1FPC

ACTIVE SITE MIMETIC INHIBITION OF THROMBIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Observed: 0.147 

wwPDB Validation   3D Report Full Report


This is version 1.3 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
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
thrombinA [auth L]36Homo 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
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
thrombinB [auth H]259Homo 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
Expand
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
HirudinC [auth I]12Hirudo medicinalisMutation(s): 0 
Find proteins for P28504 (Hirudo medicinalis)
Explore P28504 
Go to UniProtKB:  P28504
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0ZI
Query on 0ZI

Download Ideal Coordinates CCD File 
D [auth H]amino{[(4S)-4-({[5-(dimethylamino)naphthalen-1-yl]sulfonyl}amino)-5-(4-ethylpiperidin-1-yl)-5-oxopentyl]amino}methaniminium
C25 H39 N6 O3 S
IIYZWOIELWZHJV-NRFANRHFSA-O
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TYS
Query on TYS
C [auth I]L-PEPTIDE LINKINGC9 H11 N O6 STYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0ZIKi:  100   nM  Binding MOAD
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 4
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000376 (0ZI)
Query on PRD_000376
D [auth H]dansylarginine-N-(3-ethyl-1,5-pentanediyl)amidePeptide-like /  Inhibitor

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Observed: 0.147 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.1α = 90
b = 72.6β = 101
c = 73.8γ = 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: 2008-03-03
    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