2VH6

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


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 Biaryl P4 Motifs.

Young, R.J.Borthwick, A.D.Brown, D.Burns-Kurtis, C.L.Campbell, M.Chan, C.Charbaut, M.Chung, C.W.Convery, M.A.Kelly, H.A.Paul King, N.Kleanthous, S.Mason, A.M.Pateman, A.J.Patikis, A.N.Pinto, I.L.Pollard, D.R.Senger, S.Shah, G.P.Toomey, J.R.Watson, N.S.Weston, H.E.

(2008) Bioorg Med Chem Lett 18: 23

  • DOI: 10.1016/j.bmcl.2007.11.023
  • Primary Citation of Related Structures:  
    2VH6

  • PubMed Abstract: 
  • Structure and property based drug design was exploited in the synthesis of sulfonamidopyrrolidin-2-one-based factor Xa (fXa) inhibitors, incorporating biaryl P4 groups, producing highly potent inhibitors with encouraging oral pharmacokinetic profiles and significant but sub-optimal anticoagulant activities ...

    Structure and property based drug design was exploited in the synthesis of sulfonamidopyrrolidin-2-one-based factor Xa (fXa) inhibitors, incorporating biaryl P4 groups, producing highly potent inhibitors with encouraging oral pharmacokinetic profiles and significant but sub-optimal anticoagulant activities.


    Organizational Affiliation

    GlaxoSmithKline, Medicines Research Centre, Gunnels Wood Road, Stevenage, Hertfordshire SG1 2NY, UK. Rob.J.Young@gsk.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ACTIVATED FACTOR XA HEAVY CHAIN A254Homo sapiensMutation(s): 0 
Gene Names: F10
EC: 3.4.21.6
Find proteins for P00742 (Homo sapiens)
Explore P00742 
Go to UniProtKB:  P00742
NIH Common Fund Data Resources
PHAROS:  P00742
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ACTIVATED FACTOR XA LIGHT CHAIN B134Homo sapiensMutation(s): 0 
Gene Names: F10
EC: 3.4.21.6
Find proteins for P00742 (Homo sapiens)
Explore P00742 
Go to UniProtKB:  P00742
NIH Common Fund Data Resources
PHAROS:  P00742
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GSV
Query on GSV

Download Ideal Coordinates CCD File 
A
2-(5-chlorothiophen-2-yl)-N-{(3S)-1-[3-fluoro-2'-(methylsulfonyl)biphenyl-4-yl]-2-oxopyrrolidin-3-yl}ethanesulfonamide
C23 H22 Cl F N2 O5 S3
MRKBPFVJGAHTFU-IBGZPJMESA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GSVKi :  0.20000000298023224   nM  PDBBind
GSVKi:  0.20000000298023224   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.242 
  • R-Value Work: 0.197 
  • R-Value Observed: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.959α = 90
b = 72.309β = 90
c = 78.976γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2008-12-16
    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: 2019-05-08
    Changes: Data collection, Experimental preparation, Other