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 

wwPDB Validation 3D Report Full Report


This is version 1.5 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: 10.1016/j.bmcl.2006.01.046
  • Structures With Same Primary Citation

  • 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 P ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thrombin light chain
L
34Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS  P00734
Protein Feature View
  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

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 UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS  P00734
Protein Feature View
  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
synthetic peptide
P
11N/AMutation(s): 0 
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA9
Query on NA9

Download CCD File 
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
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000480
Query on PRD_000480
PHIRUDIN ANALOGUEOligopeptide /  Anticoagulant, Antithrombotic

--

Modified Residues  3 Unique
IDChainsTypeFormula2D DiagramParent
ALC
Query on ALC
PL-PEPTIDE LINKINGC9 H17 N O2ALA
HYP
Query on HYP
PL-PEPTIDE LINKINGC5 H9 N O3PRO
SMF
Query on SMF
PL-PEPTIDE LINKINGC10 H13 N O5 SPHE
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
NA9IC50:  20.200000762939453   nM  Binding MOAD
NA9IC50 :  20.200000762939453   nM  PDBBind
NA9IC50:  20.200000762939453   nM  BindingDB
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

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • 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