5EG4

BOVINE TRYPSIN IN COMPLEX WITH CYCLIC INHIBITOR

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.180 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Optimization of Cyclic Plasmin Inhibitors: From Benzamidines to Benzylamines.

Hinkes, S., Wuttke, A., Saupe, S.M., Ivanova, T., Wagner, S., Knorlein, A., Heine, A., Klebe, G., Steinmetzer, T.

(2016) J.Med.Chem. 59: 6370-6386

  • DOI: 10.1021/acs.jmedchem.6b00606

  • PubMed Abstract: 

    • New macrocyclic plasmin inhibitors based on our previously optimized P2-P3 core segment have been developed. In the first series, the P4 residue was modified, whereas the 4-amidinobenzylamide in P1 position was maintained. The originally used P4 benz ...

    New macrocyclic plasmin inhibitors based on our previously optimized P2-P3 core segment have been developed. In the first series, the P4 residue was modified, whereas the 4-amidinobenzylamide in P1 position was maintained. The originally used P4 benzylsulfonyl residue could be replaced by various sulfonyl- or urethane-like protecting groups. In the second series, the P1 benzamidine was modified and a strong potency and excellent selectivity was retained by incorporation of p-xylenediamine. Several analogues inhibit plasmin in the subnanomolar range, and their potency against related trypsin-like serine proteases including trypsin itself could be further reduced. Selected derivatives have been tested in a plasma fibrinolysis assay and are more effective than the reference inhibitor aprotinin. The crystal structure of one inhibitor was determined in complex with trypsin. The binding mode reveals a sterical clash of the inhibitor's linker segment with the 99-hairpin loop of trypsin, which is absent in plasmin.

    Organizational Affiliation: 

    Department of Pharmacy, Institute of Pharmaceutical Chemistry, Philipps University Marburg , Marbacher Weg 6, D-35032 Marburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cationic trypsin
A
223Bos taurusMutation(s): 0 
EC: 3.4.21.4
Find proteins for P00760 (Bos taurus)
Go to UniProtKB:  P00760
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ACT
Query on ACT
Download SDF File 
Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA
Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
5N7
Query on 5N7
Download SDF File 
Download CCD File 
A
(13S,16R)-N-(4-carbamimidoylbenzyl)-16-((N-cyclohexylsulfamoyl)amino)-3,9,15-trioxo-2,10,14-triaza-6(1,4)-piperazina-1,11(1,4)-dibenzenacycloheptadecaphane-13-carboxamide
MI-133
C42 H56 N10 O6 S
HGZHCKIUQIEHRY-PQQNNWGCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.32 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.180 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 61.502α = 90.00
b = 61.502β = 90.00
c = 102.239γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-07-13
    Type: Initial release
  • Version 1.1: 2016-07-27
    Type: Database references