1QUR

HUMAN ALPHA-THROMBIN IN COMPLEX WITH BIVALENT, BENZAMIDINE-BASED SYNTHETIC INHIBITOR

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.209 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Design and evaluation of novel bivalent thrombin inhibitors based on amidinophenylalanines.

Steinmetzer, T., Renatus, M., Kunzel, S., Eichinger, A., Bode, W., Wikstrom, P., Hauptmann, J., Sturzebecher, J.

(1999) Eur J Biochem 265: 598-605

  • DOI: 10.1046/j.1432-1327.1999.00742.x
  • Primary Citation of Related Structures:  
    1QUR

  • PubMed Abstract: 

    • Two bivalent thrombin inhibitors were synthesized, which consist of a benzamidine-based active-site-blocking segment, a fibrinogen recognition exosite inhibitor and a peptidic linker connecting these fragments. BZA-1 hirulog contains an Nalpha-(2-naphthylsulfonyl)-S-3-amidinophenylalanyl-is onipecotic acid residue connected via the carboxyl group to the linker segment ...

    Two bivalent thrombin inhibitors were synthesized, which consist of a benzamidine-based active-site-blocking segment, a fibrinogen recognition exosite inhibitor and a peptidic linker connecting these fragments. BZA-1 hirulog contains an Nalpha-(2-naphthylsulfonyl)-S-3-amidinophenylalanyl-is onipecotic acid residue connected via the carboxyl group to the linker segment. The active-site-directed moiety of BZA-2 hirulog [Nalpha-(2-naphthylsulfonyl-glutamyl)-R-4-amidinophenylal anyl-piperid ide] was coupled to the linker via the side chain of the glutamic acid. Both BZA-hirulogs contain almost identical linker-exo site inhibitor parts, except for the substitution of a glycine as the first linker residue in BZA-1 hirulog by a gamma-amino butyric acid in BZA-2 hirulog, thus increasing flexibility and linker length by two additional atoms. BZA-1 hirulog showed moderate potency (Ki = 0. 50 +/- 0.14 nM), while BZA-2 hirulog was characterized as a slow, tight binding inhibitor of thrombin (Ki = 0.29 +/- 0.08 pM). The stability in human plasma of both analogs was strongly improved compared with hirulog-1. For BZA-2 hirulog a significantly reduced plasma clearance was observed after intravenous injection in rats compared with BZA-1 hirulog and hirulog-1. The X-ray structure of the BZA-2 hirulog in complex with human alpha-thrombin was solved and confirmed the expected bivalent binding mode.

    Organizational Affiliation: 

    Friedrich-Schiller-Universität, Institut für Biochemie & Biophysik, Jena, Germany. steinmetzer@merlin.biologie.uni-jena.de



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HUMAN THROMBIN (ALPHA CHAIN)A [auth L]27Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
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Find proteins for P00734 (Homo sapiens)
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Go to UniProtKB:  P00734
PHAROS:  P00734
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UniProt GroupP00734
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
HUMAN THROMBIN (BETA CHAIN)B [auth H]257Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
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Find proteins for P00734 (Homo sapiens)
Explore P00734 
Go to UniProtKB:  P00734
PHAROS:  P00734
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UniProt GroupP00734
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
BIVALENT INHIBITOR (BZA-2 HIRULOG)C [auth I]19N/AMutation(s): 0 
Entity Groups  
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Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ALC
Query on ALC		C [auth I]L-PEPTIDE LINKINGC9 H17 N O2ALA
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.209 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.32α = 90
b = 72.41β = 100.27
c = 72.33γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
CNSrefinement
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-10-14
    Type: Initial release
  • Version 1.1: 2008-04-27
    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