3PO1

Thrombin in complex with Benzothiazole Guanidine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Discovery of benzothiazole guanidines as novel inhibitors of thrombin and trypsin IV.

Karle, M.Knecht, W.Xue, Y.

(2012) Bioorg.Med.Chem.Lett. 22: 4839-4843

  • DOI: 10.1016/j.bmcl.2012.05.046

  • PubMed Abstract: 
  • In a project to find novel neutral P1 fragments for the synthesis of thrombin inhibitors with improved pharmacokinetic properties, fragments containing a benzothiazole guanidine scaffold were identified as weak thrombin inhibitors. WaterLOGSY (Water- ...

    In a project to find novel neutral P1 fragments for the synthesis of thrombin inhibitors with improved pharmacokinetic properties, fragments containing a benzothiazole guanidine scaffold were identified as weak thrombin inhibitors. WaterLOGSY (Water-Ligand Observed via Gradient SpectroscopY) NMR was used to detect fragments binding to thrombin and these fragments were followed up by Biacore A100 affinity measurements and enzyme assays. A crystal structure of the most potent compound with thrombin was obtained and revealed an unexpected binding mode as well as the key interactions of the fragment with the protein. Based on these results, the structure-based design and synthesis of a small series of optimized novel substituted benzothiazole guanidines with comparatively low pK(a) values was accomplished. Testing of these compounds against human trypsin I and human trypsin IV revealed unexpected inhibitory activity and selectivity of some of the compounds, making them attractive starting points for selective trypsin inhibitors.


    Organizational Affiliation

    AstraZeneca R&D Mölndal, SE-43183 Mölndal, Sweden. Michael.Karle@astrazeneca.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Thrombin light chain
A
27Homo 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
Thrombin heavy chain
B
147Homo 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
Thrombin heavy chain
C
102Homo 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: 4
MoleculeChainsSequence LengthOrganismDetails
thrombin peptide
D
10N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

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Download CCD File 
C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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Download CCD File 
C
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
MKY
Query on MKY

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Download CCD File 
C
ethyl [(2Z)-2-(carbamimidoylimino)-6-hydroxy-1,3-benzothiazol-3(2H)-yl]acetate
C12 H14 N4 O3 S
QHEKEKSMRXTAKP-QINSGFPZSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TYS
Query on TYS
D
L-PEPTIDE LINKINGC9 H11 N O6 STYR
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MKYKd: 95000 nM BINDINGMOAD
MKYKd: 95000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.227 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 68.662α = 90.00
b = 71.414β = 99.82
c = 71.880γ = 90.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
PDB_EXTRACTdata extraction
REFMACrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2010-11-21 
  • Released Date: 2011-11-23 
  • Deposition Author(s): Xue, Y.

Revision History 

  • Version 1.0: 2011-11-23
    Type: Initial release
  • Version 1.1: 2012-07-25
    Type: Database references