1B5G

HUMAN THROMBIN COMPLEXED WITH NOVEL SYNTHETIC PEPTIDE MIMETIC INHIBITOR AND HIRUGEN

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.07 Å
  • R-Value Work: 0.164 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Bound structures of novel P3-P1' beta-strand mimetic inhibitors of thrombin.

St Charles, R., Matthews, J.H., Zhang, E., Tulinsky, A.

(1999) J Med Chem 42: 1376-1383

  • DOI: 10.1021/jm980052n
  • Primary Citation of Related Structures:  
    1B5G, 1A46, 1A5G, 1A61

  • PubMed Abstract: 

    • The X-ray crystal structures of four beta-strand-templated active site inhibitors of thrombin containing P1' groups have been determined and refined at about 2.1-A resolution to crystallographic R-values between 0.148 and 0.164. Two of the inhibitors hav ...

    The X-ray crystal structures of four beta-strand-templated active site inhibitors of thrombin containing P1' groups have been determined and refined at about 2.1-A resolution to crystallographic R-values between 0.148 and 0.164. Two of the inhibitors have an alpha-ketoamide functionality at the scissile bond; the other two have a nonhydrolyzable electrophilic group at the P1' position. The binding of lysine is compared with that of arginine at the S1 specificity site, while that of D,L-phenylalanine enantiomorphs is compared in the S3 region of thrombin. Four different P1' moieties bind at the S1' subsite in three different ways. The binding constants vary between 2.0 microM and 70 pM. The bound structures are used to intercorrelate the various binding constants and also lead to insightful inferences concerning binding at the S1' site of thrombin.

    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
    Organizational Affiliation: 

    Department of Chemistry, Michigan State University, East Lansing, Michigan 48823, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ALPHA-THROMBIN 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
GTEx:  ENSG00000180210
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ALPHA-THROMBIN 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
GTEx:  ENSG00000180210
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
HIRUGEN I12Hirudo medicinalisMutation(s): 0 
Find proteins for P09945 (Hirudo medicinalis)
Explore P09945 
Go to UniProtKB:  P09945
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0ZE
Query on 0ZE
Download Ideal Coordinates CCD File 
H
[[[(4S,5S)-4-[[(3S,6S,8aR)-6-azanyl-5-oxo-6-(phenylmethyl)-1,2,3,7,8,8a-hexahydroindolizin-3-yl]carbonylamino]-5-(1,3-b enzothiazol-2-yl)-5-hydroxy-pentyl]amino]-azanyl-methylidene]azanium
C29 H38 N7 O3 S
DKILHAQNHIMEGI-ICSWELKVSA-O		 Ligand Interaction
NA
Query on NA
Download Ideal Coordinates CCD File 
H
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N		 Ligand Interaction
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: 2.07 Å
  • R-Value Work: 0.164 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.84α = 90
b = 72.08β = 100.9
c = 73γ = 90
Software Package:
Software NamePurpose
R-AXISdata collection
R-AXISdata reduction
PROFFTrefinement
R-AXISdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-05-27
    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
  • Version 1.3: 2015-03-25
    Changes: Database references