{"id":"0bb47702-4890-56b8-ab8b-d8574564fe47","stable_key":"1310afbd-6010-586e-805d-551d846da421:b6-neuro-ginkgotoxin-binding","predicate":"occupies-substrate-site-of","statement":"Human PDXK crystallography placed ginkgotoxin at the pyridoxal-binding site alongside MgATP.","claim_class":"mechanistic","status":"source_derived_draft","evidence_grade":"ungraded","direction":"negative","is_public":true,"mechanism_event_id":"a21d568b-5346-538b-a52a-781a0749245e","mechanism_event_label":"The structure directly locates the competing toxin.","subject":{"id":"fd3806da-7e3c-571c-9775-6cd843bcbf9b","slug":"ginkgotoxin","display_name":"Ginkgotoxin / 4-prime-O-methylpyridoxine","entity_type_key":"small_molecule"},"object":{"id":"d2d46db7-13a4-595f-adaa-70ad6ca31a6c","slug":"pdxk","display_name":"Pyridoxal kinase / PDXK","entity_type_key":"protein"},"evidence_count":1,"mechanism_event":{"id":"a21d568b-5346-538b-a52a-781a0749245e","stable_key":"1310afbd-6010-586e-805d-551d846da421:b6-neuro-ginkgotoxin-binding-event","event_type":"biochemical_relationship","label":"The structure directly locates the competing toxin.","description":"Human PDXK crystallography placed ginkgotoxin at the pyridoxal-binding site alongside MgATP.","status":"provisional","compartment":null,"participants":[{"entity":{"id":"fd3806da-7e3c-571c-9775-6cd843bcbf9b","slug":"ginkgotoxin","display_name":"Ginkgotoxin / 4-prime-O-methylpyridoxine","entity_type_key":"small_molecule"},"role":"ligand","stoichiometry":null,"state_label":"","sequence_order":0,"notes":""},{"entity":{"id":"d2d46db7-13a4-595f-adaa-70ad6ca31a6c","slug":"pdxk","display_name":"Pyridoxal kinase / PDXK","entity_type_key":"protein"},"role":"enzyme","stoichiometry":null,"state_label":"","sequence_order":1,"notes":""},{"entity":{"id":"58b974f1-d389-5bf6-81cd-889c44442c42","slug":"atp","display_name":"ATP","entity_type_key":"small_molecule"},"role":"cosubstrate","stoichiometry":null,"state_label":"","sequence_order":2,"notes":""},{"entity":{"id":"bff427ab-35f9-59c2-bb24-fd5953bbaec2","slug":"magnesium-ion","display_name":"Mg2+","entity_type_key":"ion"},"role":"metal","stoichiometry":null,"state_label":"","sequence_order":3,"notes":""}]},"contexts":[{"dimension":"availability_state","value_text":"machinery_impairment","comparator":null,"unit":null,"notes":"Imported condition classification; unverified.","entity":null},{"dimension":"experimental_model","value_text":"Purified human PDXK; crystallography and inhibition kinetics","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"exposure","value_text":"2.15 angstrom ternary crystal structure.","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"limitations","value_text":"Binding in a purified protein does not establish brain concentrations.","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"nutrient_topic","value_text":"Vitamin B6 research collection; topical membership is not evidence of a direct dietary effect.","comparator":null,"unit":null,"notes":"","entity":{"slug":"vitamin-b6","display_name":"Vitamin B6","entity_type_key":"chemical_species"}},{"dimension":"organism","value_text":"Homo sapiens","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"plain_language","value_text":"The structure directly locates the competing toxin.","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"primary_references","value_text":"[gandhi-2012-pdxk-inhibitors] Crystal Structures of Human Pyridoxal Kinase in Complex with the Neurotoxins, Ginkgotoxin and Theophylline: Insights into Pyridoxal Kinase Inhibition (2012). https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0040954 DOI: 10.1371/journal.pone.0040954","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"tissue_or_cell_type","value_text":"Purified recombinant protein; no intact tissue","comparator":null,"unit":null,"notes":"","entity":null},{"dimension":"trigger_kind","value_text":"machinery_impairment","comparator":null,"unit":null,"notes":"Imported condition classification; unverified.","entity":null}],"evidence":[{"id":"af36cb99-401e-510d-8468-2839c4330b94","evidence_kind":"source_excerpt","locator":"Lines 1208-1218","start_line":1208,"end_line":1218,"excerpt":"### b6-neuro-ginkgotoxin-binding\nHuman PDXK crystallography placed ginkgotoxin at the pyridoxal-binding site alongside MgATP.\nCondition category: machinery_impairment\nnutrient_topic: Vitamin B6 research collection; topical membership is not evidence of a direct dietary effect.\nplain_language: The structure directly locates the competing toxin.\norganism: Homo sapiens\ntissue_or_cell_type: Purified recombinant protein; no intact tissue\nexperimental_model: Purified human PDXK; crystallography and inhibition kinetics\nlimitations: Binding in a purified protein does not establish brain concentrations.\nexposure: 2.15 angstrom ternary crystal structure.\n[gandhi-2012-pdxk-inhibitors] Crystal Structures of Human Pyridoxal Kinase in Complex with the Neurotoxins, Ginkgotoxin and Theophylline: Insights into Pyridoxal Kinase Inhibition (2012). https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0040954 DOI: 10.1371/journal.pone.0040954","model_system":"Purified human PDXK; 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Study references: [gandhi-2012-pdxk-inhibitors] Crystal Structures of Human Pyridoxal Kinase in Complex with the Neurotoxins, Ginkgotoxin and Theophylline: Insights into Pyridoxal Kinase Inhibition (2012). https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0040954 DOI: 10.1371/journal.pone.0040954","relationship":"supports","weight":1.0,"link_notes":"","source":{"id":"251773bb-16f5-5903-b135-db4a61d9dec4","stable_key":"import-1310afbd-6010-586e-805d-551d846da421","title":"Vitamin B6: mechanisms, deficiency and nutrient interactions (2026-09-17)","document_type":"imported_text","citation_label":"AI-assisted literature curation; primary study URLs and scope retained in the document and extraction. 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