2Y80

Structure and property based design of factor Xa inhibitors: pyrrolidin-2-ones with aminoindane and phenylpyrrolidine P4 motifs


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


Literature

Structure and Property Based Design of Factor Xa Inhibitors: Pyrrolidin-2-Ones with Aminoindane and Phenylpyrrolidine P4 Motifs.

Young, R.J.Adams, C.Blows, M.Brown, D.Burns-Kurtis, C.L.Chan, C.Chaudry, L.Convery, M.A.Davies, D.E.Exall, A.M.Foster, G.Harling, J.D.Hortense, E.Irvine, S.Irving, W.R.Jackson, S.Kleanthous, S.Pateman, A.J.Patikis, A.N.Roethka, T.J.Senger, S.Stelman, G.J.Toomey, J.R.West, R.I.Whittaker, C.Zhou, P.Watson, N.S.

(2011) Bioorg Med Chem Lett 21: 1582

  • DOI: 10.1016/j.bmcl.2011.01.131
  • Primary Citation of Related Structures:  
    2Y7Z, 2Y80, 2Y81, 2Y82

  • PubMed Abstract: 
  • The rational design, syntheses and evaluation of potent sulfonamidopyrrolidin-2-one-based factor Xa inhibitors incorporating aminoindane and phenylpyrrolidine P4 motifs are described. These series delivered highly potent anticoagulant compounds with excellent oral pharmacokinetic profiles; however, significant time dependant P450 inhibition was an issue for the aminoindane series, but this was not observed with the phenylpyrrolidine motif, which produced candidate quality molecules with potential for once-daily oral dosing in humans ...

    The rational design, syntheses and evaluation of potent sulfonamidopyrrolidin-2-one-based factor Xa inhibitors incorporating aminoindane and phenylpyrrolidine P4 motifs are described. These series delivered highly potent anticoagulant compounds with excellent oral pharmacokinetic profiles; however, significant time dependant P450 inhibition was an issue for the aminoindane series, but this was not observed with the phenylpyrrolidine motif, which produced candidate quality molecules with potential for once-daily oral dosing in humans.


    Organizational Affiliation

    GlaxoSmithKline, Medicines Research Centre, Stevenage, Hertfordshire, United Kingdom. Rob.J.Young@gsk.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ACTIVATED FACTOR XA HEAVY CHAINA254Homo sapiensMutation(s): 0 
Gene Names: F10
EC: 3.4.21.6
UniProt & NIH Common Fund Data Resources
Find proteins for P00742 (Homo sapiens)
Explore P00742 
Go to UniProtKB:  P00742
PHAROS:  P00742
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
FACTOR X LIGHT CHAINB134Homo sapiensMutation(s): 0 
Gene Names: F10
EC: 3.4.21.6
UniProt & NIH Common Fund Data Resources
Find proteins for P00742 (Homo sapiens)
Explore P00742 
Go to UniProtKB:  P00742
PHAROS:  P00742
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
439 (Subject of Investigation/LOI)
Query on 439

Download Ideal Coordinates CCD File 
C [auth A]6-CHLORO-N-{(3S)-1-[(1S)-1-(DIMETHYLAMINO)-2,3-DIHYDRO-1H-INDEN-5-YL]-2-OXO-3-PYRROLIDINYL}-2-NAPHTHALENESULFONAMIDE
C25 H26 Cl N3 O3 S
DBFTVRMJVISJEX-BJKOFHAPSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
D [auth A]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
E [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
439 BindingDB:  2Y80 Ki: min: 3, max: 9 (nM) from 2 assay(s)
PDBBind:  2Y80 Ki: 9 (nM) from 1 assay(s)
Binding MOAD:  2Y80 Ki: 9 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.192 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.727α = 90
b = 72.012β = 90
c = 78.689γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment  



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2011-03-16
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-10-16
    Changes: Data collection, Experimental preparation, Other