4ISH | pdb_00004ish

Structure of FACTOR VIIA in complex with the inhibitor BMS-593214 also known as 2'-[(6R,6AR,11BR)-2-CARBAMIMIDOYL-6,6A,7,11B-TETRAHYDRO-5H-INDENO[2,1-C]QUINOLIN-6-YL]-5'-HYDROXY-4'-METHOXYBIPHENYL-4-CARBOXYLIC ACID


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 
    0.213 (Depositor), 0.204 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 
    0.196 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 1GEClick on this verticalbar to view details

This is version 1.1 of the entry. See complete history


Literature

Discovery and gram-scale synthesis of BMS-593214, a potent, selective FVIIa inhibitor.

Priestley, E.S.De Lucca, I.Zhou, J.Zhou, J.Saiah, E.Stanton, R.Robinson, L.Luettgen, J.M.Wei, A.Wen, X.Knabb, R.M.Wong, P.C.Wexler, R.R.

(2013) Bioorg Med Chem Lett 23: 2432-2435

  • DOI: https://doi.org/10.1016/j.bmcl.2013.02.013
  • Primary Citation of Related Structures:  
    4ISH

  • PubMed Abstract: 

    A 6-amidinotetrahydroquinoline screening hit was driven to a structurally novel, potent, and selective FVIIa inhibitor through a combination of library synthesis and rational design. An efficient gram-scale synthesis of the active enantiomer BMS-593214 was developed, which required significant optimization of the key Povarov annulation. Importantly, BMS-593214 showed antithrombotic efficacy in a rabbit arterial thrombosis model. A crystal structure of BMS-593214 bound to FVIIa highlights key contacts with Asp 189, Lys 192, and the S2 pocket.


  • Organizational Affiliation

    Bristol-Myers Squibb Pharmaceutical Research Institute, Experimental Station, PO Box 80500, Wilmington, DE 19880, USA. scott.priestley@bms.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Factor VII heavy 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
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Factor VII light 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
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
1GE
Query on 1GE

Download Ideal Coordinates CCD File 
C [auth H]2'-[(6R,6aR,11bR)-2-carbamimidoyl-6,6a,7,11b-tetrahydro-5H-indeno[2,1-c]quinolin-6-yl]-5'-hydroxy-4'-methoxybiphenyl-4-carboxylic acid
C31 H27 N3 O4
UZOHOGNUODEPEP-USOMCTOXSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
D [auth H]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
1GE BindingDB:  4ISH Ki: 1.9 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free:  0.213 (Depositor), 0.204 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.186 (DCC) 
  • R-Value Observed: 0.196 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.282α = 90
b = 95.282β = 90
c = 116.735γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
CNXrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted 1GEClick on this verticalbar to view details

Entry History 

Deposition Data

  • Released Date: 2013-03-20 
  • Deposition Author(s): Wei, A.

Revision History  (Full details and data files)

  • Version 1.0: 2013-03-20
    Type: Initial release
  • Version 1.1: 2024-10-09
    Changes: Data collection, Database references, Derived calculations, Structure summary