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adenine arabinoside

CHEBI:45327 EXACT SEEDED antimicrobial unspecified

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REVIEWED records curator sign-off on identity, structure, filing class and producer claims; DEPRECATED retains a superseded or out-of-scope record.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 purine nucleoside in which adenine is attached to arabinofuranose via a β-N9-glycosidic bond.

Structure

Standard InChIKeyOIRDTQYFTABQOQ-UHTZMRCNSA-N
SMILESC1=NC2=C(C(=N1)N)N=CN2[C@H]3[C@H]([C@@H]([C@H](O3)CO)O)O
Stereochemistryfully defined

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.

TaxonBasisClusterEvidence
Streptomyces antibioticus
NCBITaxon:1890		 SOURCE_ASSERTION mibig:BGC0001735 PMID:28111097

Occurrences 6

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.

TaxonSourceReference
Eunicella cavolini
NCBITaxon:317547		 LOTUS DOI:10.1007/BF01952539
Daucus carota
NCBITaxon:4039		 LOTUS DOI:10.1016/0008-6215(84)85339-2
Tillandsia usneoides
NCBITaxon:49541		 LOTUS DOI:10.1021/NP50122A023
Streptomyces herbaceus
NCBITaxon:887449		 LOTUS DOI:10.7164/ANTIBIOTICS.32.1050
Streptomyces antibioticus
NCBITaxon:1890		 LOTUS DOI:10.7164/ANTIBIOTICS.32.1050
Streptomyces antibioticus
NCBITaxon:1890		 LOTUS DOI:10.7164/ANTIBIOTICS.45.1914

Biosynthetic gene clusters 1

AccessionHostLocus evidenceGenome
mibig:BGC0001735 Streptomyces antibioticus
NCBITaxon:1890 		CLUSTER_UNSTATED genbank:KJ856912.1

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.

Biosynthesis curated

Written by a curator with claim-level evidence on each step; not derived from a source. This is what the rest of the record exists to support.

StepEnzymeReactionSubstrate → productEvidence
1 PenF arabinoside monophosphate 5'-nucleotidase
UniProtKB:A0A1S5NPU2		 pubchem.compound:34768 → CHEBI:45327 DOI:10.3390/biom14111368

Step 1: PenF hydrolyzes vidarabine phosphate, also called vidarabine 5'-monophosphate or Ara-AMP, to adenine arabinoside (Ara-A, vidarabine) in vitro. This partial Streptomyces antibioticus NRRL 3238 pathway records the biochemically supported conversion as a proposed vidarabine biosynthetic step and leaves the upstream formation of Ara-AMP unresolved.

Mechanism & Biosynthesis Overview

PRODUCERS & OCCURRENCE 1 producer (0 causal) 6 cited occurrences BIOSYNTHETIC LOCUS 1 gene cluster 1 curated pathway step NATURAL PRODUCT adenine arabinoside CHEBI:45327 Carbohydrates TARGETS & BIOACTIVITY 0 molecular targets 0 bioactivities · 1 graph

Causal graph — biosynthesis 3 nodes, 2 edges

Proposed Streptomyces antibioticus NRRL 3238 PenF dephosphorylation of vidarabine phosphate during adenine arabinoside biosynthesis.

SubjectPredicateObjectNotesEvidence
vidarabine phosphate is dephosphorylated by PenF Recombinant PenF catalyzes hydrolytic dephosphorylation of Ara-AMP to Ara-A; the in-cluster step is proposed because the source did not identify the upstream enzyme that forms the Ara-AMP substrate.
DOI:10.3390/biom14111368
https://www.ncbi.nlm.nih.gov/nuccore/KJ856912.1
https://www.ncbi.nlm.nih.gov/protein/AKA87335.1
https://mibig.secondarymetabolites.org/repository/BGC0001735.5/BGC0001735.gbk
https://www.uniprot.org/uniprotkb/A0A1S5NPU2
  • reference
    DOI:10.3390/biom14111368
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    PenF catalyzed the hydrolysis of Ara-AMP into Ara-A
    notes
    Li et al. recombinantly expressed S. antibioticus NRRL 3238 PenF, identified its source sequence as NCBI Protein AKA87335.1, and biochemically characterized vidarabine 5'-monophosphate hydrolysis to Ara-A by HPLC and LC-MS.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/KJ856912.1
    evidence type
    DATABASE_ASSERTION
    snippet
    gene="penF"
    retrieved on
    2026-10-01
    notes
    GenBank KJ856912.1 maps Streptomyces antibioticus NRRL 3238 penF to the 18484..19560 CDS and assigns protein_id AKA87335.1.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/AKA87335.1
    evidence type
    DATABASE_ASSERTION
    snippet
    metal dependent phosphohydrolase
    retrieved on
    2026-10-01
    notes
    NCBI GenPept AKA87335.1 is the 358 aa Streptomyces antibioticus PenF coding sequence used by Li et al.; its sequence is identical to the current UniProtKB:A0A1S5NPU2 FASTA.
  • reference
    https://mibig.secondarymetabolites.org/repository/BGC0001735.5/BGC0001735.gbk
    evidence type
    DATABASE_ASSERTION
    snippet
    protein_id="AKA87335.1"
    retrieved on
    2026-10-01
    notes
    MIBiG BGC0001735.5 places penF at 18484..19560 in the Streptomyces antibioticus pentostatin and vidarabine gene cluster and annotates the CDS as AKA87335.1 metal dependent phosphohydrolase.
  • reference
    https://www.uniprot.org/uniprotkb/A0A1S5NPU2
    evidence type
    DATABASE_ASSERTION
    snippet
    GN=penF
    retrieved on
    2026-10-01
    notes
    Current UniProtKB:A0A1S5NPU2 resolves as the unreviewed 358 aa Streptomyces antibioticus metal dependent phosphohydrolase PenF; the retrieved UniProt JSON had no EMBL KJ856912.1 xref, so this grounding was accepted from the resolved accession, organism, gene, product, length and exact sequence identity to GenPept AKA87335.1.
PenF forms adenine arabinoside PenF forms adenine arabinoside from the phosphorylated precursor in vitro and is proposed to act as a 5'-nucleotidase in vidarabine biosynthesis.
DOI:10.3390/biom14111368
https://www.ncbi.nlm.nih.gov/nuccore/KJ856912.1
https://www.ncbi.nlm.nih.gov/protein/AKA87335.1
https://mibig.secondarymetabolites.org/repository/BGC0001735.5/BGC0001735.gbk
https://www.uniprot.org/uniprotkb/A0A1S5NPU2
  • reference
    DOI:10.3390/biom14111368
    evidence type
    PRIMARY_EXPERIMENT
    snippet
    PenF catalyzed the hydrolysis of Ara-AMP into Ara-A
    notes
    Li et al. recombinantly expressed S. antibioticus NRRL 3238 PenF, identified its source sequence as NCBI Protein AKA87335.1, and biochemically characterized vidarabine 5'-monophosphate hydrolysis to Ara-A by HPLC and LC-MS.
  • reference
    https://www.ncbi.nlm.nih.gov/nuccore/KJ856912.1
    evidence type
    DATABASE_ASSERTION
    snippet
    gene="penF"
    retrieved on
    2026-10-01
    notes
    GenBank KJ856912.1 maps Streptomyces antibioticus NRRL 3238 penF to the 18484..19560 CDS and assigns protein_id AKA87335.1.
  • reference
    https://www.ncbi.nlm.nih.gov/protein/AKA87335.1
    evidence type
    DATABASE_ASSERTION
    snippet
    metal dependent phosphohydrolase
    retrieved on
    2026-10-01
    notes
    NCBI GenPept AKA87335.1 is the 358 aa Streptomyces antibioticus PenF coding sequence used by Li et al.; its sequence is identical to the current UniProtKB:A0A1S5NPU2 FASTA.
  • reference
    https://mibig.secondarymetabolites.org/repository/BGC0001735.5/BGC0001735.gbk
    evidence type
    DATABASE_ASSERTION
    snippet
    protein_id="AKA87335.1"
    retrieved on
    2026-10-01
    notes
    MIBiG BGC0001735.5 places penF at 18484..19560 in the Streptomyces antibioticus pentostatin and vidarabine gene cluster and annotates the CDS as AKA87335.1 metal dependent phosphohydrolase.
  • reference
    https://www.uniprot.org/uniprotkb/A0A1S5NPU2
    evidence type
    DATABASE_ASSERTION
    snippet
    GN=penF
    retrieved on
    2026-10-01
    notes
    Current UniProtKB:A0A1S5NPU2 resolves as the unreviewed 358 aa Streptomyces antibioticus metal dependent phosphohydrolase PenF; the retrieved UniProt JSON had no EMBL KJ856912.1 xref, so this grounding was accepted from the resolved accession, organism, gene, product, length and exact sequence identity to GenPept AKA87335.1.

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

Elsewhere in the fleet

Explore across X-Mech

AntibioticMech (adenine arabinoside) ↗ MediaIngredientMech (CHEBI:45327) ↗ TaxonMech: Streptomyces antibioticus (NCBITaxon:1890) ↗ PathwayMech (mibig:BGC0001735) ↗

Open questions 1

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

Provenance

Source conceptSourceVersion
BGC0001735MIBIG5
CHEBI:45327CHEBI3-star

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