4YT7

Factor VIIa in complex with the inhibitor 2-(2-{(R)-[(4-carbamimidoylphenyl)amino][5-ethoxy-2-fluoro-3-(propan-2-yloxy)phenyl]methyl}-1H-imidazol-4-yl)benzamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Design and synthesis of potent, selective phenylimidazole-based FVIIa inhibitors.

Glunz, P.W.Cheng, X.Cheney, D.L.Weigelt, C.A.Wei, A.Luettgen, J.M.Wong, P.C.Wexler, R.R.Priestley, E.S.

(2015) Bioorg Med Chem Lett 25: 2169-2173

  • DOI: https://doi.org/10.1016/j.bmcl.2015.03.062
  • Primary Citation of Related Structures:  
    4YT6, 4YT7

  • PubMed Abstract: 

    Heterocyclic amide isosteres were incorporated into a phenylglycine-based tissue factor/factor VIIa (TF-FVIIa) inhibitor chemotype, providing potent inhibitors. An X-ray co-crystal structure of phenylimidazole 19 suggested that an imidazole nitrogen atom effectively mimics an amide carbonyl, while the phenyl ring forms key hydrophobic interactions with the S1' pocket. Exploration of phenylimidazole substitution led to the discovery of potent, selective and efficacious inhibitors of TF-FVIIa.


  • Organizational Affiliation

    Bristol-Myers Squibb R&D, 311 Pennington-Rocky Hill Rd, Pennington, NJ 08534, United States. Electronic address: peter.glunz@bms.com.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Coagulation factor VII (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
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Coagulation factor VII (light chain)B [auth L]57Homo 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 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
4K1
Query on 4K1

Download Ideal Coordinates CCD File 
C [auth H]2-[2-[(R)-[(4-carbamimidoylphenyl)amino]-(5-ethoxy-2-fluoranyl-3-propan-2-yloxy-phenyl)methyl]-1H-imidazol-4-yl]benzamide
C29 H31 F N6 O3
KAQSSNYVMPKBOO-AREMUKBSSA-N
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
GOL
Query on GOL

Download Ideal Coordinates CCD File 
I [auth H],
J [auth H]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
D [auth H]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
4K1 BindingDB:  4YT7 Ki: 1.7 (nM) from 1 assay(s)
Binding MOAD:  4YT7 Ki: 1.7 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.173 
  • R-Value Observed: 0.174 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.4α = 90
b = 94.4β = 90
c = 108.87γ = 90
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2015-04-29 
  • Deposition Author(s): Wei, A.

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-29
    Type: Initial release
  • Version 1.1: 2015-05-13
    Changes: Database references
  • Version 2.0: 2023-09-27
    Changes: Atomic model, Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy