2A2X

Orally Active Thrombin Inhibitors in Complex with Thrombin Inh12


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.198 

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Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history


Literature

Orally active thrombin inhibitors. Part 2: optimization of the P2-moiety

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

(2006) Bioorg Med Chem Lett 16: 2648-2653

  • DOI: https://doi.org/10.1016/j.bmcl.2006.01.046
  • Primary Citation of Related Structures:  
    2A2X, 2ANK, 2ANM

  • PubMed Abstract: 

    Synthesis and SAR of orally active thrombin inhibitors of the d-Phe-Pro-Arg type with focus on the P2-moiety are described. The unexpected increase in in vitro potency, oral bioavailability, and in vivo activity of inhibitors with dehydroproline as P2-isostere is discussed. Over a period of 24h the antithrombin activity of the most active inhibitors with IC(50)s in the nanomolar range was determined in dogs demonstrating high thrombin inhibitory activity in plasma and an appropriate duration of action after oral administration.


  • Organizational Affiliation

    Abbott GmbH & Co. KG, D-67061 Ludwigshafen, Germany. udo.lange@abbott.com


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Thrombin light chainA [auth L]34Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens)
Explore P00734 
Go to UniProtKB:  P00734
GTEx:  ENSG00000180210 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00734
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Thrombin heavy chainB [auth H]259Homo sapiensMutation(s): 0 
EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens)
Explore P00734 
Go to UniProtKB:  P00734
GTEx:  ENSG00000180210 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00734
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
synthetic peptideC [auth P]11N/AMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NA9
Query on NA9

Download Ideal Coordinates CCD File 
D [auth H]N-(CARBOXYMETHYL)-3-CYCLOHEXYL-D-ALANYL-N-({6-[AMINO(IMINO)METHYL]PYRIDIN-3-YL}METHYL)-N~2~-METHYL-L-ALANINAMIDE
C22 H34 N6 O4
XVBUQSSETBYPJB-KBXCAEBGSA-N
Modified Residues  3 Unique
IDChains TypeFormula2D DiagramParent
ALC
Query on ALC
C [auth P]L-PEPTIDE LINKINGC9 H17 N O2ALA
HYP
Query on HYP
C [auth P]L-PEPTIDE LINKINGC5 H9 N O3PRO
SMF
Query on SMF
C [auth P]L-PEPTIDE LINKINGC10 H13 N O5 SPHE
Binding Affinity Annotations 
IDSourceBinding Affinity
NA9 PDBBind:  2A2X IC50: 20.2 (nM) from 1 assay(s)
BindingDB:  2A2X IC50: 20.2 (nM) from 1 assay(s)
Biologically Interesting Molecules (External Reference) 1 Unique
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.198 
  • 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
CNSrefinement
PDB_EXTRACTdata extraction
FRAMBOdata collection
SAINTdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-11-14
    Type: Initial release
  • Version 1.1: 2008-04-30
    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: 2017-10-11
    Changes: Refinement description
  • Version 1.5: 2018-04-04
    Changes: Data collection
  • Version 1.6: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary