2WYJ

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 

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 Monoaryl P4 Motifs

Kleanthous, S.Borthwick, A.D.Brown, D.Burns-Kurtis, C.L.Campbell, M.Chaudry, L.Chan, C.Clarte, M.Convery, M.A.Harling, J.D.Hortense, E.Irving, W.R.Irvine, S.Pateman, A.J.Patikis, A.Pinto, I.L.Pollard, D.R.Roethka, T.J.Senger, S.Shah, G.P.Stelman, G.J.Toomey, J.R.Watson, N.S.Whittaker, C.Zhou, P.Young, R.J.

(2010) Bioorg Med Chem Lett 20: 618

  • DOI: 10.1016/j.bmcl.2009.11.077
  • Primary Citation of Related Structures:  
    2WYG, 2WYJ

  • PubMed Abstract: 
  • Structure and property based drug design was exploited in the synthesis of sulfonamidopyrrolidin-2-one-based factor Xa inhibitors, incorporating neutral and basic monoaryl P4 groups, ultimately producing potent inhibitors with effective levels of anticoagulant activity and extended oral pharmacokinetic profiles ...

    Structure and property based drug design was exploited in the synthesis of sulfonamidopyrrolidin-2-one-based factor Xa inhibitors, incorporating neutral and basic monoaryl P4 groups, ultimately producing potent inhibitors with effective levels of anticoagulant activity and extended oral pharmacokinetic profiles. However, time dependant inhibition of Cytochrome P450 3A4 was a particular issue with this series.


    Organizational Affiliation

    GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, United Kingdom.



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
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  • 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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
898 (Subject of Investigation/LOI)
Query on 898

Download Ideal Coordinates CCD File 
C [auth A](E)-2-(5-CHLOROTHIOPHEN-2-YL)-N-[(3S)-1-{4-[(1S)-1-(DIMETHYLAMINO)ETHYL]-2-FLUOROPHENYL}-2-OXOPYRROLIDIN-3-YL]ETHENESULFONAMIDE
C20 H23 Cl F N3 O3 S2
AFDHTIFDRFSZDA-WZMLOTFKSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
898 Binding MOAD:  2WYJ Ki: 1 (nM) from 1 assay(s)
BindingDB:  2WYJ Ki: min: 0.8, max: 1 (nM) from 2 assay(s)
PDBBind:  2WYJ Ki: 1 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.564α = 90
b = 72.485β = 90
c = 78.177γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment  



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2010-12-01
    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: 2019-05-29
    Changes: Data collection, Experimental preparation, Other