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 
  • R-Value Observed: 0.157 

Starting Model: other
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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: https://doi.org/10.1021/acs.jmedchem.5b01875
  • Primary Citation of Related Structures:  
    5EDB, 5EDC, 5EDE, 5EDG, 5EDH, 5EDI, 5EZX, 5EZZ, 5F00, 5F01, 5F02, 5F03, 5I2R

  • 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 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Tryptase beta-2
A, B
245Homo sapiensMutation(s): 0 
Gene Names: TPSB2TPS2
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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
5TA
Query on 5TA

Download Ideal Coordinates CCD File 
C [auth A],
D [auth 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.200 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.34α = 90
b = 78.34β = 90
c = 165.95γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XPREPdata scaling
REFMACphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-24
    Type: Initial release
  • Version 1.1: 2016-05-25
    Changes: Database references
  • Version 1.2: 2019-03-20
    Changes: Data collection, Database references, Source and taxonomy, Structure summary
  • Version 1.3: 2024-05-01
    Changes: Data collection, Database references, Refinement description