Can you download a 3D structure as pdbqt based on ZINC ID?

[lucyraven]

Hi,

I am hoping it is possible to download 3D structures (as pdbqt) from ZINC22 based on a SMILES string or a ZINC ID, but I haven't yet found a way. Can it be done?

I am designing a screening library based on subsets from many tranches and would prefer not having to download everything just to delete the majority of the files. I select the relevant molecules from the tranches based on the SMILES alone.

Best,
Lucy

[jir322]

use the 3D tranche browser. https://cartblanche22.docking.org/tranches/3d John Irwin UCSF Pharmaceutical Chemistry http://irwinlab.compbio.ucsf.edu

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On Wed, Apr 10, 2024 at 4:18 AM lucyraven ***@***.***> wrote: Hi, I am hoping it is possible to download 3D structures (as pdbqt) from ZINC22 based on a SMILES string or a ZINC ID, but I haven't yet found a way. Can it be done? I am designing a screening library based on subsets from many tranches and would prefer not having to download everything just to delete the majority of the files. I select the relevant molecules from the tranches based on the SMILES alone. Best, Lucy — Reply to this email directly, view it on GitHub <#74>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABIR2H5JUYIYXYRVBZY2K4TY4UNYZAVCNFSM6AAAAABGAHVT3KVHI2DSMVQWIX3LMV43ASLTON2WKOZSGIZTKMZVGIYDGOI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[jcastan6]

Hi Lucy, it is not possible to download individual 3D structures. However, you can download the respective tranches from the tranche browser and grab the files you need from there. Thanks! Mar

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On Wed, Apr 10, 2024 at 4:18 AM lucyraven ***@***.***> wrote: Hi, I am hoping it is possible to download 3D structures (as pdbqt) from ZINC22 based on a SMILES string or a ZINC ID, but I haven't yet found a way. Can it be done? I am designing a screening library based on subsets from many tranches and would prefer not having to download everything just to delete the majority of the files. I select the relevant molecules from the tranches based on the SMILES alone. Best, Lucy — Reply to this email directly, view it on GitHub <#74>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AECMSTFA4OJSIWUAY4PD5H3Y4UNY3AVCNFSM6AAAAABGAHVT3KVHI2DSMVQWIX3LMV43ASLTON2WKOZSGIZTKMZVGIYDGOI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[lucyraven]

Thank you both for your quick replies!

I will just download all the relevant tranches and delete what I don't need as I go along.

Also, thank you for maintaining such a valuable resource!

[jir322]

Hi Lucy Just to say what Mar said another way. In ZINC-22, we moved to a system where each molecule is not independently downloadable. This was for pragmatic reasons, though it is inconvenient. What you can do is to rebuild the molecule from SMILES. It should be identical to the one that is stored (pre-packed in groups of 5000 molecules) in our database. Use tldr.docking.org (free registration required) and use the dock3.7 or dock3.8 pipeline for 3D building. John Irwin UCSF Pharmaceutical Chemistry http://irwinlab.compbio.ucsf.edu On Wed, Apr 10, 2024 at 11:02 AM Mar Castanon ***@***.***> wrote:

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Hi Lucy, it is not possible to download individual 3D structures. However, you can download the respective tranches from the tranche browser and grab the files you need from there. Thanks! Mar On Wed, Apr 10, 2024 at 4:18 AM lucyraven ***@***.***> wrote: > Hi, > > I am hoping it is possible to download 3D structures (as pdbqt) from > ZINC22 based on a SMILES string or a ZINC ID, but I haven't yet found a > way. Can it be done? > > I am designing a screening library based on subsets from many tranches and > would prefer not having to download everything just to delete the majority > of the files. I select the relevant molecules from the tranches based on > the SMILES alone. > > Best, > Lucy > > — > Reply to this email directly, view it on GitHub > <#74>, or unsubscribe > < https://github.com/notifications/unsubscribe-auth/AECMSTFA4OJSIWUAY4PD5H3Y4UNY3AVCNFSM6AAAAABGAHVT3KVHI2DSMVQWIX3LMV43ASLTON2WKOZSGIZTKMZVGIYDGOI> > . > You are receiving this because you are subscribed to this thread.Message > ID: ***@***.***> > — Reply to this email directly, view it on GitHub <#74 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABIR2HZPESPKBP2I7WRJJP3Y4V5D3AVCNFSM6AAAAABGAHVT3KVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDANBYGE2TSMBVGY> . You are receiving this because you commented.Message ID: ***@***.***>

[lucyraven]

Hi John,
Thank you for the additional information. Depending on the number of molecules to extract this is definitely a good option that I will look into!