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Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds.
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CHEBI:173797 name and structure do not fit #4512

Closed ANiknejad closed 2 months ago

ANiknejad commented 2 months ago

hello ChEBI Team,

I am looking for '4(R),8-dimethyl-trans-2-nonenoyl-CoA' aka BiGG CE4806, aka https://www.vmh.life/#metabolite/CE4806

The metabolite currently available is https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:173797 name is '4(R),8-dimethyl-trans-2-nonenoyl-CoA' but structure is dimethyl 3-oxopentanedioate

voilà, voilà...

ANiknejad commented 2 months ago

The mol file of CE4806 should be, I guess, this one here

Ketcher 07112412252D 1 1.00000 0.00000 0

60 62 0 1 0 999 V2000 17.8692 -5.7129 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 17.0612 -5.1256 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 17.5606 -6.6630 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 16.2528 -5.7129 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 16.5617 -6.6630 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 18.1477 -7.4713 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 9.7006 -10.6062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 10.5999 -11.1058 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.8353 -11.1058 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 7.9702 -10.6062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.1049 -11.1058 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.8697 -9.1077 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.9702 -9.6072 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.8697 -8.1087 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 7.1393 -8.1087 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 8.0044 -7.6090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.7348 -6.6100 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.3702 -5.2454 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.8697 -6.1105 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 9.3693 -5.2454 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 8.0044 -6.6100 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 7.1393 -6.1105 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 10.5999 -6.1105 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 12.5980 -6.1105 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 14.5961 -6.1105 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 11.5990 -5.1114 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 11.5990 -7.1095 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 13.5971 -5.1114 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 13.5971 -7.1095 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 11.5990 -6.1105 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0 13.5971 -6.1105 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0 15.3027 -5.4043 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 15.9742 -7.4713 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 14.9751 -8.4704 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 16.9733 -8.4704 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 15.9742 -8.4704 0.0000 P 0 0 0 0 0 0 0 0 0 0 0 0 15.9742 -9.4694 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 18.8194 -5.4043 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 19.5620 -6.0727 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 19.2257 -4.4914 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 20.4271 -5.5733 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 19.5620 -7.0717 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 20.2194 -4.5958 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 21.2922 -6.0724 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 20.4271 -7.5710 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 21.2922 -7.0715 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 22.1573 -5.5730 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 11.4653 -10.6062 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 12.3304 -11.1058 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 12.3304 -12.1048 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 14.0607 -11.1058 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 14.9261 -10.6062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 13.1956 -10.6062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 15.7912 -11.1058 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 16.6565 -10.6062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 17.5216 -11.1059 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 18.3867 -10.6064 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 19.2520 -11.1059 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 14.9261 -9.6072 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 18.3869 -9.6073 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 38 1 1 0 0 2 1 1 0 0 0 3 1 1 0 0 0 4 2 1 0 0 0 5 3 1 0 0 0 3 6 1 6 0 0 4 32 1 1 0 0 5 4 1 0 0 0 5 33 1 6 0 0 9 7 1 0 0 0 7 8 1 0 0 0 8 48 1 0 0 0 10 9 1 0 0 0 13 10 1 0 0 0 10 11 2 0 0 0 12 14 1 0 0 0 13 12 1 0 0 0 16 14 1 0 0 0 16 15 2 0 0 0 16 21 1 0 0 0 19 17 1 0 0 0 17 23 1 0 0 0 19 18 1 0 0 0 21 19 1 0 0 0 19 20 1 0 0 0 21 22 1 6 0 0 23 30 1 0 0 0 30 24 1 0 0 0 24 31 1 0 0 0 31 25 1 0 0 0 32 25 1 0 0 0 30 26 2 0 0 0 30 27 1 0 0 0 31 28 2 0 0 0 31 29 1 0 0 0 33 36 1 0 0 0 36 34 1 0 0 0 36 35 1 0 0 0 36 37 2 0 0 0 39 38 1 0 0 0 40 38 1 0 0 0 41 39 2 0 0 0 42 39 1 0 0 0 43 40 2 0 0 0 44 41 1 0 0 0 43 41 1 0 0 0 45 42 2 0 0 0 46 44 2 0 0 0 47 44 1 0 0 0 46 45 1 0 0 0 48 49 1 0 0 0 49 53 1 0 0 0 49 50 2 0 0 0 53 51 2 0 0 0 51 52 1 0 0 0 52 54 1 0 0 0 54 55 1 0 0 0 55 56 1 0 0 0 56 57 1 0 0 0 57 58 1 0 0 0 52 59 1 6 0 0 57 60 1 0 0 0 M CHG 4 27 -1 29 -1 34 -1 35 -1 M END

ANiknejad commented 2 months ago

why not possible to attach a mol file to the issue, BTW ?

kaxelsen commented 2 months ago

Change the extension to txt, then it is possible

ANiknejad commented 2 months ago

CE4806_corrected copy.txt

ANiknejad commented 2 months ago

@kaxelsen I tried previously with .tsv, not working, but right .txt does, thanks a lot Cheers, Anne

ANiknejad commented 2 months ago

the issue is OPEN, CHEBI:173797 is a bad ChEBI representative!

amalik01 commented 2 months ago

Hi @ANiknejad

I have updated the name of CHEBI:173797 to dimethyl 3-oxopentanedioate Please submit a new entry for 4(R),8-dimethyl-trans-2-nonenoyl-CoA.

ANiknejad commented 2 months ago

Thank you very much, Adnan! I submitted 4(R),8-dimethyl-trans-2-nonenoyl-CoA (4-) CHEBI:231724.