1Y59

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.123 

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:  1Y5A, 1Y5B, 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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Trypsin, cationic
T
223Bos taurusEC: 3.4.21.4
Find proteins for P00760 (Bos taurus)
Go to UniProtKB:  P00760
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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T
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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T
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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T
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
TL1
Query on TL1

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T
2,5-BIS-O-{3-[AMINO(IMINO)METHYL]PHENYL}-1,4:3,6-DIANHYDRO-D-GLUCITOL
2,5-O,O-BIS-(3',3"-AMIDINOPHENYL)-1,4:3,6-DIANHYDRO-D-SORBITOL
C20 H22 N4 O4
IBIUTOFGXGGVKQ-XMTFNYHQSA-N
 Ligand Interaction
IMD
Query on IMD

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T
IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
TL1Ki: 1190 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.2 Å
  • R-Value Free: 0.167 
  • R-Value Work: 0.123 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 54.650α = 90.00
b = 54.650β = 90.00
c = 107.990γ = 120.00
Software Package:
Software NamePurpose
HKL-2000data scaling
MAR345data collection
SHELXL-97refinement
AMoREphasing
SHELXmodel building

Structure Validation

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Entry History 

Deposition Data

Revision History 

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