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 mimet ...

    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)L36Homo 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
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ALPHA-THROMBIN (LARGE SUBUNIT)H259Homo 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
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
HIRUGENI12N/AMutation(s): 0 
Find proteins for P09945 (Hirudo medicinalis)
Explore P09945 
Go to UniProtKB:  P09945
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
FPAM (FIBRINOPEPTIDE A MIMIC)T6N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TYS
Query on TYS
IL-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

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Entry History 

Deposition Data

Revision History 

  • 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