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 

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:  

  • 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.

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ACTIVATED FACTOR XA HEAVY CHAIN
A, B
241Homo sapiensMutation(s): 1 
Gene Names: F10
EC: 3.4.21.6
Find proteins for P00742 (Homo sapiens)
Go to Gene View: F10
Go to UniProtKB:  P00742
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
FACTOR X LIGHT CHAIN
K, L
55Homo sapiensMutation(s): 0 
Gene Names: F10
EC: 3.4.21.6
Find proteins for P00742 (Homo sapiens)
Go to Gene View: F10
Go to UniProtKB:  P00742
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
LZI
Query on LZI

Download SDF File 
Download CCD File 
A, 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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
LZIKi: 93 nM (99) BINDINGDB
LZIKi: 93 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.200 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 48.930α = 90.00
b = 77.110β = 92.07
c = 74.870γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
XDSdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-07-07
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-06-28
    Type: Data collection