3V7T

Crystal Structure of Human Beta-Tryptase Complexed with a Synthetic Inhibitor with a Tropanylamide Scaffold


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

A beta-tryptase inhibitor with a tropanylamide scaffold to improve in vitro stability and to lower hERG channel binding affinity

Liang, G.Choi-Sledeski, Y.M.Shum, P.Chen, X.Poli, G.B.Kumar, V.Minnich, A.Wang, Q.Tsay, J.Sides, K.Kang, J.Zhang, Y.

(2012) Bioorg Med Chem Lett 22: 1606-1610

  • DOI: 10.1016/j.bmcl.2011.12.127
  • Primary Citation of Related Structures:  
    3V7T

  • PubMed Abstract: 
  • Tropanylamide was investigated as a possible scaffold for β-tryptase inhibitors with a basic benzylamine P1 group and a substituted thiophene P4 group. Comparing to piperidinylamide, the tropanylamide scaffold is much more rigid, which presents less ...

    Tropanylamide was investigated as a possible scaffold for β-tryptase inhibitors with a basic benzylamine P1 group and a substituted thiophene P4 group. Comparing to piperidinylamide, the tropanylamide scaffold is much more rigid, which presents less opportunity for the inhibitor to bind with off-target proteins, such as cytochrome P450, SSAO, and hERG potassium channel. The proposed binding mode was further confirmed by an in-house X-ray structure through co-crystallization.


    Organizational Affiliation

    Molecular Innovative Therapeutics, Sanofi Pharmaceuticals, Bridgewater, NJ 08807, USA. guyan.liang@sanofi-aventis.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
TPSB2 proteinA, B, C, D245Homo sapiensMutation(s): 0 
Gene Names: TPSB2TPS2
EC: 3.4.21.59
Find proteins for P20231 (Homo sapiens)
Explore P20231 
Go to UniProtKB:  P20231
NIH Common Fund Data Resources
PHAROS  P20231
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0GX
Query on 0GX

Download CCD File 
A, B, C, D
{(3-exo)-3-[5-(aminomethyl)-2-fluorophenyl]-8-azabicyclo[3.2.1]oct-8-yl}(4-bromo-3-methyl-5-propoxythiophen-2-yl)methanone
C23 H28 Br F N2 O2 S
SZKGHXMOYDKXPX-OSYLJGHBSA-N
 Ligand Interaction
CO3
Query on CO3

Download CCD File 
A, B
CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0GXKi:  62   nM  Binding MOAD
0GXKi :  62   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.09 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.210 
  • Space Group: P 41
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 81.719α = 90
b = 81.719β = 90
c = 170.684γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
BUSTER-TNTrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
BUSTERrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-03-14
    Type: Initial release
  • Version 1.1: 2017-11-08
    Changes: Refinement description