tubercidin

CHEBI:48267 EXACT SEEDED antifungalcytotoxicenzyme 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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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.

An N-glycosylpyrrolopyrimidine that is adenosine in which the in the 5-membered ring that is not attached to the ribose moiety is replaced by a carbon. Tubercidin is produced in the culture broth of Streptomyces tubericidus.

Structure

Standard InChIKey	HDZZVAMISRMYHH-KCGFPETGSA-N
SMILES	C1=CN(C2=NC=NC(=C21)N)[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O
Stereochemistry	fully defined
Cross-references	pubchem:6245

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 tubercidicus NCBITaxon:47759	SOURCE_ASSERTION	mibig:BGC0001937	PMID:30153835

Occurrences 15

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
Tolypothrix distorta NCBITaxon:119534	LOTUS	DOI:10.7164/ANTIBIOTICS.41.1048
Tolypothrix byssoidea NCBITaxon:213754	CHEBI	PMID:21870828
Caulospongia biflabellata NCBITaxon:297728	LOTUS	DOI:10.1076/PHBI.40.4.302.8469
Caulospongia biflabellata NCBITaxon:297728	CHEBI	PMID:21870828
Lissoclinum timorense NCBITaxon:322851	LOTUS	DOI:10.1021/NP960457F
Actinopolyspora erythraea NCBITaxon:414996	LOTUS	DOI:10.1021/NP200603G
Actinopolyspora erythraea YIM 90600 NCBITaxon:414996	CHEBI	PMID:21870828
Hassallia byssoidea NCBITaxon:482630	LOTUS	DOI:10.1016/S0031-9422(00)97712-4
Hassallia byssoidea NCBITaxon:482630	LOTUS	DOI:10.7164/ANTIBIOTICS.41.1048
Streptomyces sparsogenes NCBITaxon:67365	LOTUS	DOI:10.1016/S0021-9673(01)83861-9
Plectonema radiosum NCBITaxon:945768	LOTUS	DOI:10.1016/0304-3835(95)03940-X
Plectonema radiosum NCBITaxon:945768	LOTUS	DOI:10.7164/ANTIBIOTICS.41.1048
Streptomyces tubercidicus NCBITaxon:47759	LOTUS	DOI:10.1007/BF02976759
Streptomyces tubercidicus NCBITaxon:47759	LOTUS	DOI:10.1186/S12934-018-0978-8
Streptomyces tubercidicus NCBITaxon:47759	CHEBI	PMID:21870828

Biosynthetic gene clusters 1

Accession	Host	Locus evidence	Genome
mibig:BGC0001937	Streptomyces tubercidicus NCBITaxon:47759	CLUSTER_UNSTATED	genbank:MG706975.1

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

Tubercidin binds Escherichia coli purine nucleoside phosphorylase in the PDB 1PR5 co-crystal structure.

Subject	Predicate	Object	Notes	Evidence
tubercidin	binds	Escherichia coli O157:H7 purine nucleoside phosphorylase DeoD	PubChem AID 977610 maps this exact InChIKey to an active 120 uM Ki row for PDB 1PR5 chain A; RCSB identifies TBN in 1PR5 as tubercidin with matching InChIKey HDZZVAMISRMYHH-KCGFPETGSA-N; and PDBe maps chains A, B and C to UniProtKB:P0ABP9.	DOI:10.1074/jbc.M304622200 DOI:10.2210/pdb1pr5/pdb reference DOI:10.1074/jbc.M304622200 evidence type PRIMARY_EXPERIMENT snippet Structural basis for substrate specificity of Escherichia coli purine nucleoside phosphorylase. notes Bennett, Li, Allan, Parker and Ealick solved PDB 1PR5 as Escherichia coli purine nucleoside phosphorylase bound to 7-deazaadenosine. reference DOI:10.2210/pdb1pr5/pdb evidence type DATABASE_ASSERTION snippet Escherichia coli Purine Nucleoside Phosphorylase Complexed with 7-deazaadenosine and Phosphate/Sulfate notes RCSB PDB identifies 1PR5 as purine nucleoside phosphorylase entity 1 bound to TBN 7-deazaadenosine entity 3, and PDBe maps entity 1 chains A, B and C to UniProtKB:P0ABP9.

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

Bioactivities 25

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

Elsewhere in the fleet

AntibioticMech — CHEBI:48267 (same structure, same inchikey)

Explore across X-Mech

AntibioticMech (tubercidin) ↗ MediaIngredientMech (CHEBI:48267) ↗ TaxonMech: Streptomyces tubercidicus (NCBITaxon:47759) ↗ PathwayMech (mibig:BGC0001937) ↗

Provenance

Source concept	Source	Version
BGC0001937	MIBIG	4
CHEBI:48267	CHEBI	3-star

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

Assay	Result	Target enzyme	Source detail
A quantitative high throughput screen for small molecules that induce DNA re-replication in MCF 10a normal breast cells.	OTHER 0.5174 uM; NOT_DETERMINED	Not recorded	pubchem.aid:624296 assay A quantitative high throughput screen for small molecules that induce DNA re-replication in MCF 10a normal breast cells. evidence reference pubchem.aid:624296 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 624296, deposited by NCGC; assay type Confirmatory. Source outcome: Inconclusive. Source endpoint: Potency. Target accession NP_056979 was left ungrounded because PubChem did not provide a UniProtKB accession. call NOT_DETERMINED measurement type OTHER value 0.5174 units uM
A quantitative high throughput screen for small molecules that induce DNA re-replication in SW480 colon adenocarcinoma cells.	OTHER 0.6513 uM; NOT_DETERMINED	Not recorded	pubchem.aid:624297 assay A quantitative high throughput screen for small molecules that induce DNA re-replication in SW480 colon adenocarcinoma cells. evidence reference pubchem.aid:624297 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 624297, deposited by NCGC; assay type Confirmatory. Source outcome: Inconclusive. Source endpoint: Potency. Target accession NP_056979 was left ungrounded because PubChem did not provide a UniProtKB accession. call NOT_DETERMINED measurement type OTHER value 0.6513 units uM
A549 Cytotoxicity Assay Measured in Cell-Based System Using Plate Reader - 7071-06_Antagonist_Dose_CherryPick_Activity	OTHER 0.0912 uM; ACTIVE	Not recorded	pubchem.aid:743412 assay A549 Cytotoxicity Assay Measured in Cell-Based System Using Plate Reader - 7071-06_Antagonist_Dose_CherryPick_Activity evidence reference pubchem.aid:743412 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 743412, deposited by Broad Institute; assay type Confirmatory. Source endpoint: AC50. call ACTIVE measurement type OTHER value 0.0912 units uM activity class CYTOTOXIC
Bursicon-induced LGR2 mediated cAMP production in LGR-2/CRE6x-Luciferase co-transfected HEK293 cells Inhibition Measured in Cell-Based System Using Plate Reader - 7011-01_Antagonist_Dose_CherryPick_Activity_Set2	OTHER 2.77 uM; ACTIVE	Not recorded	pubchem.aid:743343 assay Bursicon-induced LGR2 mediated cAMP production in LGR-2/CRE6x-Luciferase co-transfected HEK293 cells Inhibition Measured in Cell-Based System Using Plate Reader - 7011-01_Antagonist_Dose_CherryPick_Activity_Set2 evidence reference pubchem.aid:743343 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 743343, deposited by Broad Institute; assay type Confirmatory. Source endpoint: AC50. call ACTIVE measurement type OTHER value 2.77 units uM
Dose response confirmation of uHTS chemical inhibitors of both B-cell and T-cell specific antigen receptor-induced NF-kB activation in a 697B cell line using a luminescence assay	IC50 1.01 uM; ACTIVE	Not recorded	pubchem.aid:489034 assay Dose response confirmation of uHTS chemical inhibitors of both B-cell and T-cell specific antigen receptor-induced NF-kB activation in a 697B cell line using a luminescence assay evidence reference pubchem.aid:489034 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 489034, deposited by Burnham Center for Chemical Genomics; assay type Confirmatory. call ACTIVE measurement type IC50 value 1.01 units uM activity class ENZYME_INHIBITOR
Dose response confirmation of uHTS of chemical inhibitors of both B-cell and T-cell specific antigen receptor-induced NF-kB activation in a Jurkat cell line using a luminescence assay	IC50 7.83 uM; ACTIVE	Not recorded	pubchem.aid:489004 assay Dose response confirmation of uHTS of chemical inhibitors of both B-cell and T-cell specific antigen receptor-induced NF-kB activation in a Jurkat cell line using a luminescence assay evidence reference pubchem.aid:489004 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 489004, deposited by Burnham Center for Chemical Genomics; assay type Confirmatory. call ACTIVE measurement type IC50 value 7.83 units uM activity class ENZYME_INHIBITOR
Dose response counterscreen of uHTS chemical inhibitors of both B-cell and T-cell specific antigen receptor-induced NF-kB activation in a HEK-293T cell line using a luminescence assay	IC50 7.42 uM; ACTIVE	Not recorded	pubchem.aid:489020 assay Dose response counterscreen of uHTS chemical inhibitors of both B-cell and T-cell specific antigen receptor-induced NF-kB activation in a HEK-293T cell line using a luminescence assay evidence reference pubchem.aid:489020 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 489020, deposited by Burnham Center for Chemical Genomics; assay type Confirmatory. call ACTIVE measurement type IC50 value 7.42 units uM activity class ENZYME_INHIBITOR
Dose response cytoxicity of uHTS chemical inhibitors of both B-cell and T-cell specific antigen receptor-induced NF-kB activation in a HEK-293T cell line using a luminescence assay	IC50 80 uM; INACTIVE	Not recorded	pubchem.aid:489019 assay Dose response cytoxicity of uHTS chemical inhibitors of both B-cell and T-cell specific antigen receptor-induced NF-kB activation in a HEK-293T cell line using a luminescence assay evidence reference pubchem.aid:489019 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 489019, deposited by Burnham Center for Chemical Genomics; assay type Confirmatory. call INACTIVE measurement type IC50 value 80.0 units uM
Experimentally measured binding affinity data (Ki) for protein-ligand complexes derived from PDB	KI 120 uM; ACTIVE	Not recorded	PMID:12937174 assay Experimentally measured binding affinity data (Ki) for protein-ligand complexes derived from PDB evidence reference PMID:12937174 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 977610, deposited by Shanghai Institute of Organic Chemistry; assay type Other. Target accession 1PR5_A was left ungrounded because PubChem did not provide a UniProtKB accession. call ACTIVE measurement type KI value 120.0 units uM activity class ENZYME_INHIBITOR
Fluorescence Cell-Based Dose Response to Characterize Compounds Cytotoxic to RAS-Dependent BJ-TERT-LT-ST Fibroblast	EC50 0.104 uM; ACTIVE	Not recorded	pubchem.aid:2631 assay Fluorescence Cell-Based Dose Response to Characterize Compounds Cytotoxic to RAS-Dependent BJ-TERT-LT-ST Fibroblast evidence reference pubchem.aid:2631 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 2631, deposited by Broad Institute; assay type Confirmatory. call ACTIVE measurement type EC50 value 0.104 units uM activity class CYTOTOXIC
HEK293 Cytotoxicity Assay Measured in Cell-Based System Using Plate Reader - 7071-01_Antagonist_Dose_CherryPick_Activity	OTHER 1.6 uM; ACTIVE	Not recorded	pubchem.aid:743446 assay HEK293 Cytotoxicity Assay Measured in Cell-Based System Using Plate Reader - 7071-01_Antagonist_Dose_CherryPick_Activity evidence reference pubchem.aid:743446 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 743446, deposited by Broad Institute; assay type Confirmatory. Source endpoint: AC50. call ACTIVE measurement type OTHER value 1.6 units uM activity class CYTOTOXIC
HSF-1 induced GFP reporter and Doxycycline induced RFP reporter Measured in Cell-Based System Using Plate Reader - 2038-03_Inhibitor_DoseNoFile_CherryPick_Activity_Set3	OTHER 10.488 uM; ACTIVE	Not recorded	pubchem.aid:493083 assay HSF-1 induced GFP reporter and Doxycycline induced RFP reporter Measured in Cell-Based System Using Plate Reader - 2038-03_Inhibitor_DoseNoFile_CherryPick_Activity_Set3 evidence reference pubchem.aid:493083 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 493083, deposited by Broad Institute; assay type Confirmatory. Source endpoint: AC50. Target accession AAH94064 was left ungrounded because PubChem did not provide a UniProtKB accession. call ACTIVE measurement type OTHER value 10.488 units uM
HSF-1 induced GFP reporter and Doxycycline induced RFP reporter Measured in Cell-Based System Using Plate Reader - 2038-03_Inhibitor_DoseNoFile_CherryPick_Internal-Standard_Set3	OTHER 3.174 uM; ACTIVE	Not recorded	pubchem.aid:493085 assay HSF-1 induced GFP reporter and Doxycycline induced RFP reporter Measured in Cell-Based System Using Plate Reader - 2038-03_Inhibitor_DoseNoFile_CherryPick_Internal-Standard_Set3 evidence reference pubchem.aid:493085 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 493085, deposited by Broad Institute; assay type Confirmatory. Source endpoint: AC50. Target accession AAH94064 was left ungrounded because PubChem did not provide a UniProtKB accession. call ACTIVE measurement type OTHER value 3.174 units uM
HTS for Inhibitors of HP1-beta Chromodomain Interactions with Methylated Histone Tails	OTHER 11.2202 uM; INACTIVE	Not recorded	pubchem.aid:540317 assay HTS for Inhibitors of HP1-beta Chromodomain Interactions with Methylated Histone Tails evidence reference pubchem.aid:540317 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 540317, deposited by NCGC; assay type Confirmatory. Source endpoint: Potency. Target accession NP_001120700 was left ungrounded because PubChem did not provide a UniProtKB accession. call INACTIVE measurement type OTHER value 11.2202 units uM
HepG2 Cytotoxicity Assay Measured in Cell-Based System Using Plate Reader - 7071-02_Antagonist_Dose_CherryPick_Activity	OTHER 0.25 uM; ACTIVE	Not recorded	pubchem.aid:743416 assay HepG2 Cytotoxicity Assay Measured in Cell-Based System Using Plate Reader - 7071-02_Antagonist_Dose_CherryPick_Activity evidence reference pubchem.aid:743416 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 743416, deposited by Broad Institute; assay type Confirmatory. Source endpoint: AC50. call ACTIVE measurement type OTHER value 0.25 units uM activity class CYTOTOXIC
High Throughput Screen to Identify Inhibitors of Mycobacterium tuberculosis H37Rv	IC50 2.438 uM; ACTIVE	Not recorded	pubchem.aid:1626 assay High Throughput Screen to Identify Inhibitors of Mycobacterium tuberculosis H37Rv evidence reference pubchem.aid:1626 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1626, deposited by SRMLSC; assay type Confirmatory. call ACTIVE measurement type IC50 value 2.438 units uM activity class ENZYME_INHIBITOR
High Throughput Screening for Foot and Mouth Disease Virus Antivirals	OTHER 28.1838 uM; NOT_DETERMINED	Not recorded	pubchem.aid:1159524 assay High Throughput Screening for Foot and Mouth Disease Virus Antivirals evidence reference pubchem.aid:1159524 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1159524, deposited by NCGC; assay type Confirmatory. Source outcome: Inconclusive. Source endpoint: Potency. call NOT_DETERMINED measurement type OTHER value 28.1838 units uM
LGR2:Counterscreen with MC4R Measured in Cell-Based System Using Plate Reader - 7011-02_Antagonist_Dose_CherryPick_Activity	OTHER 3.98 uM; ACTIVE	Not recorded	pubchem.aid:743444 assay LGR2:Counterscreen with MC4R Measured in Cell-Based System Using Plate Reader - 7011-02_Antagonist_Dose_CherryPick_Activity evidence reference pubchem.aid:743444 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 743444, deposited by Broad Institute; assay type Confirmatory. Source endpoint: AC50. Target accession AAC47329 was left ungrounded because PubChem did not provide a UniProtKB accession. call ACTIVE measurement type OTHER value 3.98 units uM
Luminescence Cell-Based Dose Confimation HTS to Identify Inhibitors of Heat Shock Factor 1 (HSF1)	EC50 3.057 uM; ACTIVE	Not recorded	pubchem.aid:2382 assay Luminescence Cell-Based Dose Confimation HTS to Identify Inhibitors of Heat Shock Factor 1 (HSF1) evidence reference pubchem.aid:2382 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 2382, deposited by Broad Institute; assay type Confirmatory. Target accession AAH94064 was left ungrounded because PubChem did not provide a UniProtKB accession. call ACTIVE measurement type EC50 value 3.057 units uM activity class ENZYME_INHIBITOR
Luminescence Cell-Based Dose Confimation HTS to Identify Inhibitors of of 5'UTR Stem-Loop Driven Alpha-Synuclein mRNA Translation in H4 Neuroglioblastoma Cells	EC50 0.1 uM; ACTIVE	Not recorded	pubchem.aid:1988 assay Luminescence Cell-Based Dose Confimation HTS to Identify Inhibitors of of 5'UTR Stem-Loop Driven Alpha-Synuclein mRNA Translation in H4 Neuroglioblastoma Cells evidence reference pubchem.aid:1988 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1988, deposited by Broad Institute; assay type Confirmatory. call ACTIVE measurement type EC50 value 0.1 units uM activity class ENZYME_INHIBITOR
Luminescence Cell-Based Dose Confirmation HTS to Identify Compounds Cytotoxic to BJeLR RAS-Dependent Fibroblast	EC50 5.45 uM; NOT_DETERMINED	Not recorded	pubchem.aid:1936 assay Luminescence Cell-Based Dose Confirmation HTS to Identify Compounds Cytotoxic to BJeLR RAS-Dependent Fibroblast evidence reference pubchem.aid:1936 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1936, deposited by Broad Institute; assay type Confirmatory. Source outcome: Inconclusive. call NOT_DETERMINED measurement type EC50 value 5.45 units uM
Luminescence Cell-Based Dose Response HTS to Identify Compounds Cytotoxic to BJ-TERT RAS-Independent Fibroblast	EC50 2.082 uM; NOT_DETERMINED	Not recorded	pubchem.aid:1933 assay Luminescence Cell-Based Dose Response HTS to Identify Compounds Cytotoxic to BJ-TERT RAS-Independent Fibroblast evidence reference pubchem.aid:1933 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1933, deposited by Broad Institute; assay type Confirmatory. Source outcome: Inconclusive. call NOT_DETERMINED measurement type EC50 value 2.082 units uM
Luminescence Cell-Based Dose Response HTS to Identify Compounds Cytotoxic to BJ-TERT-LT-ST RAS-Independent Fibroblast	EC50 5.044 uM; ACTIVE	Not recorded	pubchem.aid:1935 assay Luminescence Cell-Based Dose Response HTS to Identify Compounds Cytotoxic to BJ-TERT-LT-ST RAS-Independent Fibroblast evidence reference pubchem.aid:1935 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1935, deposited by Broad Institute; assay type Confirmatory. call ACTIVE measurement type EC50 value 5.044 units uM activity class CYTOTOXIC
Luminescence Cell-Based Dose Response HTS to Identify Compounds Cytotoxic to DRD Non-Viral Oncogenic Fibroblast	EC50 4.118 uM; ACTIVE	Not recorded	pubchem.aid:1934 assay Luminescence Cell-Based Dose Response HTS to Identify Compounds Cytotoxic to DRD Non-Viral Oncogenic Fibroblast evidence reference pubchem.aid:1934 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1934, deposited by Broad Institute; assay type Confirmatory. call ACTIVE measurement type EC50 value 4.118 units uM activity class CYTOTOXIC
Luminescence Cell-Based Dose Response HTS to Identify Inhibitors of Luciferase Translation or Activity in H4 Neuroglioblastoma Cells	EC50 0.1 uM; ACTIVE	Not recorded	pubchem.aid:1990 assay Luminescence Cell-Based Dose Response HTS to Identify Inhibitors of Luciferase Translation or Activity in H4 Neuroglioblastoma Cells evidence reference pubchem.aid:1990 evidence type DATABASE_ASSERTION notes PubChem BioAssay AID 1990, deposited by Broad Institute; assay type Confirmatory. call ACTIVE measurement type EC50 value 0.1 units uM activity class ENZYME_INHIBITOR notes 109 further PubChem assay results are in data/raw/pubchem_bioassay.tsv but not written here.