4YT6

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 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: 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 ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence 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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence 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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4JY (Subject of Investigation/LOI)
Query on 4JY

Download Ideal Coordinates CCD File 
C [auth H]4-[[(R)-(5-ethoxy-2-fluoranyl-3-propan-2-yloxy-phenyl)-(4-phenyl-1H-imidazol-2-yl)methyl]amino]benzenecarboximidamide
C28 H30 F N5 O2
FEJKACPKVXNBAK-AREMUKBSSA-N
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
E [auth H], F [auth H], G [auth H], HSULFATE 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
4JY Binding MOAD:  4YT6 Ki: 11 (nM) from 1 assay(s)
BindingDB:  4YT6 Ki: 11 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Free: 0.202 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.178 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.24α = 90
b = 95.24β = 90
c = 117.18γ = 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

  • Deposited Date: 2015-03-17 
  • 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