{"schema":"https://ver.cy/schemas/card/1.0.0","id":"vr.tr.crotonoyl-coa","code":"thing-q303169","url":"https://ver.cy/models/thing/q303169/","name":"crotonoyl-CoA","alternateNames":[],"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":"Crotonoyl-CoA, usually called crotonyl-CoA, is the coenzyme A thioester of crotonic acid, ordinarily referring to the trans (E) but-2-enoyl compound that participates in intermediary metabolism and supplies crotonyl groups for protein lysine crotonylation.","purpose":"Enable an AI agent to identify crotonoyl-CoA, assess the identity and condition of a preparation, and judge its suitability for a specified biochemical use.","scope":{"in":["Resolution of the registry name to a verified molecular structure and chemical identifiers","Acyl-chain connectivity, double-bond geometry and linkage to coenzyme A","Protonation, counterions, hydration and preparation composition","Identity, concentration, purity and degradation measurements","Evidence for participation in specified enzyme reactions","Preparation-specific storage, handling and hazard information"],"out":["Coenzyme A and other acyl-CoA compounds as independently modelled substances","Enzymes that produce or consume the compound","Complete metabolic pathways and their regulation","Protein crotonylation as a biological process","Commercial reagent products, packaging and supplier organisations","Organism-level effects inferred solely from detection of the metabolite"],"boundaries":[]},"distinguishingFeatures":["Require structural evidence that the registry name denotes the intended unsaturated four-carbon acyl-CoA rather than treating spelling similarity to crotonyl-CoA as sufficient identification.","Distinguish a covalent acyl-CoA thioester from free crotonic acid, free coenzyme A or a mixture of those substances.","Record double-bond position and geometry explicitly; a cis or differently positioned unsaturated acyl group must not be silently equated with a trans-2 assignment.","Distinguish the unsaturated acyl group from the saturated acyl group of butyryl-CoA using evidence appropriate to the analytical method.","Separate the molecular entity from its salt or hydrated preparation so that counterion and water content do not silently alter mass-based concentration calculations."],"structure":{"bundles":[{"id":"molecular-identity","name":"Molecular identity","description":"Resolve what crotonoyl-CoA denotes before assigning properties or biochemical roles.","layers":[{"id":"registry-name-resolution","name":"Registry name resolution","description":"Connect the supplied name to independently documented chemical identity.","findings":[{"id":"crotonoyl-crotonyl-equivalence","name":"Crotonoyl and crotonyl equivalence","description":"Treat the apparent relationship between these names as an identity question requiring verification.","questions":[{"text":"Which authoritative chemical record establishes what the registry name crotonoyl-CoA denotes?","id":"crotonoyl-crotonyl-equivalence-q01","kind":"definition"},{"text":"Does that record explicitly support equivalence to crotonyl-CoA, and which structure-specific identifiers does it assign?","id":"crotonoyl-crotonyl-equivalence-q02","kind":"provenance"}]}]},{"id":"structural-boundaries","name":"Structural boundaries","description":"Specify the acyl group, its geometry and its attachment to coenzyme A.","findings":[{"id":"acyl-coa-structure-assignment","name":"Acyl-CoA structure assignment","description":"Make structural assignments explicit enough to exclude neighbouring acyl-CoA entities.","questions":[{"text":"What evidence establishes the four-carbon acyl connectivity, double-bond position and E/Z geometry?","id":"acyl-coa-structure-assignment-q01","kind":"definition"},{"text":"What evidence distinguishes the intended coenzyme A thioester from butyryl-CoA, positional or geometric isomers, and free-acid mixtures?","id":"acyl-coa-structure-assignment-q02","kind":"boundary"}]}]}]},{"id":"chemical-form-and-amount","name":"Chemical form and amount","description":"Relate the molecular entity to the material weighed, dissolved and delivered.","layers":[{"id":"salt-and-solvation","name":"Salt and solvation","description":"Identify the form to which formula and mass statements apply.","findings":[{"id":"preparation-formula-basis","name":"Preparation formula basis","description":"Keep molecular identity distinct from the composition of a supplied preparation.","questions":[{"text":"Which protonation state, counterions and hydration or solvation levels are documented for this preparation?","id":"preparation-formula-basis-q01","kind":"definition"},{"text":"Does the stated formula mass describe the parent entity, a specified salt or a preparation with variable water content?","id":"preparation-formula-basis-q02","kind":"boundary"}]}]},{"id":"assay-available-amount","name":"Assay-available amount","description":"Establish the concentration of intact compound under intended assay conditions.","findings":[{"id":"intact-acyl-coa-quantitation","name":"Intact acyl-CoA quantitation","description":"Require a concentration basis that accounts for preparation composition and analytical selectivity.","questions":[{"text":"How was intact crotonoyl-CoA concentration measured, and what calibration and uncertainty accompany the result?","id":"intact-acyl-coa-quantitation-q01","kind":"measurement"},{"text":"How should the required assay volume be calculated after accounting for chemical form, purity and dilution?","id":"intact-acyl-coa-quantitation-q02","kind":"action"}]}]}]},{"id":"analytical-identity-and-integrity","name":"Analytical identity and integrity","description":"Evaluate whether a preparation contains the intended intact species at acceptable quality.","layers":[{"id":"identity-evidence","name":"Identity evidence","description":"Combine measurements that resolve the specific identity claims being made.","findings":[{"id":"orthogonal-structure-confirmation","name":"Complementary structure confirmation","description":"Record what chromatography, mass spectrometry, spectroscopy or reference comparison actually establishes.","questions":[{"text":"Which observations support intact acyl-CoA identity, and which independently resolve double-bond position or geometry?","id":"orthogonal-structure-confirmation-q01","kind":"measurement"},{"text":"Was the comparison standard authenticated for the same isomer and chemical form?","id":"orthogonal-structure-confirmation-q02","kind":"provenance"}]}]},{"id":"impurities-and-transformation","name":"Impurities and transformation","description":"Track components and changes that could compromise an acyl-CoA preparation.","findings":[{"id":"impurity-specific-acceptance","name":"Impurity-specific acceptance","description":"Assess free coenzyme A, free acid, related acyl-CoAs and unidentified components without assuming their origin.","questions":[{"text":"Which impurities are detected, at what levels, and with what detection limits and response-factor assumptions?","id":"impurity-specific-acceptance-q01","kind":"measurement"},{"text":"What evidence distinguishes components present initially from products formed during storage or assay preparation?","id":"impurity-specific-acceptance-q02","kind":"provenance"},{"text":"Which impurity limits are necessary for the intended enzyme assay or analytical calibration?","id":"impurity-specific-acceptance-q03","kind":"action"}]}]}]},{"id":"biochemical-participation","name":"Biochemical participation","description":"Connect the verified compound to experimentally supported transformations and uses.","layers":[{"id":"reaction-specific-role","name":"Reaction-specific role","description":"Describe documented production and consumption without treating pathway labels as sufficient evidence.","findings":[{"id":"enzyme-transformation-evidence","name":"Enzyme transformation evidence","description":"Resolve reported hydration, reduction or other transformations into explicit, supported reactions.","questions":[{"text":"Which reactions directly demonstrate consumption or formation of the verified species, with what products and stoichiometry?","id":"enzyme-transformation-evidence-q01","kind":"provenance"},{"text":"Which enzyme, cofactors, pH and substrate geometry were used to establish each reaction?","id":"enzyme-transformation-evidence-q02","kind":"boundary"}]}]},{"id":"assay-and-biological-interpretation","name":"Assay and biological interpretation","description":"Separate demonstrated reagent function from broader claims about metabolism or acyl transfer.","findings":[{"id":"use-specific-evidence","name":"Use-specific evidence","description":"Qualify intended uses through direct measurements and appropriate controls.","questions":[{"text":"What evidence supports use of this species as the intended enzyme substrate, analytical standard or crotonyl-group donor?","id":"use-specific-evidence-q01","kind":"provenance"},{"text":"Which controls distinguish the intended reaction from spontaneous change, impurity activity or assay interference?","id":"use-specific-evidence-q02","kind":"action"},{"text":"What additional evidence is required before a measured pool or reaction rate supports a claim about cellular flux or protein crotonylation?","id":"use-specific-evidence-q03","kind":"boundary"}]}]}]},{"id":"storage-and-handling","name":"Storage and handling","description":"Define evidence-based conditions for retaining and using a qualified preparation.","layers":[{"id":"stability-window","name":"Stability window","description":"Relate retained integrity to solvent, pH, temperature and storage history.","findings":[{"id":"condition-dependent-requalification","name":"Condition-dependent requalification","description":"Use measured retention of intact compound to establish storage and reuse limits.","questions":[{"text":"How much intact compound remains after defined storage intervals, temperatures, solution conditions and freeze-thaw cycles?","id":"condition-dependent-requalification-q01","kind":"measurement"},{"text":"Which documented conditions and acceptance thresholds determine whether a stored aliquot can be used or requires requalification?","id":"condition-dependent-requalification-q02","kind":"action"}]}]},{"id":"preparation-specific-safety","name":"Preparation-specific safety","description":"Attach handling requirements to the actual substance form and formulation.","findings":[{"id":"applicable-hazard-record","name":"Applicable hazard record","description":"Distinguish documented hazards from missing assessments and formulation-dependent requirements.","questions":[{"text":"Which current safety data and regulatory identifiers apply to this exact chemical form and preparation?","id":"applicable-hazard-record-q01","kind":"provenance"},{"text":"What handling and disposal measures follow from those records and from any solvent or additive present?","id":"applicable-hazard-record-q02","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 crotonoyl-CoA this model covers, and on what evidence?","id":"evidence-confidence-notes-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 crotonoyl-CoA 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 crotonoyl-CoA this model covers, and on what evidence?","id":"evidence-real-world-use-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 crotonoyl-CoA 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 crotonoyl-CoA this model covers, and on what evidence?","id":"evidence-neighbours-q01","kind":"provenance"}]}]}]}]},"agentConduct":{"may":["Describe crotonyl-CoA and its place in metabolism and histone modification from biochemical sources.","Annotate metabolic pathways with it using recognized databases."],"mustNot":["Present research findings on crotonylation as established medical fact.","Promote supplements or diets as raising or lowering it without evidence.","Confuse the trans and cis forms or related acyl-CoA species in reports."],"requiresHuman":["Publishing claims about it that inform clinical decisions."]},"ethics":{"considerations":["Early research on its role in gene regulation can be overstated to sell products.","Accurate pathway data matters for diagnosis of metabolic disorders."],"affectedParties":["Researchers","Patients with metabolic disorders"]},"owners":{"steward":"Nobody owns the molecule; curated metabolic databases maintain records of it.","roles":[],"masterSystems":["Metabolic pathway and compound databases"]},"relations":[{"target":"Q27104386","type":"parent","note":"registry parent class"},{"target":"Q33616143","type":"parent","note":"registry parent class"}],"interaction":{"identity":{"applicability":"required","items":["Vercy registry: vr.tr.crotonoyl-coa","Wikidata: Q303169 (https://www.wikidata.org/wiki/Q303169)"]},"properties":{"applicability":"required","items":["Verified molecular identity: Source-supported preferred name, structure representation and identifiers; unresolved where unverified","Acyl-chain structure: Carbon connectivity, double-bond position and E/Z assignment, each with evidence","Coenzyme A linkage and stereochemistry: Acyl attachment site, linkage type and assigned stereochemistry","Preparation chemical form: Protonation convention, counterion identity and stoichiometry, hydration and solvation","Intact compound concentration: mol/L or mmol/L, with method, calibration and uncertainty","Purity and impurity profile: Mass fraction, mole fraction or chromatographic area percentage, with method and identified impurities","Preparation condition: Physical form, solvent, pH, temperature, elapsed storage time and freeze-thaw history","Reaction-specific biochemical role: Named reaction, enzyme, role, direction, organism or experimental system, and supporting evidence","Handling evidence status: Applicable safety documentation, assessed hazards, unassessed hazards and jurisdiction"]},"recognition":{"applicability":"required","items":["Not visible; detected by laboratory methods such as mass spectrometry."]},"capabilities":{"applicability":"required","items":["Resolve a label or registry reference to a source-supported structure and flag unresolved naming or isomer ambiguity.","Compare a preparation with an authenticated reference using complementary analytical evidence.","Calculate an assay amount from verified chemical form, purity and intact-compound concentration.","Assess whether a preparation meets the identity and impurity requirements of a specified enzyme assay.","Track storage history and analytical change to determine whether requalification is needed.","Link measured consumption or formation to a specified reaction while preserving uncertainty about biological interpretation."]},"hazards":{"applicability":"required","items":["Misannotation can mislead metabolic research and diagnosis."]},"interfaces":{"applicability":"required","items":["The Globally Harmonized System of Classification and Labelling of Chemicals, issued by the United Nations, provides the framework for assessing and communicating preparation-specific chemical hazards where adopted."]},"context":{"applicability":"required","items":["Crotonyl-CoA occurs in intermediary metabolism and is studied as a substrate or intermediate in enzyme reactions involving short-chain acyl groups.","Biochemical research uses it as a crotonyl-group donor to investigate protein lysine crotonylation.","Suitability for an experiment depends on the preparation's chemical identity, purity, concentration and stability."]}},"sources":[{"title":"Wikidata item Q303169: crotonoyl-CoA","url":"https://www.wikidata.org/wiki/Q303169","note":"identity and sense of the item"},{"title":"Wikipedia: Crotonyl-CoA","url":"https://en.wikipedia.org/wiki/Crotonyl-CoA","note":"general description of the item"}],"openQuestions":["Does crotonoyl-CoA denote the same entity as crotonyl-CoA, and does this registry entry specify trans-2 geometry or leave geometry unresolved?","Which authoritative structure record, CAS number, PubChem CID or other identifiers match the intended entity rather than a particular salt or broader isomer class?","Which analytical methods and authenticated standards can distinguish relevant isomers and quantify intact compound separately from free coenzyme A and related acyl-CoAs?","What preparation-specific solubility and stability data support stock preparation, storage duration and freeze-thaw limits?","Which biochemical uses, hazard classifications and exposure guidance are directly supported for the verified entity and its supplied forms?"],"resources":{"spec":"/models/things/publications/thing-q303169/spec.json"},"provenance":{"origin":"thing registry research (pass 2)","builtFrom":["models/things/publications/thing-q303169/spec.json"],"providers":["Codex"],"researchStatus":"unreviewed","generatedAt":"2026-09-12T08:55:11Z","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}}