1A5G

HUMAN THROMBIN COMPLEXED WITH NOVEL SYNTHETIC PEPTIDE MIMETIC INHIBITOR AND HIRUGEN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Work: 0.158 

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:  

  • 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 ...

    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 Coagulation Fibrinolysis 4: 305


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ALPHA-THROMBIN (SMALL SUBUNIT)
L
36Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to Gene View: F2
Go to UniProtKB:  P00734
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
ALPHA-THROMBIN (LARGE SUBUNIT)
H
259Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens)
Go to Gene View: F2
Go to UniProtKB:  P00734
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
HIRUGEN
I
12Hirudo medicinalisMutation(s): 0 
Find proteins for P09945 (Hirudo medicinalis)
Go to UniProtKB:  P09945
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
H
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
00L
Query on 00L

Download SDF File 
Download CCD File 
H
(1S,7S)-7-amino-7-benzyl-N-[(1S)-4-carbamimidamido-1-{(1S)-1-hydroxy-2-oxo-2-[(2-phenylethyl)amino]ethyl}butyl]-8-oxohexahydro-1H-pyrazolo[1,2-a]pyridazine-1-carboxamide
MOL-126
C30 H42 N8 O4
BCHJOEWNJFXZEK-DNHJLFCISA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000618 (00L)
Query on PRD_000618
HMOL-126Peptide-like / Thrombin inhibitor

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Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TYS
Query on TYS
I
L-PEPTIDE LINKINGC9 H11 N O6 STYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.06 Å
  • R-Value Work: 0.158 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 70.810α = 90.00
b = 72.250β = 100.80
c = 72.790γ = 90.00
Software Package:
Software NamePurpose
PROFFTrefinement
R-AXISdata collection
R-AXISdata reduction
R-AXISdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-05-27
    Type: Initial release
  • Version 1.1: 2008-03-24
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.3: 2012-12-12
    Type: Other