3HAT

ACTIVE SITE MIMETIC INHIBITION OF THROMBIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Observed: 0.140 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Active-site mimetic inhibition of thrombin.

Mathews, I.I.Tulinsky, A.

(1995) Acta Crystallogr D Biol Crystallogr 51: 550-559

  • DOI: 10.1107/S0907444994013132
  • Primary Citation of Related Structures:  
    3HAT, 1FPC

  • PubMed Abstract: 
  • The structures of two mimetic inhibitor complexes of human alpha-thrombin have been determined by X-ray crystallography. One mimics a beta-turn with a bicyclic ring system; the other mimics two different active-site binding modes. The beta-turn mimetic is used to approximate a turn found in the conformation of fibrinopeptide A, which is catalytically released by thrombin in the activation of fibrinogen to fibrin ...

    The structures of two mimetic inhibitor complexes of human alpha-thrombin have been determined by X-ray crystallography. One mimics a beta-turn with a bicyclic ring system; the other mimics two different active-site binding modes. The beta-turn mimetic is used to approximate a turn found in the conformation of fibrinopeptide A, which is catalytically released by thrombin in the activation of fibrinogen to fibrin. The binding of the second mimetic is a hybrid between normal substrate and the abnormal binding of the potent natural leech inhibitor hirudin. The binding of the beta-turn mimetic is tenuous, because it is like a substrate, while that of the substrate-hirudin hybrid is that of a tenacious inhibitor (which it is). Structurally retrospect modifications for rational design and improvement of both mimetic inhibitors are proposed.


    Related Citations: 
    • The Structure of a Designed Peptidomimetic Inhibitor Complex of Alpha-Thrombin
      Wu, T.-P., Yee, V., Tulinsky, A., Chrusciel, R.A., Nakanishi, H., Shen, R., Priebe, C., Kahn, M.
      (1993) Protein Eng 6: 471
    • Active Site and Exosite Binding of Alpha-Thrombin
      Tulinsky, A., Qiu, X.
      (1993) Blood Coagul Fibrinolysis 4: 305
    • Interactions of a Fluorescent Active-Site-Directed Inhibitor of Thrombin: Dansylarginine N-(3-Ethyl-1,5-Pentanediyl)Amide
      Nesheim, M.E., Prendergast, F.G., Mann, K.G.
      (1979) Biochemistry 18: 996

    Organizational Affiliation

    Department of Chemistry, Michigan State University, East Lansing 48824, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ALPHA-THROMBIN (SMALL SUBUNIT)A [auth L]36Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens)
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Go to UniProtKB:  P00734
PHAROS:  P00734
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ALPHA-THROMBIN (LARGE SUBUNIT)B [auth H]259Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens)
Explore P00734 
Go to UniProtKB:  P00734
PHAROS:  P00734
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
HIRUGENC [auth I]12N/AMutation(s): 0 
UniProt
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: 4
MoleculeChainsSequence LengthOrganismDetailsImage
FPAM (FIBRINOPEPTIDE A MIMIC)D [auth T]6N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TYS
Query on TYS
C [auth I]L-PEPTIDE LINKINGC9 H11 N O6 STYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Observed: 0.140 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.1α = 90
b = 72.4β = 101
c = 73γ = 90
Software Package:
Software NamePurpose
PROLSQrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1995-02-27
    Type: Initial release
  • Version 1.1: 2008-05-22
    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