Looking for sugars...

Hello everyone,

I have drawn a sugar (furanose form) in 2 different reactions
(see 2 reactions below). However, I am not able to find
reaction "sugar2" with JChem and this sugar (furanose form) as a query, while this structure is found in reaction "sugar1". Is it normal ?
This situation occurs sometimes with sugars and I don't understand the reason. Could you give me an explanation ?
Thank you for your answer.
Best regards,

Vincent

Hi Vincent,

We tried to reproduce the failure, but the missing hit in search (query: the product furanose in sugar1 and sugar2 reactions; target: sugar2.mrv; substructure search) couldn't be reproduced with the latest JChem (5.11.4) version.

Which version of JChem are you using? Have you applied any other search options than default?

Best regards,

Krisztina

Hello Krisztina,

the version of JChem we are using is 5.8.
We didn't apply any other option than substructural search.
Thank you,
Regards,

Vincent

Could you send us the query file as well?

Thanks,

Krisztina

Here it is !
It is simply the sugar with the furanose form.
Best regards,

Vincent

Hi Vincent,

Sorry, but we couldn't reproduce the missing hit neither with JChem 5.8.3 -  running the search in file and in database as well.

What is the result in your environment of running the following command line commands from the installed JChem/bin/ directory?

jcsearch -q sugar-query.mrv sugar2.mrv 


jcsearch -q sugar-query.mrv sugar1.mrv 

Best regards,

Krisztina

 

Hello Krisztina,

we have maybe found two causes for this failure :

1. before drawing reaction "sugar2", I drawn an iron atom connected to the cyclohexyl toward a coordination bond (see file "sugar3"). And I was neither able to find this reaction.


2. Today, "reaction2" is found with exactly the same query although that was not possible yesterday, when I first submitted this message. And this is not the first time that we are able to find a reaction with a substructural search the day after we drawn it in JChem (we use JChem 5.8.2 Dotnet).

Thank you for your help,

Vincent

Hi Vincent,

 

This issue looks to be hard to reproduce. Some problems may depend on the way the query is drawn; for example on atom index differences, etc.

 

Next time when you are able to reproduce this problem I recommend to save the query immediately and send to us.

 

Thanks and best regards,

Szabolcs