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
Blocked rows
The PubChem PDB-derived rows for the NaturalProductMech
CHEBI:22450record point at SERCA structures that are protein-groundable but ligand-mismatched:data/raw/pubchem_bioassay.tsv:7982, AID 1811, target2O9J_A,PMID:17259168data/raw/pubchem_bioassay.tsv:7983, AID 1811, target2OA0_A,PMID:17259168data/raw/pubchem_bioassay.tsv:7984, AID 977610,Ki = 0.12 uM, target2O9J_A,PMID:17259168data/raw/pubchem_bioassay.tsv:7985, AID 977610,Ki = 0.12 uM, target2OA0_A,PMID:17259168Why 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:CHEBI:22450SZINUGQCTHLQAZ-DQYPLSBCSA-N54682463The PDB evidence itself is valid for a rabbit SERCA protein:
2O9Jprimary DOI:10.1074/jbc.M6116532002O9JPDB DOI:10.2210/pdb2o9j/pdb2OA0PDB DOI:10.2210/pdb2oa0/pdb2O9J_Aand2OA0_Ato reviewedUniProtKB:P04191/AT2A1_RABITHowever, both PDB entries contain
CZA, and the RCSBCZAchem comp hasInChIKey=RLOAZVAJNNPPDI-DQYPLSBCSA-Nand related PubChem CID65261, notSZINUGQCTHLQAZ-DQYPLSBCSA-N.Suggested resolution
Do one of these before adding a
cyclopiazonic-acid-serca-bindinggraph:65261/ PDBCZAand attach the2O9J/2OA0rows there, orCHEBI:22450is not an exact-structure overstatement.Acceptance checks:
P04191,10.1074/jbc.M611653200,10.2210/pdb2o9j/pdb, and10.2210/pdb2oa0/pdbremain clean except for the intentional graph or blocker