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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.0 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: 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 ...

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence 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)
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
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)
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
7KR (Subject of Investigation/LOI)
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
 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
7KR BindingDB:  5TQF Ki: min: 5, max: 58 (nM) from 2 assay(s)
Binding MOAD:  5TQF Ki: 5 (nM) from 1 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

  • Deposited Date: 2016-10-24 
  • 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