{"schema":"https://ver.cy/schemas/card/1.0.0","id":"vr.tr.dihydrothymine","code":"thing-q3027885","url":"https://ver.cy/models/thing/q3027885/","name":"dihydrothymine","alternateNames":["(5R)-dihydrothymine","(5S)-dihydrothymine"],"kind":"thing","status":"published","version":"0.1.0-research.1","language":"en","classifiers":{"family":"Thing Registry","category":"Physical world and living systems","entryKind":"thing","plane":"PHY","domain":["PHY.MAT"],"industry":[],"navPath":"","tags":[],"facets":{}},"whatItIs":"Dihydrothymine is the 5,6-dihydro derivative of thymine, a reduced pyrimidine base with molecular formula C5H8N2O2 that occurs as an intermediate in thymine catabolism.","purpose":"Enable an agent to identify dihydrothymine, assess the composition and condition of a sample, and determine its suitability for chemical analysis or biochemical research.","scope":{"in":["Molecular identity and identifier reconciliation for 5,6-dihydrothymine","C5 stereochemical specification and measured enantiomer composition","Sample purity, concentration, physical form and storage history","Analytical discrimination from thymine and related pyrimidine metabolites","Evidence linking dihydrothymine to biochemical transformations","Material-specific handling evidence and research-use suitability"],"out":["Thymine, dihydrouracil and other neighbouring substances as independent chemical entities","Dihydrothymidine, nucleotides and dihydrothymine residues within nucleic acids","Complete enzyme, organism and pyrimidine-metabolism models","Patient diagnosis, disease classification and treatment decisions","Manufacturing processes and commercial formulations containing dihydrothymine"],"boundaries":[]},"distinguishingFeatures":["Its thymine-derived ring has a saturated C5-C6 bond; the neutral molecular formula is C5H8N2O2. [ChEBI](https://www.ebi.ac.uk/chebi/CHEBI:27468)","Its C5 methyl substituent distinguishes it from unsubstituted 5,6-dihydrouracil.","The free molecule has no attached sugar or phosphate, distinguishing it from dihydrothymidine and nucleotide derivatives.","It lacks the additional C5 and C6 hydroxyl substituents that define thymine glycol.","A stereochemically unspecified identity does not establish a racemic sample; C5 configuration and enantiomer proportions require separate evidence."],"structure":{"bundles":[{"id":"molecular-identity-and-stereochemistry","name":"Molecular identity and stereochemistry","description":"Establish what the dihydrothymine name identifies and what it leaves unspecified.","layers":[{"id":"constitutional-identity","name":"Constitutional identity","description":"Recognize the reduced thymine structure and reconcile its names.","findings":[{"id":"reduced-thymine-identity","name":"Reduced thymine identity","description":"Use the saturated C5-C6 bond and retained C5 methyl group as structural anchors; ChEBI records the stereochemically unspecified SMILES CC1CNC(=O)NC1=O. [ChEBI](https://www.ebi.ac.uk/chebi/CHEBI:27468)","questions":[{"text":"Does the candidate structure have the dihydrothymine ring connectivity and C5 methyl substituent?","id":"reduced-thymine-identity-q01","kind":"definition"},{"text":"Which read source establishes that each supplied name, CAS number or database identifier denotes this structure?","id":"reduced-thymine-identity-q02","kind":"provenance"}]}]},{"id":"stereochemical-scope","name":"Stereochemical scope","description":"Separate molecular configuration from the composition of a supplied sample.","findings":[{"id":"c5-configuration-evidence","name":"C5 configuration evidence","description":"Record C5 configuration and enantiomer proportions without interpreting an unspecified structure as a measured racemate.","questions":[{"text":"Does the record specify R, S, a mixture or no C5 configuration?","id":"c5-configuration-evidence-q01","kind":"definition"},{"text":"What chiral measurement or traceable preparation evidence establishes the sample's enantiomer composition?","id":"c5-configuration-evidence-q02","kind":"measurement"},{"text":"Can the configuration be represented within this registry entry without creating an unsupported separate thing?","id":"c5-configuration-evidence-q03","kind":"boundary"}]}]}]},{"id":"material-composition-and-condition","name":"Material composition and condition","description":"Characterize the actual dihydrothymine material presented for use.","layers":[{"id":"assay-and-related-substances","name":"Assay and related substances","description":"Distinguish dihydrothymine content from impurities, solvent and water.","findings":[{"id":"usable-dihydrothymine-content","name":"Usable dihydrothymine content","description":"Require the assay basis and identify relevant related-substance contamination, including thymine and dihydrouracil where applicable.","questions":[{"text":"Is the reported purity an absolute assay, chromatographic area percentage or another quantity?","id":"usable-dihydrothymine-content-q01","kind":"measurement"},{"text":"Which related pyrimidines, residual solvents and water contributions were measured, and at what detection limits?","id":"usable-dihydrothymine-content-q02","kind":"measurement"}]}]},{"id":"physical-form-and-stability","name":"Physical form and stability","description":"Connect physical-property and stability observations to the tested material and conditions.","findings":[{"id":"condition-dependent-material-state","name":"Condition-dependent material state","description":"Record observed form, dissolution behaviour and chemical integrity without assigning unsupported melting, boiling or shelf-life values.","questions":[{"text":"What form, solvent, pH and temperature apply to the reported solubility or thermal observation?","id":"condition-dependent-material-state-q01","kind":"measurement"},{"text":"What data establish dihydrothymine integrity during storage, solution preparation and repeated thawing where applicable?","id":"condition-dependent-material-state-q02","kind":"provenance"},{"text":"What observed change requires reanalysis or rejection before use?","id":"condition-dependent-material-state-q03","kind":"action"}]}]}]},{"id":"analytical-recognition-and-quantification","name":"Analytical recognition and quantification","description":"Establish whether dihydrothymine is present and how much is present.","layers":[{"id":"structural-discrimination","name":"Structural discrimination","description":"Test the dihydrothymine assignment against realistic chemical alternatives.","findings":[{"id":"orthogonal-identity-check","name":"Orthogonal identity check","description":"Combine appropriate reference-standard, chromatographic, mass-spectral or NMR evidence and state whether stereoisomers are resolved.","questions":[{"text":"What evidence distinguishes the signal from thymine, dihydrouracil, thymine glycol and dihydrothymidine?","id":"orthogonal-identity-check-q01","kind":"measurement"},{"text":"Does the method identify total dihydrothymine or resolve individual C5 enantiomers?","id":"orthogonal-identity-check-q02","kind":"boundary"},{"text":"Which authenticated standard or spectral record supports the identification?","id":"orthogonal-identity-check-q03","kind":"provenance"}]}]},{"id":"matrix-specific-quantification","name":"Matrix-specific quantification","description":"Preserve the measurement basis for standards, reaction mixtures and biological specimens.","findings":[{"id":"defensible-concentration","name":"Defensible concentration","description":"Tie dihydrothymine concentration to calibration, recovery, matrix effects and any normalization applied.","questions":[{"text":"What calibration range, recovery, quantification limit and uncertainty apply in this matrix?","id":"defensible-concentration-q01","kind":"measurement"},{"text":"Is the result an absolute concentration, a normalized specimen value or a ratio to another metabolite?","id":"defensible-concentration-q02","kind":"definition"},{"text":"What specimen preparation or analytical interference could change the apparent dihydrothymine amount?","id":"defensible-concentration-q03","kind":"boundary"}]}]}]},{"id":"biochemical-transformations-and-context","name":"Biochemical transformations and context","description":"Represent evidenced formation, consumption and occurrence of dihydrothymine.","layers":[{"id":"reaction-participation","name":"Reaction participation","description":"Resolve the thymine degradation branch and its enzyme-specific substrate requirements.","findings":[{"id":"formation-and-ring-opening","name":"Formation and ring opening","description":"Require source-checked reaction records for thymine reduction and subsequent dihydrothymine ring opening, explicitly checking methyl-group retention and stereochemistry.","questions":[{"text":"Which enzyme, organism and reaction evidence establish formation of the specified dihydrothymine stereoisomer from thymine?","id":"formation-and-ring-opening-q01","kind":"provenance"},{"text":"Does the evidenced ring-opening product retain the methyl substituent, distinguishing the thymine branch from the uracil branch?","id":"formation-and-ring-opening-q02","kind":"definition"},{"text":"What stereochemical and assay conditions determine whether this material is a suitable enzyme substrate?","id":"formation-and-ring-opening-q03","kind":"action"}]}]},{"id":"biological-occurrence","name":"Biological occurrence","description":"Connect observations to a defined organism, specimen and experimental setting.","findings":[{"id":"contextualized-metabolite-observation","name":"Contextualized metabolite observation","description":"Keep endogenous occurrence, experimentally added material and clinical interpretation distinct.","questions":[{"text":"Which organism, specimen, compartment and collection conditions apply to the observation?","id":"contextualized-metabolite-observation-q01","kind":"provenance"},{"text":"Was dihydrothymine endogenous, added as a standard or generated during the experiment or sample handling?","id":"contextualized-metabolite-observation-q02","kind":"boundary"},{"text":"What additional evidence is required before relating its concentration to enzyme activity or metabolic flux?","id":"contextualized-metabolite-observation-q03","kind":"boundary"}]}]}]},{"id":"research-use-and-handling","name":"Research use and handling","description":"Translate material evidence into decisions about dihydrothymine use and handling.","layers":[{"id":"fitness-for-research-use","name":"Fitness for research use","description":"Determine whether a dihydrothymine lot meets the requirements of a specified experiment.","findings":[{"id":"standard-or-substrate-qualification","name":"Standard or substrate qualification","description":"Match identity, assay, stereochemical composition and stability evidence to the intended calibration or biochemical role.","questions":[{"text":"Does this use require total dihydrothymine, a specified enantiomer or a certified quantitative standard?","id":"standard-or-substrate-qualification-q01","kind":"action"},{"text":"Do the lot certificate and independent checks establish adequate assay, impurity limits and solution stability?","id":"standard-or-substrate-qualification-q02","kind":"provenance"}]}]},{"id":"hazard-and-regulatory-evidence","name":"Hazard and regulatory evidence","description":"Associate handling decisions with the supplied dihydrothymine material and applicable jurisdiction.","findings":[{"id":"documented-handling-basis","name":"Documented handling basis","description":"Record verified SDS and regulatory information while distinguishing missing hazard data from an affirmative classification.","questions":[{"text":"Which current SDS covers this dihydrothymine form or solution, and what handling and disposal conditions does it specify?","id":"documented-handling-basis-q01","kind":"provenance"},{"text":"Are an EC identifier, GHS classification or exposure limit explicitly documented for the relevant identity and jurisdiction?","id":"documented-handling-basis-q02","kind":"provenance"},{"text":"Which documented precautions apply to weighing the solid or handling its actual solvent formulation?","id":"documented-handling-basis-q03","kind":"action"}]}]}]},{"id":"evidence-and-external-alignment","name":"Evidence and external alignment","description":"What the world already says about this thing, gathered so the model can be checked against it.","layers":[{"id":"reported-evidence","name":"Reported evidence","description":"Findings from the breadth pass, kept separate from the structural claims.","findings":[{"id":"evidence-confidence-notes","name":"Check these first","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these check these first hold for the sense of dihydrothymine this model covers, and on what evidence?","id":"evidence-confidence-notes-q01","kind":"provenance"}]},{"id":"evidence-kinds","name":"Kinds and varieties","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these kinds and varieties hold for the sense of dihydrothymine this model covers, and on what evidence?","id":"evidence-kinds-q01","kind":"provenance"}]},{"id":"evidence-identifiers","name":"Identifiers and schemes","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these identifiers and schemes hold for the sense of dihydrothymine this model covers, and on what evidence?","id":"evidence-identifiers-q01","kind":"provenance"}]},{"id":"evidence-real-world-use","name":"Real-world use","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these real-world use hold for the sense of dihydrothymine this model covers, and on what evidence?","id":"evidence-real-world-use-q01","kind":"provenance"}]},{"id":"evidence-measurements","name":"Typical measurements","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these typical measurements hold for the sense of dihydrothymine this model covers, and on what evidence?","id":"evidence-measurements-q01","kind":"provenance"}]},{"id":"evidence-failure-modes-and-hazards","name":"Failure modes and hazards","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these failure modes and hazards hold for the sense of dihydrothymine this model covers, and on what evidence?","id":"evidence-failure-modes-and-hazards-q01","kind":"provenance"}]},{"id":"evidence-neighbours","name":"Neighbouring kinds and how to tell them apart","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these neighbouring kinds and how to tell them apart hold for the sense of dihydrothymine this model covers, and on what evidence?","id":"evidence-neighbours-q01","kind":"provenance"}]}]}]}]},"agentConduct":{"may":["Explain the role of dihydrothymine in thymine breakdown from cited sources.","Report laboratory measurements of dihydrothymine with method and reference range."],"mustNot":["Diagnose an enzyme deficiency in a person from a single measurement.","Present research findings as clinical guidance on drug dosing.","Confuse dihydrothymine with thymine or dihydrouracil in records."],"requiresHuman":["Using metabolite results in decisions about a patient's chemotherapy."]},"ethics":{"considerations":["Pyrimidine breakdown defects affect how some patients tolerate certain cancer drugs, so accuracy matters.","Metabolic test results are sensitive health data."],"affectedParties":["Patients tested","Clinicians","Researchers"]},"owners":{"steward":"Nobody owns the compound; the laboratory answers for its samples and results.","roles":[],"masterSystems":["Metabolite and chemical substance databases"]},"relations":[{"target":"Q47069735","type":"parent","note":"registry parent class"}],"interaction":{"identity":{"applicability":"required","items":["Vercy registry: vr.tr.dihydrothymine","Wikidata: Q3027885 (https://www.wikidata.org/wiki/Q3027885)"]},"properties":{"applicability":"required","items":["Chemical identity anchors: 5,6-dihydrothymine; C5H8N2O2; CHEBI:27468; CAS 696-04-8","C5 stereochemical composition: R, S, racemic, measured non-racemic mixture or unspecified; enantiomer fractions in %","Dihydrothymine assay and impurity profile: Mass fraction % or molar fraction %, with method and reporting basis","Sample concentration: mol/L, µmol/L or mg/L; matrix and dilution basis required","Physical form and solution conditions: Observed solid or solution form; solvent, pH, temperature in °C and pressure where relevant","Thermal and solubility measurements: Melting or decomposition interval in °C; solubility in g/L or mol/L with conditions","Analytical identification confidence: Tentative, reference-standard matched or orthogonally confirmed; supporting method records","Biochemical participation: Precursor, product, enzyme, organism, compartment and supporting experiment","Storage and handling evidence: Storage conditions, preparation date, stability evidence and jurisdiction-specific SDS status"]},"recognition":{"applicability":"required","items":["A white solid supplied as a reference standard, identified by label and analysis.","Detected in body fluids only by laboratory methods such as chromatography."]},"capabilities":{"applicability":"required","items":["Resolve a named material or database record to dihydrothymine while preserving stereochemical uncertainty.","Select identity tests that distinguish dihydrothymine from related pyrimidines and sugar-containing derivatives.","Prepare or evaluate a quantified research solution using documented assay, solvent and stability information.","Assess whether a lot qualifies as a calibration standard or biochemical substrate.","Link measured dihydrothymine to an evidenced metabolic reaction and specimen context.","Accept, quarantine or request requalification of material using its identity, purity and condition records."]},"hazards":{"applicability":"required","items":["Confusion with related bases leads to wrong interpretation of tests.","Unvalidated assays can give misleading results."]},"interfaces":{"applicability":"required","items":["The Globally Harmonized System of Classification and Labelling of Chemicals, published by the United Nations Economic Commission for Europe, provides the framework for evaluating and communicating chemical hazards without establishing a specific hazard classification for dihydrothymine."]},"context":{"applicability":"required","items":["Dihydrothymine is encountered in biochemical research on thymine breakdown and pyrimidine metabolism.","It can serve as an analytical reference substance when measuring metabolites or investigating the enzymes involved in this pathway."]}},"sources":[{"title":"Wikidata item Q3027885: dihydrothymine","url":"https://www.wikidata.org/wiki/Q3027885","note":"identity and sense of the item"},{"title":"Wikipedia: Dihydrothymine","url":"https://en.wikipedia.org/wiki/Dihydrothymine","note":"general description of the item"}],"openQuestions":["Should the registry definition explicitly cover all C5 stereochemical forms, and which external identifiers denote unspecified, racemic or individual-enantiomer material?","Which primary biochemical sources establish the physiological stereoisomer and the correctly methylated ring-opening product, resolving inconsistent pathway summaries?","What experimentally supported solubility, thermal-transition and decomposition data exist for well-characterized dihydrothymine material?","What storage and solution-stability evidence supports particular solvent, pH, temperature and holding-time limits?","Which authoritative records establish applicable EC identifiers, hazard classifications and exposure limits, and where is information simply unavailable?"],"resources":{"spec":"/models/things/publications/thing-q3027885/spec.json"},"provenance":{"origin":"thing registry research (pass 2)","builtFrom":["models/things/publications/thing-q3027885/spec.json"],"providers":["Codex"],"researchStatus":"unreviewed","generatedAt":"2026-09-12T09:11:23Z","builder":"tools/build_cards.py@1.0.0"},"completeness":{"sections":{"classifiers":"filled","whatItIs":"filled","purpose":"filled","distinguishingFeatures":"filled","structure":"filled","agentConduct":"filled","ethics":"filled","owners":"filled","relations":"filled","interaction.identity":"filled","interaction.properties":"filled","interaction.recognition":"filled","interaction.capabilities":"filled","interaction.hazards":"filled","interaction.interfaces":"filled","interaction.context":"filled","sources":"filled"},"notes":{"_gate":"Published through the thing publication gate 1.0 on 2026-10-07T10:10:29+00:00: completeness 1.00; sense: Wikidata description; 2 live sources; review by codex: pass"},"score":1.0}}