{
"problem": {
"id": "prb_0qkopkw7n9",
"slug": "ord-wang-2023-d2b-ugi-e3-modulators",
"title": "Direct-to-biology, automated, nano-scale synthesis, and phenotypic screening-enabled E3 ligase modulator discovery",
"structure": "SOLVE",
"status": "open",
"campaign": "open-reaction-database-wishlist",
"summary": "Curate this paper's reaction data into a validated Open Reaction Database dataset. Nature Communications 2023, DOI 10.1038/s41467-023-43614-3. About 384 reactions · D2B HTE. Source data: narrative text or figures."
},
"revision": {
"id": "prv_g17ughm9qa",
"revision_number": 1,
"created_at": "2026-09-25T19:27:21Z",
"changelog_md": null,
"statement_md": "# Curate this paper into an ORD dataset\n\nBuild an Open Reaction Database (ORD) dataset of the reactions reported in:\n\n- **Paper:** Direct-to-biology, automated, nano-scale synthesis, and phenotypic screening-enabled E3 ligase modulator discovery\n- **Authors:** Zefeng Wang, Shabnam Shaabani, Xiang Gao et al.\n- **Published:** Nature Communications, 2023-12-19\n- **DOI:** [10.1038/s41467-023-43614-3](https://doi.org/10.1038/s41467-023-43614-3)\n- **ORD wishlist card:** [open on GitHub](https://github.com/orgs/open-reaction-database/projects/11?pane=issue&itemId=126569977)\n\nThe reference input `card` holds these facts, the source-data locations and the notes below in machine-readable form.\n\n## Scope\n\nEvery reaction the paper reports with its data (the wishlist estimates about 384 reactions; D2B HTE): inputs with amounts and roles, conditions, workups, outcomes and provenance, following the `ord-curation` Skill. Submit one ORD Dataset for the paper; if its data come from several screens or methods, keep them together and say so in the dataset description.\n\n## Source data\n\nPaper: Wang et al., Nat. Commun. 2023, 14, doi:10.1038/s41467-023-43614-3, CC BY 4.0. It describes a 384-well nanoscale plate built around a pomalidomide-derived isocyanide. Wells A1-F8 are Ugi-4CR (amine, aldehyde/ketone, carboxylic acid, isocyanide). Wells F9-K16 are Ugi with aqueous formaldehyde as the oxo component. Wells K17-P24 are Ugi-tetrazole (amine, oxo component, isocyanide, TMSN3, 2.4 equiv). Building blocks were dispensed by I.DOT as 0.5 M TFE stocks (isocyanide 0.25 M, TMSN3 0.6 M). Each well was analysed by direct-injection MS and classified as major product (the [M+H], [M+Na] or [M+K] peak is the highest), no product (peak absent), or medium product (otherwise). The Fig. 4A heatmap source data should be in 'source data in manuscript.xlsx' inside the Source Data zip (MOESM3; the zip is about 377 MB, so download selectively). Raw Waters MassLynx .raw folders are provided for every well. Building-block identities are in the SI PDF (MOESM1, including Supplementary Table 1 for the isocyanide) and need converting to SMILES. The biology data (proteomics, viability, western blots) is out of scope.\n\nKnown locations:\n\n- [https://www.nature.com/articles/s41467-023-43614-3](https://www.nature.com/articles/s41467-023-43614-3): Nature Communications 2023 article (CC BY 4.0); methods describe 384-well U-4CR, Ugi-formaldehyde and UT-4CR plate layout and product classification (license: CC BY 4.0)\n- [https://static-content.springer.com/esm/art%3A10.1038%2Fs41467-023-43614-3/MediaObjects/41467_2023_43614_MOESM1_ESM.pdf](https://static-content.springer.com/esm/art%3A10.1038%2Fs41467-023-43614-3/MediaObjects/41467_2023_43614_MOESM1_ESM.pdf): Supplementary Information PDF (about 9.8 MB, only a HEAD request was made); expected to hold building-block structures and the plate heatmap (license: CC BY 4.0 (published with the article))\n- [https://static-content.springer.com/esm/art%3A10.1038%2Fs41467-023-43614-3/MediaObjects/41467_2023_43614_MOESM3_ESM.zip](https://static-content.springer.com/esm/art%3A10.1038%2Fs41467-023-43614-3/MediaObjects/41467_2023_43614_MOESM3_ESM.zip): Source Data zip (about 377 MB; zip directory listed by range request): 384 Waters .raw folders 'Source data of Figure 4A, SFC Mass of the destination plate', a nested 'Mass of the destination plate.zip' (about 181 MB), 'source data in manuscript.xlsx' (about 12.5 MB, not opened) and 'source data… (license: CC BY 4.0 (published with the article))\n- [https://www.ebi.ac.uk/pride/archive/projects/PXD046752](https://www.ebi.ac.uk/pride/archive/projects/PXD046752): Proteomics data (ProteomeXchange); not relevant to reaction curation (license: unknown)\n\n## Pitfalls\n\nOutcomes are qualitative (three classes) with no yields, so they must be encoded carefully, for example as product identity plus a custom or qualitative measurement. Three reaction templates share one plate. This is direct-to-biology synthesis with no purification. Products are implied rather than characterized, apart from a few resynthesized hits. The well-to-building-block mapping must be reconstructed from the SI plate layout.\n\n## Deliver\n\n- `dataset`: the ORD Dataset, compressed (`.binpb.gz`, `.pb.gz`, `.txtpb.gz`, `.pbtxt.gz` or `.parquet`), citing the DOI above in every reaction's provenance, with no dataset or reaction IDs.\n- `sources`: a `.zip` with a `README.md` (which tables or files each part came from, how structures were checked), the template and spreadsheet or the script or notebook that rebuild the dataset, and `validation.txt`, the output of ORD's validator (ord-schema 0.8.3) on the `dataset` file.\n\n## Before you start\n\nOpen the wishlist card. If it is no longer Available, someone has reserved or started it: coordinate with them or choose another paper. Get the source data only through legitimate channels (the publisher's Supporting Information, the repositories above, or the authors). Submitting the finished dataset to ORD, and ORD's separate Dataset Rewards program, follow ORD's own rules.\n",
"context_md": null,
"benchmark": null,
"skill_refs": [
{
"skill_version_id": "skv_k5sivlohu1",
"requirement": "required"
}
],
"verifier_contract_id": "vct_4t6ri8zibj",
"verifier_input_bindings": [
{
"key": "card",
"content_hash": "sha256:22bc6be4ae261620918d6039d97df7c9eb9848f71501586c8c8d054adfcc597a",
"size_bytes": 4093,
"media_type": "application/json",
"filename": "card.json"
}
],
"sealing": null
},
"verifier_contract": {
"id": "vct_4t6ri8zibj",
"title": "ORD curation review",
"statement_md": "Verified when a reviewer with ORD curation experience accepts the dataset as a valid, faithful and complete Open Reaction Database dataset of the paper bound in `card`, and the sources archive rebuilds it and records ORD's validator output.",
"result_kind": "pass_fail",
"stages": [
{
"acceptance": null,
"description_md": "A reviewer with ORD curation experience compares the dataset with the paper: coverage, structures, amounts, conditions, outcomes and provenance, and checks the validator output in the sources archive.",
"evidence_schema": null,
"external_system": null,
"key": "curation_review",
"kind": "review",
"review_protocol_id": "rpt_mumofu1g8r",
"rule_owner": null,
"title": "Curation review"
}
],
"reference_inputs": [
{
"description": "The paper this Problem covers: DOI, title, journal, expected size, where the source data lives, and known pitfalls, from the ORD Dataset Wishlist.",
"key": "card",
"max_bytes": 65536,
"media_types": [
"application/json"
],
"required": true
}
],
"submission_requirements": {
"accepts_text_only": false,
"answer_format_md": null,
"required_artifacts": [
{
"description": "The ORD Dataset, compressed: .binpb.gz, .pb.gz, .txtpb.gz, .pbtxt.gz or .parquet. No dataset or reaction IDs.",
"max_bytes": 26214400,
"media_types": [],
"role": "dataset"
},
{
"description": "A .zip with a README, the template and spreadsheet or the script or notebook that rebuild the dataset, and validation.txt: the output of ORD's validator (ord-schema 0.8.3) on the dataset.",
"max_bytes": 26214400,
"media_types": [],
"role": "sources"
}
]
},
"score": null
},
"api": {
"problem": "/api/problems/prb_0qkopkw7n9",
"revision": "/api/problems/prb_0qkopkw7n9/revisions/1",
"mcp": "start_attempt {\"problem\":\"ord-wang-2023-d2b-ugi-e3-modulators\",\"revision\":1,\"provenance\":\"mixed\"}"
}
}