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 
  • R-Value Observed: 0.229 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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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
  • Primary Citation of Related Structures:  
    3PO1

  • 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-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 ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Thrombin light chainA27Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens)
Explore P00734 
Go to UniProtKB:  P00734
PHAROS:  P00734
Entity Groups  
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UniProt GroupP00734
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Thrombin heavy chainB147Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens)
Explore P00734 
Go to UniProtKB:  P00734
PHAROS:  P00734
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UniProt GroupP00734
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Thrombin heavy chainC102Homo sapiensMutation(s): 0 
Gene Names: F2
EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens)
Explore P00734 
Go to UniProtKB:  P00734
PHAROS:  P00734
Entity Groups  
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UniProt GroupP00734
Protein Feature View
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
thrombin peptideD10Homo sapiensMutation(s): 0 
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Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MKY
Query on MKY

Download Ideal Coordinates CCD File 
E [auth C]ethyl [(2Z)-2-(carbamimidoylimino)-6-hydroxy-1,3-benzothiazol-3(2H)-yl]acetate
C12 H14 N4 O3 S
QHEKEKSMRXTAKP-QINSGFPZSA-N
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
G [auth C]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
F [auth C]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TYS
Query on TYS
D L-PEPTIDE LINKINGC9 H11 N O6 STYR
Binding Affinity Annotations 
IDSourceBinding Affinity
MKY PDBBind:  3PO1 Kd: 9.50e+4 (nM) from 1 assay(s)
Binding MOAD:  3PO1 Kd: 9.50e+4 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.662α = 90
b = 71.414β = 99.82
c = 71.88γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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