Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 24.35 kDa 
• Atom Count: 1855 
• Modelled Residue Count: 223 
• Deposited Residue Count: 223 
• Unique protein chains: 1

5EG4

BOVINE TRYPSIN IN COMPLEX WITH CYCLIC INHIBITOR

• PDB DOI: 10.2210/pdb5EG4/pdb

• Classification: HYDROLASE
• Organism(s): Bos taurus
• Mutation(s): No 


• Deposited: 2015-10-26 Released: 2016-07-13 
• Deposition Author(s): Knoerlein, A., Wagner, S., Heine, A., Steinmetzer, T., Klebe, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.32 Å
• R-Value Free: 0.218 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 

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

• PubMed: 27280436 
• DOI: 10.1021/acs.jmedchem.6b00606
• Primary Citation of Related Structures:  
  5EG4


• 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 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Cationic trypsin	A	223	Bos taurus	Mutation(s): 0  EC: 3.4.21.4
UniProt
Find proteins for P00760 (Bos taurus) Explore P00760  Go to UniProtKB:  P00760

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5N7	E [auth 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 C42 H56 N10 O6 S HGZHCKIUQIEHRY-PQQNNWGCSA-N
SO4	C [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACT	D [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
5N7	Binding MOAD:  5EG4	Ki: 21 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.32 Å
• R-Value Free: 0.218 
• R-Value Work: 0.180 
• R-Value Observed: 0.182 
• Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.502	α = 90
b = 61.502	β = 90
c = 102.239	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-10-26 
• Released Date: 2016-07-13 
Deposition Author(s): Knoerlein, A., Wagner, S., Heine, A., Steinmetzer, T., Klebe, G.

Revision History  

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