5F03

TRYPTASE B2 IN COMPLEX WITH 5-(3-Aminomethyl-phenoxymethyl)-3-[3-(2-chloro-pyridin-3-ylethynyl)-phenyl]-oxazolidin-2-one; compound with trifluoro-acetic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.155 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

A Real-World Perspective on Molecular Design.

Kuhn, B.Guba, W.Hert, J.Banner, D.Bissantz, C.Ceccarelli, S.Haap, W.Korner, M.Kuglstatter, A.Lerner, C.Mattei, P.Neidhart, W.Pinard, E.Rudolph, M.G.Schulz-Gasch, T.Woltering, T.Stahl, M.

(2016) J.Med.Chem. 59: 4087-4102

  • DOI: 10.1021/acs.jmedchem.5b01875
  • Primary Citation of Related Structures:  
  • Also Cited By: 6DMI

  • PubMed Abstract: 
  • We present a series of small molecule drug discovery case studies where computational methods were prospectively employed to impact Roche research projects, with the aim of highlighting those methods that provide real added value. Our brief accounts ...

    We present a series of small molecule drug discovery case studies where computational methods were prospectively employed to impact Roche research projects, with the aim of highlighting those methods that provide real added value. Our brief accounts encompass a broad range of methods and techniques applied to a variety of enzymes and receptors. Most of these are based on judicious application of knowledge about molecular conformations and interactions: filling of lipophilic pockets to gain affinity or selectivity, addition of polar substituents, scaffold hopping, transfer of SAR, conformation analysis, and molecular overlays. A case study of sequence-driven focused screening is presented to illustrate how appropriate preprocessing of information enables effective exploitation of prior knowledge. We conclude that qualitative statements enabling chemists to focus on promising regions of chemical space are often more impactful than quantitative prediction.


    Organizational Affiliation

    Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche Ltd. , Grenzacherstrasse 124, 4070 Basel, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tryptase beta-2
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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
5TA
Query on 5TA

Download SDF File 
Download CCD File 
A, B
(5~{S})-5-[[3-(aminomethyl)phenoxy]methyl]-3-[3-[2-(2-chloranylpyridin-3-yl)ethynyl]phenyl]-1,3-oxazolidin-2-one
C24 H20 Cl N3 O3
DALBYXAUBIFWAM-QFIPXVFZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.155 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 78.340α = 90.00
b = 78.340β = 90.00
c = 165.950γ = 120.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACphasing
REFMACrefinement
XPREPdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-02-24
    Type: Initial release
  • Version 1.1: 2016-05-25
    Type: Database references
  • Version 1.2: 2019-03-20
    Type: Data collection, Database references, Source and taxonomy, Structure summary