benzylpenicillin sodium

CHEBI:51765 EXACT SEEDED

What these status tags mean

Curation status describes a workflow state. SEEDED means the record entered through the source-seeding workflow; it does not imply that no later curation occurred. PROPOSED marks an addition awaiting review; REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record. These are workflow decisions, not independently verified human review. Agent-assisted contributions may appear in the record history.

Grounding describes the identifier mapping: EXACT uses an ontology identity asserted by the source; MINTED keeps a local identifier when no defensible ontology identity is available; REVIEW_NEEDED flags an exact structure whose ontology identity needs adjudication. The grounding note retains any unresolved alternatives. These tags do not establish the strength of producer or activity evidence.

Structure

Standard InChIKey	FCPVYOBCFFNJFS-LQDWTQKMSA-M
SMILES	CC1([C@@H](N2[C@H](S1)[C@@H](C2=O)NC(=O)CC3=CC=CC=C3)C(=O)[O-])C.[Na+]
Stereochemistry	fully defined
Cross-references	pubchem:23668834

Filing pathway

Amino acids and peptides — computed by NPClassifier npclassifier.gnps2.org@2026-09-07, which is why it is pinned rather than recomputed. The gene cluster's asserted class is nrps, from MIBiG.

Producer organisms 2

A claim that this taxon makes the compound. The basis says what the evidence addressed — a knockout and a database assertion are not the same claim.

Taxon	Basis	Cluster	Evidence
Penicillium chrysogenum Strain: AS-P-78 NCBITaxon:5076	SOURCE_ASSERTION	mibig:BGC0000404	DOI:10.1016/j.fgb.2006.03.001, DOI:10.1016/s0140-6736(00)87452-8 reference DOI:10.1016/j.fgb.2006.03.001 evidence type DATABASE_ASSERTION notes MIBiG BGC0000404 entry version 4; claim-specific citation selected through a reviewed producer_reference correction. This remains a database assertion, not independently graded experimental evidence. reference DOI:10.1016/s0140-6736(00)87452-8 evidence type CURATOR_INFERENCE notes Citation routing only. The imported compound-bioactivity reference DOI:10.1016/s0140-6736(00)87452-8 (Chain et al., Lancet 1940;236(6104):226-228) is a 1940 clinical mouse-protection study that predates DNA sequencing and does not characterize Penicillium chrysogenum AS-P-78 or GenBank DQ192518.1 (coordinates 17440..28759). Route the BGC0000404:1 producer and locus claims to Fierro et al. 2006 (PMID:16713314, DOI:10.1016/j.fgb.2006.03.001), which sequenced and characterized the DQ192518.1 penicillin region in P. chrysogenum AS-P-78, without upgrading SOURCE_ASSERTION or CLUSTER_UNSTATED grades or altering taxon or structure identity. See issue #1023. Original imported citation DOI:10.1016/s0140-6736(00)87452-8 (COMPOUND_BIOACTIVITY) remains in the raw inventory, not as support for this claim. MIBiG source row BGC0000404:1; SHA256 9460d29fcad2b7ecb913298bc80838656966e219ec0654094d28b71942eaeb19. Curator: antigravity; date: 2026-10-23. Taxon, locus, chemistry and evidence grades are unchanged. reference DOI:10.1016/j.fgb.2006.03.001 evidence type CURATOR_INFERENCE notes Strain context: AS-P-78. Fierro et al. 2006 (PMID:16713314, DOI:10.1016/j.fgb.2006.03.001) and GenBank DQ192518.1 explicitly identify Penicillium chrysogenum strain AS-P-78 as the sequenced and amplified 106.5 kb penicillin region host for BGC0000404:1. Preserve NCBITaxon:5076 and existing SOURCE_ASSERTION/CLUSTER_UNSTATED grades; sodium-salt structure representation remains tracked in #1015. See issue #1022. Taxon identity and evidence grade are unchanged; this is not a species-wide experiment. MIBiG source row BGC0000404:1; SHA256 9460d29fcad2b7ecb913298bc80838656966e219ec0654094d28b71942eaeb19. Curator: antigravity; date: 2026-10-23.
Penicillium chrysogenum Strain: Wisconsin 54-1255 NCBITaxon:5076	SOURCE_ASSERTION	mibig:BGC0000405	DOI:10.1016/j.fgb.2007.03.008, PMID:1368505 reference DOI:10.1016/j.fgb.2007.03.008 evidence type DATABASE_ASSERTION notes MIBiG BGC0000405 entry version 5; claim-specific citation selected through a reviewed producer_reference correction. This remains a database assertion, not independently graded experimental evidence. reference PMID:1368505 evidence type CURATOR_INFERENCE notes Citation routing only. The imported entry-level reference PMID:1368505 (Smith et al., Bio/Technology 1990;8(1):39-41, DOI:10.1038/nbt0190-39) reports 1990 heterologous cosmid pDJB3-G1 expression in Neurospora crassa and Aspergillus niger and predates GenBank EF601124.1 (coordinates 22186..33473) by 17 years. Route the BGC0000405:3 (benzylpenicillin) producer and locus claims to van den Berg et al. 2007 (PMID:17548217, DOI:10.1016/j.fgb.2007.03.008), which sequenced and functionally characterized the 56.8 kb EF601124.1 penicillin cluster in P. chrysogenum Wisconsin 54-1255, without altering taxon, structure identity, or evidence grades. See issue #1023. Original imported citation PMID:1368505 (ENTRY) remains in the raw inventory, not as support for this claim. MIBiG source row BGC0000405:3; SHA256 847cf368dc26e162604ac12681781efc5814bcc31c4e19e94b09578562a1dd42. Curator: antigravity; date: 2026-10-23. Taxon, locus, chemistry and evidence grades are unchanged. reference DOI:10.1016/j.fgb.2007.03.008 evidence type CURATOR_INFERENCE notes Strain context: Wisconsin 54-1255. Van den Berg et al. 2007 (PMID:17548217, DOI:10.1016/j.fgb.2007.03.008) and GenBank EF601124.1 explicitly identify Penicillium chrysogenum strain Wisconsin 54-1255 as the sequenced and functionally characterized 56.8 kb penicillin cluster host for BGC0000405:3 (benzylpenicillin). Preserve NCBITaxon:5076 and existing SOURCE_ASSERTION/CLUSTER_DEMONSTRATED grades; sodium-salt structure representation remains tracked in #1015. See issue #1022. Taxon identity and evidence grade are unchanged; this is not a species-wide experiment. MIBiG source row BGC0000405:3; SHA256 847cf368dc26e162604ac12681781efc5814bcc31c4e19e94b09578562a1dd42. Curator: antigravity; date: 2026-10-23.

Occurrences 0

None cited.

Biosynthetic gene clusters 2

Accession	Host	Locus evidence	Genome
mibig:BGC0000404	Penicillium chrysogenum NCBITaxon:5076	CLUSTER_UNSTATED	genbank:DQ192518.1
mibig:BGC0000405	Penicillium chrysogenum NCBITaxon:5076	CLUSTER_DEMONSTRATED	genbank:EF601124.1

A locus claim and a taxon claim are different questions. Heterologous expression settles the first and leaves the second where the isolation report left it.

Mechanism & Biosynthesis Overview

Explore across X-Mech

AntibioticMech (benzylpenicillin sodium) ↗ MediaIngredientMech (CHEBI:51765) ↗ TaxonMech: Penicillium chrysogenum (NCBITaxon:5076) ↗ TaxonMech: Penicillium chrysogenum (NCBITaxon:5076) ↗ PathwayMech (mibig:BGC0000404) ↗ PathwayMech (mibig:BGC0000405) ↗

Open questions 2

name-disagreement — ChEBI calls this structure 'benzylpenicillin sodium' and MIBiG calls it 'penicillin'. They share a Standard InChIKey, so if the names denote different compounds then one upstream record has the wrong structure. Check which.

shared-structure — This structure is reported by more than one MIBiG entry: BGC0000404, BGC0000405. Confirm they describe the same compound rather than an upstream cross-reference error.

Provenance

Source concept	Source	Version
BGC0000404	MIBIG	4
BGC0000405	MIBIG	5
CHEBI:51765	CHEBI	3-star

This page is generated from data/natural_products/amino_acids_and_peptides/benzylpenicillin-sodium.yaml, which is generated from the committed inventories. Neither is edited by hand.