5TP0

Human mesotrypsin in complex with diminazene


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.137 
  • R-Value Work: 0.118 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Small molecule inhibitors of mesotrypsin from a structure-based docking screen.

Kayode, O.Huang, Z.Soares, A.S.Caulfield, T.R.Dong, Z.Bode, A.M.Radisky, E.S.

(2017) PLoS ONE 12: e0176694-e0176694

  • DOI: 10.1371/journal.pone.0176694

  • PubMed Abstract: 
  • PRSS3/mesotrypsin is an atypical isoform of trypsin, the upregulation of which has been implicated in promoting tumor progression. To date there are no mesotrypsin-selective pharmacological inhibitors which could serve as tools for deciphering the pa ...

    PRSS3/mesotrypsin is an atypical isoform of trypsin, the upregulation of which has been implicated in promoting tumor progression. To date there are no mesotrypsin-selective pharmacological inhibitors which could serve as tools for deciphering the pathological role of this enzyme, and could potentially form the basis for novel therapeutic strategies targeting mesotrypsin. A virtual screen of the Natural Product Database (NPD) and Food and Drug Administration (FDA) approved Drug Database was conducted by high-throughput molecular docking utilizing crystal structures of mesotrypsin. Twelve high-scoring compounds were selected for testing based on lowest free energy docking scores, interaction with key mesotrypsin active site residues, and commercial availability. Diminazene (CID22956468), along with two similar compounds presenting the bis-benzamidine substructure, was validated as a competitive inhibitor of mesotrypsin and other human trypsin isoforms. Diminazene is the most potent small molecule inhibitor of mesotrypsin reported to date with an inhibitory constant (Ki) of 3.6±0.3 μM. Diminazene was subsequently co-crystalized with mesotrypsin and the crystal structure was solved and refined to 1.25 Å resolution. This high resolution crystal structure can now offer a foundation for structure-guided efforts to develop novel and potentially more selective mesotrypsin inhibitors based on similar molecular substructures.


    Organizational Affiliation

    Department of Cancer Biology, Mayo Clinic Comprehensive Cancer Center, Jacksonville, Florida, United States of America.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Trypsin-3
A
224Homo sapiensMutation(s): 0 
Gene Names: PRSS3 (PRSS4, TRY3, TRY4)
EC: 3.4.21.4
Find proteins for P35030 (Homo sapiens)
Go to Gene View: PRSS3
Go to UniProtKB:  P35030
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BRN
Query on BRN

Download SDF File 
Download CCD File 
A
BERENIL
DIMINAZINE ACETURATE; 1,3-TRIS-(4'AMIDINOPHENYL)TRIAZINE
C14 H15 N7
XNYZHCFCZNMTFY-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.137 
  • R-Value Work: 0.118 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 40.916α = 90.00
b = 64.443β = 90.00
c = 80.675γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
HKL-2000data reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer InstituteUnited StatesR01CA154387

Revision History 

  • Version 1.0: 2017-05-17
    Type: Initial release
  • Version 1.1: 2017-08-23
    Type: Data collection
  • Version 1.2: 2017-09-06
    Type: Author supporting evidence
  • Version 1.3: 2017-11-22
    Type: Refinement description