Skip to content

Do not seed cyclopiazonic-acid CZA PDB rows on CHEBI:22450 #147

Description

@realmarcin

Blocked rows

The PubChem PDB-derived rows for the NaturalProductMech CHEBI:22450 record point at SERCA structures that are protein-groundable but ligand-mismatched:

  • data/raw/pubchem_bioassay.tsv:7982, AID 1811, target 2O9J_A, PMID:17259168
  • data/raw/pubchem_bioassay.tsv:7983, AID 1811, target 2OA0_A, PMID:17259168
  • data/raw/pubchem_bioassay.tsv:7984, AID 977610, Ki = 0.12 uM, target 2O9J_A, PMID:17259168
  • data/raw/pubchem_bioassay.tsv:7985, AID 977610, Ki = 0.12 uM, target 2OA0_A, PMID:17259168

Why this should not become a graph yet

The record is data/natural_products/unclassified/6ar-11as-11br-10-acetyl-11-hydroxy-7-7-dimethyl-2-6-6a-7-11a-11b-hexahydro-9h-py.yaml:

  • identifier: CHEBI:22450
  • record Standard InChIKey: SZINUGQCTHLQAZ-DQYPLSBCSA-N
  • source PubChem CID: 54682463

The PDB evidence itself is valid for a rabbit SERCA protein:

  • RCSB 2O9J primary DOI: 10.1074/jbc.M611653200
  • RCSB 2O9J PDB DOI: 10.2210/pdb2o9j/pdb
  • RCSB 2OA0 PDB DOI: 10.2210/pdb2oa0/pdb
  • PDBe maps both 2O9J_A and 2OA0_A to reviewed UniProtKB:P04191 / AT2A1_RABIT

However, both PDB entries contain CZA, and the RCSB CZA chem comp has InChIKey=RLOAZVAJNNPPDI-DQYPLSBCSA-N and related PubChem CID 65261, not SZINUGQCTHLQAZ-DQYPLSBCSA-N.

Suggested resolution

Do one of these before adding a cyclopiazonic-acid-serca-binding graph:

  • add a separate exact record for PubChem 65261 / PDB CZA and attach the 2O9J/2OA0 rows there, or
  • model the tautomer/protomer relationship explicitly enough that a graph on CHEBI:22450 is not an exact-structure overstatement.

Acceptance checks:

  • exact ignored-file-inclusive searches for P04191, 10.1074/jbc.M611653200, 10.2210/pdb2o9j/pdb, and 10.2210/pdb2oa0/pdb remain clean except for the intentional graph or blocker
  • the PDB ligand Standard InChIKey matches the record that receives the SERCA causal graph

Activity

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment

Metadata

Metadata

Assignees

No one assigned

    Labels

    No labels
    No labels

    Type

    No type

    Projects

    No projects

      Milestone

      No milestone

      Relationships

      None yet

      Development

      No branches or pull requests

      Issue actions