4MPU

Human beta-tryptase co-crystal structure with (6S,8R)-N,N'-bis[3-({4-[3-(aminomethyl)phenyl]piperidin-1-yl}carbonyl)phenyl]-8-hydroxy-6-(1-hydroxycyclobutyl)-5,7-dioxaspiro[3.4]octane-6,8-dicarboxamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.649 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.178 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Target-Directed Self-Assembly of Homodimeric Drugs Against beta-Tryptase.

Giardina, S.F.Werner, D.S.Pingle, M.Foreman, K.W.Bergstrom, D.E.Arnold, L.D.Barany, F.

(2018) Acs Med.Chem.Lett. 9: 827-831

  • DOI: 10.1021/acsmedchemlett.8b00204
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Tryptase, a serine protease released from mast cells, is implicated in many allergic and inflammatory disorders. Human tryptase is a donut-shaped tetramer with the active sites facing inward forming a central pore. Bivalent ligands spanning two activ ...

    Tryptase, a serine protease released from mast cells, is implicated in many allergic and inflammatory disorders. Human tryptase is a donut-shaped tetramer with the active sites facing inward forming a central pore. Bivalent ligands spanning two active sites potently inhibit this configuration, but these large compounds have poor drug-like properties. To overcome some of these challenges, we developed self-assembling molecules, called coferons, which deliver a larger compound in two parts. Using a pharmacophoric core and reversibly binding linkers to span two active sites, we have successfully produced three novel homodimeric tryptase inhibitors. Upon binding to tryptase, compounds reassembled into flexible homodimers, with significant improvements in IC 50 (0.19 ± 0.08 μM) over controls (5.50 ± 0.09 μM), and demonstrate good activity in mast cell lines. These studies provide validation for this innovative technology that is especially well-suited for the delivery of dimeric drugs to modulate intracellular macromolecular targets.


    Organizational Affiliation

    Coferon, Inc., 25 Health Sciences Drive, Mailbox 123, Stony Brook, New York 11790, United States.,Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 575 Stadium Mall, West Lafayette, Indiana 47907, United States.,Department of Microbiology and Immunology, Weill Cornell Medicine, 1300 York Avenue, Box 62, New York, New York 10065, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tryptase alpha/beta-1
A, B
245Homo sapiensMutation(s): 0 
Gene Names: TPSAB1 (TPS1, TPS2, TPSB1)
EC: 3.4.21.59
Find proteins for Q15661 (Homo sapiens)
Go to Gene View: TPSAB1
Go to UniProtKB:  Q15661
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
PG4
Query on PG4

Download SDF File 
Download CCD File 
A, B
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
X2A
Query on X2A

Download SDF File 
Download CCD File 
B
(6S,8R)-N,N'-bis[3-({4-[3-(aminomethyl)phenyl]piperidin-1-yl}carbonyl)phenyl]-8-hydroxy-6-(1-hydroxycyclobutyl)-5,7-dioxaspiro[3.4]octane-6,8-dicarboxamide
C50 H58 N6 O8
SNRGDRCFKQFZAO-LOYCUKJKSA-N
 Ligand Interaction
MES
Query on MES

Download SDF File 
Download CCD File 
A, B
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.649 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.178 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 78.157α = 90.00
b = 78.157β = 90.00
c = 165.039γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
ADSCdata collection
HKL-2000data reduction
MOLREPphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-03-18
    Type: Initial release
  • Version 1.1: 2019-09-25
    Type: Data collection, Database references