5I46

Factor VIIA in complex with the inhibitor (2R,15R)-2-[(1-aminoisoquinolin-6-yl)amino]-8-fluoro-7-hydroxy-4,15,17-trimethyl-13-oxa-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: 0.239 
  • R-Value Work: 0.217 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Atropisomer Control in Macrocyclic Factor VIIa Inhibitors.

Glunz, P.W.Mueller, L.Cheney, D.L.Ladziata, V.Zou, Y.Wurtz, N.R.Wei, A.Wong, P.C.Wexler, R.R.Priestley, E.S.

(2016) J.Med.Chem. 59: 4007-4018

  • DOI: 10.1021/acs.jmedchem.6b00244

  • PubMed Abstract: 
  • Incorporation of a methyl group onto a macrocyclic FVIIa inhibitor improves potency 10-fold but is accompanied by atropisomerism due to restricted bond rotation in the macrocyclic structure, as demonstrated by NMR studies. We designed a conformationa ...

    Incorporation of a methyl group onto a macrocyclic FVIIa inhibitor improves potency 10-fold but is accompanied by atropisomerism due to restricted bond rotation in the macrocyclic structure, as demonstrated by NMR studies. We designed a conformational constraint favoring the desired atropisomer in which this methyl group interacts with the S2 pocket of FVIIa. A macrocyclic inhibitor incorporating this constraint was prepared and demonstrated by NMR to reside predominantly in the desired conformation. This modification improved potency 180-fold relative to the unsubstituted, racemic macrocycle and improved selectivity. An X-ray crystal structure of a closely related analogue in the FVIIa active site was obtained and matches the NMR and modeled conformations, confirming that this conformational constraint does indeed direct the methyl group into the S2 pocket as designed. The resulting rationally designed, conformationally stable template enables further optimization of these macrocyclic inhibitors.


    Organizational Affiliation

    Bristol-Myers Squibb Research & Development, 311 Pennington-Rocky Hill Road, Pennington, New Jersey 08534, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Coagulation factor VII (Heavy Chain)
H
254Homo sapiensMutation(s): 0 
Gene Names: F7
EC: 3.4.21.21
Find proteins for P08709 (Homo sapiens)
Go to Gene View: F7
Go to UniProtKB:  P08709
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Coagulation factor VII (Light Chain)
L
55Homo sapiensMutation(s): 0 
Gene Names: F7
EC: 3.4.21.21
Find proteins for P08709 (Homo sapiens)
Go to Gene View: F7
Go to UniProtKB:  P08709
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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

Download SDF File 
Download CCD File 
H
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
67O
Query on 67O

Download SDF File 
Download CCD File 
H
(2R,15R)-2-[(1-aminoisoquinolin-6-yl)amino]-8-fluoro-7-hydroxy-4,15,17-trimethyl-13-oxa-4,11-diazatricyclo[14.2.2.1~6,10~]henicosa-1(18),6(21),7,9,16,19-hexaene-3,12-dione
C30 H30 F N5 O4
XABZFDVRWXGDRR-MRDQGFSESA-N
 Ligand Interaction
MES
Query on MES

Download SDF File 
Download CCD File 
H
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Free: 0.239 
  • R-Value Work: 0.217 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 95.300α = 90.00
b = 95.300β = 90.00
c = 117.300γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2016-02-11 
  • Released Date: 2016-06-22 
  • Deposition Author(s): Wei, A.

Revision History 

  • Version 1.0: 2016-06-22
    Type: Initial release