2FES

Orally active thrombin inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.170 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

Literature

Orally active thrombin inhibitors. Part 1: optimization of the P1-moiety.

Mack, H.Baucke, D.Hornberger, W.Lange, U.E.W.Seitz, W.Hoeffken, H.W.

(2006) Bioorg.Med.Chem.Lett. 16: 2641-2647

  • DOI: 10.1016/j.bmcl.2006.02.040
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The synthesis and SAR of novel nanomolar thrombin inhibitors with the common backbone HOOC-CH(2)-d-cyclohexylalanyl-3,4-dehydroprolyl-NH-CH(2)-aryl-C(=NH)NH(2) are described together with their ecarin clotting time (ECT) prolongation as measure for t ...

    The synthesis and SAR of novel nanomolar thrombin inhibitors with the common backbone HOOC-CH(2)-d-cyclohexylalanyl-3,4-dehydroprolyl-NH-CH(2)-aryl-C(=NH)NH(2) are described together with their ecarin clotting time (ECT) prolongation as measure for thrombin inhibition ex vivo. The aryl P1-moiety mimicking the arginine part of the d-Phe-Pro-Arg derived thrombin inhibitors turned out to be a key component for in vitro potency and in vivo activity. Optimization of this part led to compounds with improved antithrombin activity in rats and dogs after oral administration compared to the recently launched anticoagulant melagatran.


    Organizational Affiliation

    Abbott GmbH & Co. KG, D-67061 Ludwigshafen, Germany. helmut.mack@abbott.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thrombin light chain
L
36Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to Gene View: F2
Go to UniProtKB:  P00734
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Thrombin heavy chain
H
259Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to Gene View: F2
Go to UniProtKB:  P00734
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Decapeptide Hirudin Analogue
D
11N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3SP
Query on 3SP

Download SDF File 
Download CCD File 
H
N-(CARBOXYMETHYL)-3-CYCLOHEXYL-D-ALANYL-N-({5-[(E)-AMINO(IMINO)METHYL]THIEN-2-YL}METHYL)-L-PROLINAMIDE
C22 H33 N5 O4 S
WWADFOUMUCMPEO-SJORKVTESA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3SPIC50: 0.98 nM BINDINGMOAD
3SPIC50: 0.98 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.170 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 71.240α = 90.00
b = 72.390β = 101.01
c = 73.060γ = 90.00
Software Package:
Software NamePurpose
CNXrefinement
X-GENdata scaling
CNXphasing
SAINTdata reduction
X-GENdata reduction
SAINTdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2005-12-16 
  • Released Date: 2006-05-09 
  • Deposition Author(s): Hoeffken, H.W.

Revision History 

  • Version 1.0: 2006-05-09
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Type: Other
  • Version 1.4: 2017-10-18
    Type: Refinement description
  • Version 1.5: 2018-04-04
    Type: Data collection