2VWM

Aminopyrrolidine Factor Xa inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.204 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Design of Novel Aminopyrrolidine Factor Xa Inhibitors from a Screening Hit.

Zbinden, K.G.Anselm, L.Banner, D.W.Benz, J.M.Blasco, F.Decoret, G.Himber, J.Kuhn, B.Panday, N.Ricklin, F.Risch, P.Schlatter, D.Stahl, M.Thomi, S.Unger, R.Haap, W.

(2009) Eur J Med Chem 44: 2787

  • DOI: 10.1016/j.ejmech.2008.12.025
  • Primary Citation of Related Structures:  
    2VVC, 2VWL, 2VWM, 2VWN, 2VWO, 2VVU, 2VVV

  • PubMed Abstract: 
  • Starting from a hit identified by focused screening, 3-aminopyrrolidine factor Xa inhibitors were designed. The binding mode as determined by X-ray structural analysis as well as the pharmacokinetic behaviour of selected compounds is discussed.


    Organizational Affiliation

    F Hoffmann - La Roche Ltd, Basel, Switzerland. katrin.groebke_zbinden@roche.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ACTIVATED FACTOR XA HEAVY CHAINA, B241Homo sapiensMutation(s): 1 
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 CHAINC [auth K], D [auth L]55Homo 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 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LZI
Query on LZI

Download Ideal Coordinates CCD File 
E [auth A], G [auth B](4R)-4-{[(5-chlorothiophen-2-yl)carbonyl]amino}-N-(cyclopropylmethyl)-1-(2-{[2-fluoro-4-(2-oxopyridin-1(2H)-yl)phenyl]amino}-2-oxoethyl)-L-prolinamide
C27 H27 Cl F N5 O4 S
LRFNMAKOTZSBFP-UTKZUKDTSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
F [auth A], H [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LZIKi :  93   nM  PDBBind
LZIKi:  93   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.200 
  • R-Value Observed: 0.204 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.93α = 90
b = 77.11β = 92.07
c = 74.87γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-07
    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: 2017-06-28
    Changes: Data collection