4ZXY

FACTOR VIIA IN COMPLEX WITH THE INHIBITOR (2R)-2-[(1-aminoisoquinolin-6-yl)amino]-4,11-diazatricyclo[14.2.2.1~6,10~]henicosa-1(18),6(21),7,9,16,19-hexaene-3,12-dione


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure-Based Design of Macrocyclic Coagulation Factor VIIa Inhibitors.

Priestley, E.S.Cheney, D.L.DeLucca, I.Wei, A.Luettgen, J.M.Rendina, A.R.Wong, P.C.Wexler, R.R.

(2015) J Med Chem 58: 6225-6236

  • DOI: 10.1021/acs.jmedchem.5b00788
  • Primary Citation of Related Structures:  
    4ZXY, 4ZXX

  • PubMed Abstract: 
  • On the basis of a crystal structure of a phenylpyrrolidine lead and subsequent molecular modeling results, we designed and synthesized a novel series of macrocyclic FVIIa inhibitors. The optimal 16-membered macrocycle was 60-fold more potent than an ...

    On the basis of a crystal structure of a phenylpyrrolidine lead and subsequent molecular modeling results, we designed and synthesized a novel series of macrocyclic FVIIa inhibitors. The optimal 16-membered macrocycle was 60-fold more potent than an acyclic analog. Further potency optimization by incorporation of P1' alkyl sulfone and P2 methyl groups provided a macrocycle with TF/FVIIa Ki = 1.6 nM, excellent selectivity against a panel of seven serine proteases, and FVII-deficient prothrombin time EC2x = 1.2 μM. Discovery of this potent, selective macrocyclic scaffold opens new possibilities for the development of orally bioavailable FVIIa inhibitors.


    Organizational Affiliation

    Department of Global Chemistry, ‡Department of Neuroscience, §Department of Safety Assessment and Laboratory Animal Research, ∥Department of Discovery Pharmaceutical Sciences, and ⊥Department of Pharmacokinetics, Pharmacodynamics, and Drug Metabolism, Merck Research Laboratories , 2015 Galloping Hill Road, Kenilworth, New Jersey 07033, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Coagulation factor VIIa heavy chainH254Homo sapiensMutation(s): 0 
Gene Names: F7
EC: 3.4.21.21
Find proteins for P08709 (Homo sapiens)
Explore P08709 
Go to UniProtKB:  P08709
NIH Common Fund Data Resources
PHAROS  P08709
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Coagulation factor VIIa light chainL55Homo sapiensMutation(s): 0 
Gene Names: F7
EC: 3.4.21.21
Find proteins for P08709 (Homo sapiens)
Explore P08709 
Go to UniProtKB:  P08709
NIH Common Fund Data Resources
PHAROS  P08709
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4T1
Query on 4T1

Download CCD File 
H
(2R)-2-[(1-aminoisoquinolin-6-yl)amino]-4,11-diazatricyclo[14.2.2.1~6,10~]henicosa-1(18),6(21),7,9,16,19-hexaene-3,12-dione
C28 H27 N5 O2
LXFPTSIBSQOGTO-AREMUKBSSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
H
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
H
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
H
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4T1Ki:  920   nM  Binding MOAD
4T1Ki:  400   nM  BindingDB
4T1Ki:  920   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.4α = 90
b = 94.4β = 90
c = 107.85γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2015-05-20 
  • Released Date: 2015-07-22 
  • Deposition Author(s): Wei, A.

Revision History 

  • Version 1.0: 2015-07-22
    Type: Initial release
  • Version 1.1: 2015-08-26
    Changes: Database references