5TQF

Factor VIIa in complex with the inhibitor (11R)-11-[(1-aminoisoquinolin-6-yl)amino]-16-(cyclopropylsulfonyl)-13-methyl-2,13-diazatricyclo[13.3.1.1~6,10~]icosa-1(19),6(20),7,9,15,17-hexaene-3,12-dione


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Design and Synthesis of Novel Meta-Linked Phenylglycine Macrocyclic FVIIa Inhibitors.

Richter, J.M.Cheney, D.L.Bates, J.A.Wei, A.Luettgen, J.M.Rendina, A.R.Harper, T.M.Narayanan, R.Wong, P.C.Seiffert, D.Wexler, R.R.Priestley, E.S.

(2017) ACS Med Chem Lett 8: 67-72

  • DOI: https://doi.org/10.1021/acsmedchemlett.6b00375
  • Primary Citation of Related Structures:  
    5TQE, 5TQF, 5TQG

  • PubMed Abstract: 

    Two novel series of meta-linked phenylglycine-based macrocyclic FVIIa inhibitors have been designed to improve the rodent metabolic stability and PK observed with the precursor para-linked phenylglycine macrocycles. Through iterative structure-based design and optimization, the TF/FVIIa K i was improved to subnanomolar levels with good clotting activity, metabolic stability, and permeability.


  • Organizational Affiliation

    Research & Development, Bristol-Myers Squibb , Hopewell, New Jersey 08534, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence 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)
Go to UniProtKB:  P08709
PHAROS:  P08709
GTEx:  ENSG00000057593 
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence 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)
Go to UniProtKB:  P08709
PHAROS:  P08709
GTEx:  ENSG00000057593 
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
7KR
Query on 7KR

Download Ideal Coordinates CCD File 
C [auth H](11R)-11-[(1-aminoisoquinolin-6-yl)amino]-16-(cyclopropylsulfonyl)-13-methyl-2,13-diazatricyclo[13.3.1.1~6,10~]icosa-1(19),6(20),7,9,15,17-hexaene-3,12-dione
C31 H31 N5 O4 S
LGIRRDHRFMYVGC-GDLZYMKVSA-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],
K [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
7KR BindingDB:  5TQF Ki: min: 5, max: 58 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.184 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 95.3α = 90
b = 95.3β = 90
c = 116.6γ = 90
Software Package:
Software NamePurpose
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
AMoREphasing
BUSTERrefinement

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • Released Date: 2017-02-01 
  • Deposition Author(s): Wei, A.

Revision History  (Full details and data files)

  • Version 1.0: 2017-02-01
    Type: Initial release
  • Version 1.1: 2023-10-04
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2024-10-09
    Changes: Structure summary