3V7T

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

• PDB DOI: https://doi.org/10.2210/pdb3V7T/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Komagataella pastoris
• Mutation(s): No 


• Deposited: 2011-12-22 Released: 2012-03-14 
• Deposition Author(s): Zhang, Y., Colonna, C., Michot, N.

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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 

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

• PubMed: 22264487 
• DOI: https://doi.org/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 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.

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Organizational Affiliation: 

Molecular Innovative Therapeutics, Sanofi Pharmaceuticals, Bridgewater, NJ 08807, USA. [e-mail]

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

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

Macromolecule Content

• Total Structure Weight: 112.07 kDa 
• Atom Count: 8,360 
• Modelled Residue Count: 968 
• Deposited Residue Count: 980 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
TPSB2 protein	A, B, C, D	245	Homo sapiens	Mutation(s): 0  Gene Names: TPSB2 EC: 3.4.21.59
UniProt & NIH Common Fund Data Resources
Find proteins for P20231 (Homo sapiens) Explore P20231  Go to UniProtKB:  P20231
PHAROS:  P20231 GTEx:  ENSG00000197253

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0GX	E [auth A], G [auth B], I [auth C], J [auth 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
CO3	F [auth A], H [auth B]	CARBONATE ION C O3 BVKZGUZCCUSVTD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
0GX	PDBBind:  3V7T	Ki: 62 (nM) from 1 assay(s)

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 = 81.719	α = 90
b = 81.719	β = 90
c = 170.684	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-14 
Deposition Author(s): Zhang, Y., Colonna, C., Michot, N.

Revision History  

• Version 1.0: 2012-03-14
  Type: Initial release
  
• Version 1.1: 2017-11-08
  Changes: Refinement description
• Version 1.2: 2024-11-27
  Changes: Data collection, Database references, Derived calculations, Structure summary