1YPM

X-ray crystal structure of thrombin inhibited by synthetic cyanopeptide analogue RA-1014


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.191 

wwPDB Validation 3D Report Full Report


This is version 1.6 of the entry. See complete history


Literature

Design and X-ray crystal structures of human thrombin with synthetic cyanopeptide-analogues.

Radau, G.Fokkens, J.

(2007) Pharmazie 62: 83-88

  • Primary Citation of Related Structures:  
    1YPM, 1YPL

  • PubMed Abstract: 
  • Based on the X-ray crystals of cocrystallized cyanopeptide-trypsin and cyanopeptide-thrombin-com-plexes, a rational drug design succeeded in the establishment of suitable lead structures for the development of new potential inhibitors of thrombin. Th ...

    Based on the X-ray crystals of cocrystallized cyanopeptide-trypsin and cyanopeptide-thrombin-com-plexes, a rational drug design succeeded in the establishment of suitable lead structures for the development of new potential inhibitors of thrombin. This report deals with the design and X-ray crystallography data of new synthetic, low-molecular weight cyanopeptide-analogues, RA-1008 and RA-1014, complexed with human alpha-thrombin at 1.85 A resolution. The crystal structures of the complexes reveal, by analogy with modeling studies, that the salt bridge of Asp189 to this type of synthetic thrombin inhibitors leads to an almost identically binding into the S1 specificity pocket in comparison to the complex of the natural products, whereas in the overall binding modes the P2-P4 substructures differ from those of the leads. The strongest member of the second series of described thrombin inhibitors, RA-1014, shows in the crystal complex with thrombin a slightly higher affinity towards the enzyme than RA-1008 as confirmed by inhibition tests. This result and other key informations will be helpful to design a more potent series of inhibitors.


    Organizational Affiliation

    Institute of Pharmacy, Ernst-Moritz-Arndt-University Greifswald, Germany. radau@uni-greifswald.de



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
thrombin light chainL27Homo 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:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Thrombin heavy chainH257Homo 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: 3
MoleculeChainsSequence LengthOrganismDetailsImage
HirudinI10Hirudo medicinalisMutation(s): 0 
Find proteins for P01050 (Hirudo medicinalis)
Explore P01050 
Go to UniProtKB:  P01050
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RA4
Query on RA4

Download CCD File 
H
N-(4-NITROBENZOYL)-L-LEUCYL-N-(4-{[AMINO(IMINO)METHYL]AMINO}BUTYL)-L-PROLINAMIDE
C23 H35 N7 O5
FIZYZWLGMGGGBJ-OALUTQOASA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TYS
Query on TYS
IL-PEPTIDE LINKINGC9 H11 N O6 STYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RA4Ki:  1900   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.191 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.652α = 90
b = 71.721β = 99.73
c = 71.331γ = 90
Software Package:
Software NamePurpose
SHELXmodel building
SHELXL-97refinement
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2005-01-31 
  • Released Date: 2006-01-17 
  • Deposition Author(s): Fokkens, J., Radau, G.

Revision History 

  • Version 1.0: 2006-01-17
    Type: Initial release
  • Version 1.1: 2008-04-30
    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
  • Version 1.4: 2013-03-13
    Changes: Other
  • Version 1.5: 2013-11-13
    Changes: Other
  • Version 1.6: 2017-10-11
    Changes: Refinement description