Do not seed neocarzinostatin apoprotein binding as enzyme inhibition

[realmarcin]

Problem

data/natural_products/unclassified/neocarzinostatin-chromophore.yaml inherits two PubChem/PDB bioactivity rows from data/raw/pubchem_bioassay.tsv for Standard InChIKey QZGIWPZCWHMVQL-UIYAJPBUSA-N, CID 447545:

• AID 977611, Kd 0.0001 uM, target 1O5P_A, PMID:15640161
• AID 1811, active call, target 1O5P_A, PMID:15640161

The seeder currently marks these as activity_class: ENZYME_INHIBITOR, but 1O5P_A is not an inhibited host enzyme. RCSB identifies 1O5P as Solution Structure of holo-Neocarzinostatin, with CHR neocarzinostatin chromophore as the non-polymer ligand, and PDBe maps chain A to the mature Streptomyces carzinostaticus neocarzinostatin apoprotein on UniProtKB:P0A3R9 residues 35-147.

Why this blocks protein graph curation

The row is an exact protein/chromophore structure, so it looks attractive in the PubChem/PDB target queue. Biologically, though, it represents the enediyne chromophore bound to its producer carrier apoprotein in the holo-antibiotic complex, not enzymatic inhibition and not a host bioactivity target.

Possible fixes

• exclude known holoprotein/carrier PDB rows from PubChem-derived bioactivities; or
• add a record field or graph scope that can express carrier apoprotein protection/release without pretending it is BIOACTIVITY or ENZYME_INHIBITOR.

Checks already run

• exact ignored-file-inclusive search for 1O5P, PMID:15640161, and neocarzinostatin chromophore found only the seeded record and raw PubChem/CHEBI rows in the bounded working corpus
• exact ignored-file-inclusive search for P0A3R9, 10.1074/jbc.M411579200, 10.2210/pdb1o5p/pdb, and neocarzinostatin-apoprotein found no existing curated graph in the bounded working corpus