4JZE

Structure of factor VIIA in complex with the inhibitor 2-{2-[(1-aminoisoquinolin-6-yl)carbamoyl]-6-methoxypyridin-3-yl}-5-{[(2S)-1-hydroxy-3,3-dimethylbutan-2-yl]carbamoyl}benzoic acid

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 

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Ligand Structure Quality Assessment 


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


Literature

Discovery of nonbenzamidine factor VIIa inhibitors using a biaryl acid scaffold.

Bolton, S.A., Sutton, J.C., Anumula, R., Bisacchi, G.S., Jacobson, B., Slusarchyk, W.A., Treuner, U.D., Wu, S.C., Zhao, G., Pi, Z., Sheriff, S., Smirk, R.A., Bisaha, S., Cheney, D.L., Wei, A., Schumacher, W.A., Hartl, K.S., Liu, E., Zahler, R., Seiler, S.M.

(2013) Bioorg Med Chem Lett 23: 5239-5243

  • DOI: 10.1016/j.bmcl.2013.06.028
  • Primary Citation of Related Structures:  
    4JZD, 4JZE, 4JZF

  • PubMed Abstract: 

    • In this Letter, we describe the synthesis of several nonamidine analogs of biaryl acid factor VIIa inhibitor 1 containing weakly basic or nonbasic P1 groups. 2-Aminoisoquinoline was found to be an excellent surrogate for the benzamidine group (compound 2) wherein potent inhibition of factor VIIa is maintained relative to most other related serine proteases ...

    In this Letter, we describe the synthesis of several nonamidine analogs of biaryl acid factor VIIa inhibitor 1 containing weakly basic or nonbasic P1 groups. 2-Aminoisoquinoline was found to be an excellent surrogate for the benzamidine group (compound 2) wherein potent inhibition of factor VIIa is maintained relative to most other related serine proteases. In an unanticipated result, the m-benzamide P1 (compounds 21a and 21b) proved to be a viable benzamidine replacement, albeit with a 20-40 fold loss in potency against factor VIIa.

    Organizational Affiliation: 

    Bristol-Myers Squibb Research & Development, Hopewell, NJ 08534-5400, USA. scott.bolton@bms.com



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Factor VIIa (Heavy Chain)A [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
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(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Factor VIIa (Light Chain)B [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
1NK
Query on 1NK
Download Ideal Coordinates CCD File 
C [auth H]2-{2-[(1-aminoisoquinolin-6-yl)carbamoyl]-6-methoxypyridin-3-yl}-5-{[(2S)-1-hydroxy-3,3-dimethylbutan-2-yl]carbamoyl}benzoic acid
C30 H31 N5 O6
GCBXPOHPNDVIFD-HSZRJFAPSA-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]		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
1NK PDBBind:  4JZE IC50: 7 (nM) from 1 assay(s)
BindingDB:  4JZE IC50: 7 (nM) from 1 assay(s)
Binding MOAD:  4JZE IC50: 7 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.197 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.9α = 90
b = 94.9β = 90
c = 115.4γ = 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: 2013-04-02 
  • Released Date: 2013-08-21 
    • Deposition Author(s): Wei, A., Anumula, R.

Revision History  (Full details and data files)

  • Version 1.0: 2013-08-21
    Type: Initial release
  • Version 1.1: 2013-09-04
    Changes: Database references