sangivamycin

CHEBI:85997 EXACT SEEDED enzyme inhibitor

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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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 nucleoside analogue that is adenosine in which the nitrogen at position 7 is replaced by a carbamoyl-substituted carbon. It is a potent inhibitor of protein kinase C.

Structure

Standard InChIKey	OBZJZDHRXBKKTJ-JTFADIMSSA-N
SMILES	NC(=O)C1=CN([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)C2=C1C(N)=NC=N2
Stereochemistry	fully defined
Cross-references	npatlas:NPA05297, pubchem:14978

Filing pathway

Carbohydrates — 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 other, from MIBiG.

Producer organisms 1

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
Streptomyces rimosus NCBITaxon:1927	SOURCE_ASSERTION	mibig:BGC0000879	PMID:18721750

Occurrences 2

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
Streptomyces NCBITaxon:1883	LOTUS	DOI:10.1021/JM00311A005
Streptomyces sparsogenes NCBITaxon:67365	LOTUS	DOI:10.1016/S0021-9673(01)83861-9

Biosynthetic gene clusters 1

Accession	Host	Locus evidence	Genome
mibig:BGC0000879	Streptomyces rimosus NCBITaxon:1927	CLUSTER_UNSTATED	genbank:EU573979.1

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

Causal graph — bioactivity 2 nodes, 1 edge

Sangivamycin binds human G protein-coupled receptor kinase 6 in the PDB 3NYN co-crystal structure.

Subject	Predicate	Object	Notes	Evidence
sangivamycin	binds	human G protein-coupled receptor kinase 6	PubChem BioAssay AID 977611 maps this exact Standard InChIKey to an active 1 uM Kd row for PDB 3NYN chain A; PDBe maps 3NYN_A to Homo sapiens UniProtKB:P43250, and RCSB reports SGV sangivamycin with the record's Standard InChIKey as a 3NYN non-polymer ligand.	DOI:10.1038/emboj.2010.206 DOI:10.2210/pdb3nyn/pdb reference DOI:10.1038/emboj.2010.206 evidence type PRIMARY_EXPERIMENT snippet Molecular basis for activation of G protein-coupled receptor kinases. notes Boguth et al. solved PDB 3NYN as a sangivamycin-bound human GRK6 structure. reference DOI:10.2210/pdb3nyn/pdb evidence type DATABASE_ASSERTION notes RCSB PDB identifies 3NYN as a human GRK6 crystal structure containing SGV sangivamycin, and PDBe maps chain A to the canonical Homo sapiens GRK6 sequence in UniProtKB:P43250.

Every edge carries its own citation; an uncited edge is refused by the corpus tests.

Bioactivities 1

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
Experimentally measured binding affinity data (Kd) for protein-ligand complexes derived from PDB	KD 1 uM; ACTIVE	Not recorded	PMID:20729810 assay Experimentally measured binding affinity data (Kd) for protein-ligand complexes derived from PDB evidence reference PMID:20729810 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 977611, deposited by Shanghai Institute of Organic Chemistry; assay type Other. Target accession 3NYN_A was left ungrounded because PubChem did not provide a UniProtKB accession. call ACTIVE measurement type KD value 1.0 units uM activity class ENZYME_INHIBITOR

Explore across X-Mech

AntibioticMech (sangivamycin) ↗ MediaIngredientMech (CHEBI:85997) ↗ TaxonMech: Streptomyces rimosus (NCBITaxon:1927) ↗ PathwayMech (mibig:BGC0000879) ↗

Provenance

Source concept	Source	Version
BGC0000879	MIBIG	5
CHEBI:85997	CHEBI	3-star

This page is generated from data/natural_products/carbohydrates/sangivamycin.yaml, which is generated from the committed inventories. Neither is edited by hand.