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: 1.65 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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: https://doi.org/10.1021/acsmedchemlett.8b00204
  • Primary Citation of Related Structures:  
    4MPU, 4MPV

  • 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 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

    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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tryptase alpha/beta-1
A, B
245Homo sapiensMutation(s): 0 
Gene Names: TPS1TPS2TPSAB1TPSB1
EC: 3.4.21.59
UniProt & NIH Common Fund Data Resources
Find proteins for Q15661 (Homo sapiens)
Explore Q15661 
Go to UniProtKB:  Q15661
PHAROS:  Q15661
GTEx:  ENSG00000172236 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15661
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
X2A
Query on X2A

Download Ideal Coordinates CCD File 
F [auth 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
MES
Query on MES

Download Ideal Coordinates CCD File 
C [auth A],
G [auth B]
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
PG4
Query on PG4

Download Ideal Coordinates CCD File 
E [auth A],
K [auth B]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A],
H [auth B],
I [auth B],
J [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.157α = 90
b = 78.157β = 90
c = 165.039γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

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