoquinoline and isoquinoline groups have successfully replaced the more basic P1 benzamidine group of an acylsulfonamide factor VIIa inhibitor. Inhibitory activity was optimized by the identification of additional hydrophobic and hydrophilic P' binding interactions. The molecular details of these interactions were elucidated by X-ray crystallography and molecular modeling. We also show that decreasing the basicity of the P1 group results in improved oral bioavailability in this chemotype.

    Organizational Affiliation: 

    Bristol-Myers Squibb R&D, Pennington, NJ 08534, United States. peter.glunz@bms.com



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Factor VII light chainA [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
GTEx:  ENSG00000057593 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08709
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Factor VII heavy chainB [auth L]55Homo 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
GTEx:  ENSG00000057593 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08709
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1OJ
Query on 1OJ
Download Ideal Coordinates CCD File 
C [auth H](2R)-2-[3-ethoxy-4-(propan-2-yloxy)phenyl]-2-(isoquinolin-6-ylamino)-N-[(3-sulfamoylphenyl)sulfonyl]ethanamide
C28 H30 N4 O7 S2
QHVDUHFNSHQJRC-HHHXNRCGSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
E [auth H],
F [auth H],
G [auth H],
H		SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
I [auth H],
J [auth H],
K [auth H],
L [auth H]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
D [auth H]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
1OJ BindingDB:  4JYV Ki: min: 17, max: 32 (nM) from 2 assay(s)
PDBBind:  4JYV Ki: 17 (nM) from 1 assay(s)
Binding MOAD:  4JYV Ki: 17 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.2α = 90
b = 95.2β = 90
c = 117.5γ = 90
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
BUSTERrefinement

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

  • Deposited Date: 2013-04-01 
  • Released Date: 2013-07-24 
    • Deposition Author(s): Wei, A., Anumula, R.

Revision History  (Full details and data files)

  • Version 1.0: 2013-07-24
    Type: Initial release
  • Version 1.1: 2013-09-11
    Changes: Database references