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 
  • R-Value Observed: 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:  
    2FES, 2FEQ

  • 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 throm ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Thrombin light chain L36Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Explore P00734 
Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS:  P00734
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Thrombin heavy chain H259Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Explore P00734 
Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS:  P00734
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Decapeptide Hirudin Analogue D11Hirudo medicinalisMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3SP
Query on 3SP

Download Ideal Coordinates 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
Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
ALC
Query on ALC
DL-PEPTIDE LINKINGC9 H17 N O2ALA
HYP
Query on HYP
DL-PEPTIDE LINKINGC5 H9 N O3PRO
SMF
Query on SMF
DL-PEPTIDE LINKINGC10 H13 N O5 SPHE
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
3SPIC50 :  0.9800000190734863   nM  PDBBind
3SPIC50:  0.9800000190734863   nM  Binding MOAD
3SPIC50:  1   nM  BindingDB
Biologically Interesting Molecules (External Reference) 2 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.170 
  • R-Value Observed: 0.170 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.24α = 90
b = 72.39β = 101.01
c = 73.06γ = 90
Software Package:
Software NamePurpose
SAINTdata scaling
X-GENdata reduction
CNXrefinement
SAINTdata reduction
X-GENdata scaling
CNXphasing

Structure Validation

View Full Validation Report



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
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Changes: Other
  • Version 1.4: 2017-10-18
    Changes: Refinement description
  • Version 1.5: 2018-04-04
    Changes: Data collection