2XBW

Factor Xa in complex with a pyrrolidine-3,4-dicarboxylic acid inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.192 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Discovery of a Factor Xa Inhibitor (3R,4R)-1-(2,2-Difluoro-Ethyl)-Pyrrolidine-3,4-Dicarboxylic Acid 3-[(5-Chloro-Pyridin-2-Yl)-Amide] 4-{[2-Fluoro-4-(2-Oxo-2H-Pyridin-1-Yl)-Phenyl]-Amide} as a Clinical Candidate.

Anselm, L.Banner, D.W.Benz, J.Groebke Zbinden, K.Himber, J.Hilpert, H.Huber, W.Kuhn, B.Mary, J.L.Otteneder, M.B.Panday, N.Ricklin, F.Stahl, M.Thomi, S.Haap, W.

(2010) Bioorg.Med.Chem. 20: 5313

  • DOI: 10.1016/j.bmcl.2010.06.126
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • A series of (3R,4R)-pyrrolidine-3,4-dicarboxylic acid amides was investigated with respect to their factor Xa inhibitory activity, selectivity, pharmacokinetic properties, and ex vivo antithrombotic activity. The clinical candidate from this series, ...

    A series of (3R,4R)-pyrrolidine-3,4-dicarboxylic acid amides was investigated with respect to their factor Xa inhibitory activity, selectivity, pharmacokinetic properties, and ex vivo antithrombotic activity. The clinical candidate from this series, R1663, exhibits excellent selectivity against a panel of serine proteases and good pharmacokinetic properties in rats and monkeys. A Phase I clinical study with R1663 has been finalized.


    Organizational Affiliation

    F. Hoffmann-La Roche Ltd, Pharma Research, Basel, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ACTIVATED FACTOR XA HEAVY CHAIN
A
241Homo sapiensGene 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
L
55Homo sapiensGene 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 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
455
Query on 455

Download SDF File 
Download CCD File 
A
(3R,4R)-1-SULFAMOYL-PYRROLIDINE-3,4-DICARBOXYLIC ACID 3-[(4-CHLORO-PHENYL)-AMIDE] 4-{[2-FLUORO-4-(2-OXO-2H-PYRIDIN-1-YL)-PHENYL]-AMIDE}
C23 H21 Cl F N5 O5 S
GYWPDZGVFZEVMA-ROUUACIJSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
455Ki: 10 nM (100) BINDINGDB
455Ki: 10 nM BINDINGMOAD
455Ki: 10 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.192 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 105.680α = 90.00
b = 105.680β = 90.00
c = 49.650γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
XDSdata scaling
MOLREPphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-08-04
    Type: Initial release
  • Version 1.1: 2012-02-29
    Type: Non-polymer description, Other, Version format compliance
  • Version 1.2: 2017-06-28
    Type: Data collection