1Y5B

Dianhydrosugar-based benzamidine, factor Xa specific inhibitor in complex with bovine trypsin mutant

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.160 

wwPDB Validation   3D Report Full Report


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


Literature

Understanding binding selectivity toward trypsin and factor Xa: the role of aromatic interactions

Di Fenza, A., Heine, A., Koert, U., Klebe, G.

(2007) ChemMedChem 2: 297-308

  • DOI: 10.1002/cmdc.200600185
  • Primary Citation of Related Structures:  
    1Y5B, 1Y5A, 1Y59, 1Y5U

  • PubMed Abstract: 

    • A congeneric series of four bis-benzamidine inhibitors sharing a dianhydrosugar isosorbide scaffold in common has been studied by crystal structure analysis and enzyme kinetics with respect to their binding to trypsin and factor Xa. Within the series, aromatic interactions are an important determinant for selectivity discrimination among both serine proteases ...

    A congeneric series of four bis-benzamidine inhibitors sharing a dianhydrosugar isosorbide scaffold in common has been studied by crystal structure analysis and enzyme kinetics with respect to their binding to trypsin and factor Xa. Within the series, aromatic interactions are an important determinant for selectivity discrimination among both serine proteases. To study the selectivity-determining features in detail, we used trypsin mutants in which the original binding site is gradually substituted to finally resemble the factor Xa binding pocket. The influence of these mutations has been analyzed on the binding of the closely related inhibitors. We present the crystal structures of the inhibitor complexes obtained by co-crystallizing an "intermediate" trypsin mutant. They could be determined to a resolution of up to 1.2 A, and we measured the inhibitory activity (K(i)) of each ligand against factor Xa, trypsin, and the various mutants. From these data we were able to derive a detailed structure-activity relationship which demonstrates the importance of aromatic interactions in protein-ligand recognition and their role in modulating enzyme selectivity. Pronounced preference is experienced to accommodate the benzamidine anchor with meta topology in the S(1) specificity pocket. One ligand possessing only para topology deviates strongly from the other members of the series and adopts a distinct binding mode addressing the S(1)' site instead of the distal S(3)/S(4) binding pocket.

    Organizational Affiliation: 

    Institute of Pharmaceutical Chemistry, University of Marburg, Marbacher Weg 6, 35032 Marburg, Germany.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Trypsin, cationicA [auth T]223Bos taurusMutation(s): 2 
EC: 3.4.21.4
Find proteins for P00760 (Bos taurus)
Explore P00760 
Go to UniProtKB:  P00760
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TL3
Query on TL3
Download Ideal Coordinates CCD File 
 E [auth T]2,5-BIS-O-{4-[AMINO(IMINO)METHYL]PHENYL}-1,4:3,6-DIANHYDRO-D-GLUCITOL
C20 H22 N4 O4
CDEVHSIVANGYRI-XMTFNYHQSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
 B [auth T], C [auth T]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
IMD
Query on IMD
Download Ideal Coordinates CCD File 
 F [auth T]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O		 Ligand Interaction
CA
Query on CA
Download Ideal Coordinates CCD File 
 D [auth T]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TL3Kd:  1260   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.160 
  • R-Value Observed: 0.160 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.366α = 90
b = 54.366β = 90
c = 105.14γ = 120
Software Package:
Software NamePurpose
SHELXmodel building
SHELXL-97refinement
CrystalCleardata reduction
HKL-2000data scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-12-13
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description