1W7G

Alpha-thrombin complex with sulfated hirudin (residues 54-65) and L- Arginine template inhibitor CS107


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.243 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Design, Synthesis and Evaluation of Graftable Thrombin Inhibitors for the Preparation of Blood-Compatible Polymer Materials.

Salvagnini, C.Michaux, C.Remiche, J.Wouters, J.Charlier, P.Marchand-Brynaert, J.

(2005) Org Biomol Chem 3: 4209

  • DOI: 10.1039/b510239a
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Piperazinyl-amide derivatives of N-alpha-(3-trifluoromethyl-benzenesulfonyl)-L-arginine (1) were synthesized as graftable thrombin inhibitors. The possible disturbance of biological activity due to a variable spacer-arm fixed on the N-4 piperazinyl p ...

    Piperazinyl-amide derivatives of N-alpha-(3-trifluoromethyl-benzenesulfonyl)-L-arginine (1) were synthesized as graftable thrombin inhibitors. The possible disturbance of biological activity due to a variable spacer-arm fixed on the N-4 piperazinyl position was evaluated in vitro, against human alpha-thrombin, and in blood coagulation assay. Molecular modelling (in silico analysis) and X-ray diffraction studies of thrombin-inhibitor complexes were also performed. The fixation of bioactive molecules on poly(butylene terephthalate) (PBT) and poly(ethylene terephthalate) (PET) membranes was performed by wet chemistry treatment and evaluated by XPS analysis. Surface grafting of inhibitor 1d improved the membrane hemocompatibility by reducing blood clot formation on the modified surface.


    Related Citations: 
    • Crystallographic Analysis at 3.0-A Resolution of the Binding to Human Thrombin of Four Active Site-Directed Inhibitors
      Banner, D.W., Hadvary, P.
      (1991) J Biol Chem 30: 20085

    Organizational Affiliation

    Unité de Chimie Organique et Médicinale, Université catholique de Louvain, Bâtiment Lavoisier, place Louis Pasteur 1, B-1348, Louvain-la-Neuve, Belgium.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
THROMBINH259Homo 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: 2
MoleculeChainsSequence LengthOrganismDetails
HIRUDIN II12Hirudo medicinalisMutation(s): 0 
Find proteins for P09945 (Hirudo medicinalis)
Explore P09945 
Go to UniProtKB:  P09945
Protein Feature View
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
THROMBINL36Homo 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
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MIU
Query on MIU

Download CCD File 
H
N-{(1S)-1-{[4-(3-AMINOPROPYL)PIPERAZIN-1-YL]CARBONYL}-4-[(DIAMINOMETHYLENE)AMINO]BUTYL}-3-(TRIFLUOROMETHYL)BENZENESULFONAMIDE
C20 H32 F3 N7 O3 S
KGJKWHCPJPBEJP-KRWDZBQOSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MIUKi:  1900   nM  BindingDB
MIUKi:  13000   nM  Binding MOAD
MIUKi :  8000   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.243 
  • R-Value Observed: 0.243 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.51α = 90
b = 71.343β = 100.59
c = 72.555γ = 90
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-05-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.2: 2019-01-30
    Changes: Data collection, Experimental preparation