rifamycin SV

CHEBI:29673 EXACT SEEDED antibacterialantimycobacterial

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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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.

A member of the class of rifamycins that exhibits antibiotic and antitubercular properties.

Structure

Standard InChIKey	HJYYPODYNSCCOU-ODRIEIDWSA-N
SMILES	C[C@H]1/C=C/C=C(\C(=O)NC2=CC(=C3C(=C2O)C(=C(C4=C3C(=O)[C@](O4)(O/C=C/[C@@H]([C@H]([C@H]([C@@H]([C@@H]([C@@H]([C@H]1O)C)O)C)OC(=O)C)C)OC)C)C)O)O)/C
Stereochemistry	fully defined
Cross-references	pubchem:6324616

Filing pathway

Polyketides — 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 pks, 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
Amycolatopsis mediterranei S699 NCBITaxon:713604	SOURCE_ASSERTION	mibig:BGC0000136	PMID:9512878
Salinispora arenicola CNS-205 NCBITaxon:391037	SOURCE_ASSERTION	mibig:BGC0000137	PMID:16517661

Occurrences 4

Somebody found the compound in this organism and cited it. That is not a claim that the organism makes it, and nothing here promotes one to the other.

Taxon	Source	Reference
Salinispora arenicola NCBITaxon:168697	LOTUS	DOI:10.1021/NP0604580
Amycolatopsis mediterranei NCBITaxon:33910	LOTUS	DOI:10.1016/S1074-5521(98)90141-7
Amycolatopsis mediterranei NCBITaxon:33910	LOTUS	DOI:10.1111/LAM.12332
Amycolatopsis mediterranei NCBITaxon:33910	CHEBI	PMID:25256628

Biosynthetic gene clusters 2

Accession	Host	Locus evidence	Genome
mibig:BGC0000136	Amycolatopsis mediterranei S699 NCBITaxon:713604	CLUSTER_UNSTATED	genbank:AF040570.3
mibig:BGC0000137	Salinispora arenicola CNS-205 NCBITaxon:391037	CLUSTER_UNSTATED	genbank:CP000850.1

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

Bioactivities 7

Entries preserve source qualifiers, targets and evidence. Repeated assay names or values are not independent replications; inspect source detail for differences.

Assay	Result	Target enzyme	Source detail
RNAP-Inhibition Assay from Article 10.1021/acschembio.6b01133: "Affinity Selection-Mass Spectrometry Identifies a Novel Antibacterial RNA Polymerase Inhibitor."	IC50 0.02 uM; ACTIVE	UniProtKB:P0A8V2	PMID:28323406 assay RNAP-Inhibition Assay from Article 10.1021/acschembio.6b01133: "Affinity Selection-Mass Spectrometry Identifies a Novel Antibacterial RNA Polymerase Inhibitor." evidence reference PMID:28323406 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1802841, deposited by BindingDB; assay type Confirmatory. call ACTIVE measurement type IC50 value 0.02 units uM target enzyme UniProtKB:P0A8V2 activity class ANTIBACTERIAL
RNAP-Inhibition Assay from Article 10.1021/acschembio.6b01133: "Affinity Selection-Mass Spectrometry Identifies a Novel Antibacterial RNA Polymerase Inhibitor."	IC50 0.03 uM; ACTIVE	UniProtKB:P0A8V2	PMID:28323406 assay RNAP-Inhibition Assay from Article 10.1021/acschembio.6b01133: "Affinity Selection-Mass Spectrometry Identifies a Novel Antibacterial RNA Polymerase Inhibitor." evidence reference PMID:28323406 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1802841, deposited by BindingDB; assay type Confirmatory. call ACTIVE measurement type IC50 value 0.03 units uM target enzyme UniProtKB:P0A8V2 activity class ANTIBACTERIAL
RNAP-Inhibition Assay from Article 10.1021/acschembio.6b01133: "Affinity Selection-Mass Spectrometry Identifies a Novel Antibacterial RNA Polymerase Inhibitor."	IC50 70 uM; INACTIVE	UniProtKB:Q3YUZ7	PMID:28323406 assay RNAP-Inhibition Assay from Article 10.1021/acschembio.6b01133: "Affinity Selection-Mass Spectrometry Identifies a Novel Antibacterial RNA Polymerase Inhibitor." evidence reference PMID:28323406 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1802841, deposited by BindingDB; assay type Confirmatory. call INACTIVE measurement type IC50 value 70.0 units uM target enzyme UniProtKB:Q3YUZ7
RNAP-Inhibition Assay from Article 10.1021/acschembio.6b01133: "Affinity Selection-Mass Spectrometry Identifies a Novel Antibacterial RNA Polymerase Inhibitor."	IC50 80 uM; INACTIVE	UniProtKB:Q3YUZ7	PMID:28323406 assay RNAP-Inhibition Assay from Article 10.1021/acschembio.6b01133: "Affinity Selection-Mass Spectrometry Identifies a Novel Antibacterial RNA Polymerase Inhibitor." evidence reference PMID:28323406 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1802841, deposited by BindingDB; assay type Confirmatory. call INACTIVE measurement type IC50 value 80.0 units uM target enzyme UniProtKB:Q3YUZ7
RNAP-Inhibition Assay from Article 10.1021/acschembio.6b01133: "Affinity Selection-Mass Spectrometry Identifies a Novel Antibacterial RNA Polymerase Inhibitor."	IC50 100 uM; INACTIVE	UniProtKB:Q3YUZ7	PMID:28323406 assay RNAP-Inhibition Assay from Article 10.1021/acschembio.6b01133: "Affinity Selection-Mass Spectrometry Identifies a Novel Antibacterial RNA Polymerase Inhibitor." evidence reference PMID:28323406 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1802841, deposited by BindingDB; assay type Confirmatory. call INACTIVE measurement type IC50 value 100.0 units uM target enzyme UniProtKB:Q3YUZ7
Human OATP1A2 (SLCO family of organic anion transporting polypeptides)	ACTIVE	Not recorded	PMID:12085361 assay Human OATP1A2 (SLCO family of organic anion transporting polypeptides) evidence reference PMID:12085361 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1345149, deposited by IUPHAR-DB; assay type Other. Target accession NP_602307 was left ungrounded because PubChem did not provide a UniProtKB accession. call ACTIVE
Human OATP1B1 (SLCO family of organic anion transporting polypeptides)	ACTIVE	Not recorded	PMID:12085361 assay Human OATP1B1 (SLCO family of organic anion transporting polypeptides) evidence reference PMID:12085361 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1345178, deposited by IUPHAR-DB; assay type Other. Target accession NP_006437 was left ungrounded because PubChem did not provide a UniProtKB accession. call ACTIVE

Elsewhere in the fleet

AntibioticMech — CHEBI:29673 (same structure, same inchikey)

Explore across X-Mech

AntibioticMech (rifamycin SV) ↗ MediaIngredientMech (CHEBI:29673) ↗ TaxonMech: Amycolatopsis mediterranei S699 (NCBITaxon:713604) ↗ TaxonMech: Salinispora arenicola CNS-205 (NCBITaxon:391037) ↗ PathwayMech (mibig:BGC0000136) ↗ PathwayMech (mibig:BGC0000137) ↗

Open questions 1

shared-structure — This structure is reported by more than one MIBiG entry: BGC0000136, BGC0000137. Confirm they describe the same compound rather than an upstream cross-reference error.

Provenance

Source concept	Source	Version
BGC0000136	MIBIG	5
BGC0000137	MIBIG	3
CHEBI:29673	CHEBI	3-star

This page is generated from data/natural_products/polyketides/rifamycin-sv.yaml, which is generated from the committed inventories. Neither is edited by hand.