data_CHT
#
_chem_comp.id CHT
_chem_comp.name 'CHOLINE ION'
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula 'C5 H14 N O'
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 1
_chem_comp.pdbx_initial_date 2001-02-07
_chem_comp.pdbx_modified_date 2024-09-27
_chem_comp.pdbx_ambiguous_flag N
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces ?
_chem_comp.formula_weight 104.171
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code CHT
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1H8G
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
_chem_comp.pdbx_pcm Y
#
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.alt_atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.charge
_chem_comp_atom.pdbx_align
_chem_comp_atom.pdbx_aromatic_flag
_chem_comp_atom.pdbx_leaving_atom_flag
_chem_comp_atom.pdbx_stereo_config
_chem_comp_atom.pdbx_backbone_atom_flag
_chem_comp_atom.pdbx_n_terminal_atom_flag
_chem_comp_atom.pdbx_c_terminal_atom_flag
_chem_comp_atom.model_Cartn_x
_chem_comp_atom.model_Cartn_y
_chem_comp_atom.model_Cartn_z
_chem_comp_atom.pdbx_model_Cartn_x_ideal
_chem_comp_atom.pdbx_model_Cartn_y_ideal
_chem_comp_atom.pdbx_model_Cartn_z_ideal
_chem_comp_atom.pdbx_component_atom_id
_chem_comp_atom.pdbx_component_comp_id
_chem_comp_atom.pdbx_ordinal
CHT C4 C4 C 0 1 N N N N N N 66.094 81.817 11.179 1.539 -0.771 0.051 C4 CHT 1
CHT C5 C5 C 0 1 N N N N N N 64.698 81.250 10.695 0.200 -0.739 0.790 C5 CHT 2
CHT C6 C6 C 0 1 N N N N N N 62.720 80.380 11.944 -0.870 -0.546 -1.348 C6 CHT 3
CHT C7 C7 C 0 1 N N N N N N 63.715 82.456 12.660 -0.342 1.426 -0.089 C7 CHT 4
CHT C8 C8 C 0 1 N N N N N N 62.494 82.327 10.580 -2.091 -0.038 0.653 C8 CHT 5
CHT O6 O6 O 0 1 N N N N N N 66.277 83.061 10.567 2.101 0.543 0.025 O6 CHT 6
CHT N1 N1 N 1 1 N N N N N N 63.417 81.589 11.477 -0.776 0.026 0.001 N1 CHT 7
CHT HC41 1HC4 H 0 0 N N N N N N 66.184 81.861 12.289 2.221 -1.448 0.566 HC41 CHT 8
CHT HC42 2HC4 H 0 0 N N N N N N 66.937 81.112 10.992 1.383 -1.120 -0.970 HC42 CHT 9
CHT HC51 1HC5 H 0 0 N N N N N N 64.548 81.543 9.629 0.332 -0.264 1.762 HC51 CHT 10
CHT HC52 2HC5 H 0 0 N N N N N N 64.777 80.140 10.612 -0.163 -1.757 0.929 HC52 CHT 11
CHT H61 1H6 H 0 1 N N N N N N 61.791 80.625 12.510 0.105 -0.498 -1.832 H61 CHT 12
CHT H62 2H6 H 0 1 N N N N N N 62.506 79.684 11.099 -1.192 -1.585 -1.281 H62 CHT 13
CHT H63 3H6 H 0 1 N N N N N N 63.398 79.727 12.541 -1.594 0.021 -1.934 H63 CHT 14
CHT H71 1H7 H 0 1 N N N N N N 62.786 82.701 13.226 -1.144 2.028 -0.518 H71 CHT 15
CHT H72 2H7 H 0 1 N N N N N N 64.487 81.996 13.319 -0.103 1.798 0.907 H72 CHT 16
CHT H73 3H7 H 0 1 N N N N N N 64.268 83.377 12.363 0.541 1.493 -0.724 H73 CHT 17
CHT H81 1H8 H 0 1 N N N N N N 61.565 82.572 11.146 -2.412 -1.078 0.721 H81 CHT 18
CHT H82 2H8 H 0 1 N N N N N N 62.968 83.228 10.127 -2.021 0.386 1.655 H82 CHT 19
CHT H83 3H8 H 0 1 N N N N N N 62.283 81.773 9.635 -2.815 0.529 0.068 H83 CHT 20
CHT HO6 6HO H 0 1 N N N N N N 67.115 83.401 10.857 2.942 0.478 -0.448 HO6 CHT 21
#
loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_aromatic_flag
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_ordinal
CHT C4 C5 SING N N 1
CHT C4 O6 SING N N 2
CHT C4 HC41 SING N N 3
CHT C4 HC42 SING N N 4
CHT C5 N1 SING N N 5
CHT C5 HC51 SING N N 6
CHT C5 HC52 SING N N 7
CHT C6 N1 SING N N 8
CHT C6 H61 SING N N 9
CHT C6 H62 SING N N 10
CHT C6 H63 SING N N 11
CHT C7 N1 SING N N 12
CHT C7 H71 SING N N 13
CHT C7 H72 SING N N 14
CHT C7 H73 SING N N 15
CHT C8 N1 SING N N 16
CHT C8 H81 SING N N 17
CHT C8 H82 SING N N 18
CHT C8 H83 SING N N 19
CHT O6 HO6 SING N N 20
#
loop_
_pdbx_chem_comp_descriptor.comp_id
_pdbx_chem_comp_descriptor.type
_pdbx_chem_comp_descriptor.program
_pdbx_chem_comp_descriptor.program_version
_pdbx_chem_comp_descriptor.descriptor
CHT SMILES ACDLabs 10.04 'OCC[N+](C)(C)C'
CHT SMILES_CANONICAL CACTVS 3.341 'C[N+](C)(C)CCO'
CHT SMILES CACTVS 3.341 'C[N+](C)(C)CCO'
CHT SMILES_CANONICAL 'OpenEye OEToolkits' 1.5.0 'C[N+](C)(C)CCO'
CHT SMILES 'OpenEye OEToolkits' 1.5.0 'C[N+](C)(C)CCO'
CHT InChI InChI 1.03 'InChI=1S/C5H14NO/c1-6(2,3)4-5-7/h7H,4-5H2,1-3H3/q+1'
CHT InChIKey InChI 1.03 OEYIOHPDSNJKLS-UHFFFAOYSA-N
#
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
CHT 'SYSTEMATIC NAME' ACDLabs 10.04 2-hydroxy-N,N,N-trimethylethanaminium
CHT 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.5.0 2-hydroxyethyl-trimethyl-azanium
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
CHT 'Create component' 2001-02-07 EBI
CHT 'Modify descriptor' 2011-06-04 RCSB
CHT 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id CHT
_pdbx_chem_comp_pcm.modified_residue_id CYS
_pdbx_chem_comp_pcm.type None
_pdbx_chem_comp_pcm.category 'Covalent chemical modification'
_pdbx_chem_comp_pcm.position 'Amino-acid side chain'
_pdbx_chem_comp_pcm.polypeptide_position 'Any position'
_pdbx_chem_comp_pcm.comp_id_linking_atom C4
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom SG
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ?
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
#
_pdbe_chem_comp_drugbank_details.comp_id CHT
_pdbe_chem_comp_drugbank_details.drugbank_id DB00122
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name Choline
_pdbe_chem_comp_drugbank_details.description
'A basic constituent of lecithin that is found in many plants and animal organs. It is important as a precursor of acetylcholine, as a methyl donor in various metabolic processes, and in lipid metabolism.'
_pdbe_chem_comp_drugbank_details.cas_number 62-49-7
_pdbe_chem_comp_drugbank_details.mechanism_of_action
"Choline is a major part of the polar head group of phosphatidylcholine. Phosphatidylcholine's role in the maintenance of cell membrane integrity is vital to all of the basic biological processes: information flow, intracellular communication and bioenergetics. Inadequate choline intake would negatively affect all these processes. Choline is also a major part of another membrane phospholipid, sphingomyelin, also important for the maintenance of cell structure and function. It is noteworthy and not surprising that choline deficiency in cell culture causes apoptosis or programmed cell death. This appears to be due to abnormalities in cell membrane phosphatidylcholine content and an increase in ceramide, a precursor, as well as a metabolite, of sphingomyelin. Ceramide accumulation, which is caused by choline deficiency, appears to activate Caspase, a type of enzyme that mediates apoptosis. Betaine or trimethylglycine is derived from choline via an oxidation reaction. Betaine is one of the factors that maintains low levels of homocysteine by resynthesizing L-methionine from homocysteine. Elevated homocysteine levels are a significant risk factor for atherosclerosis, as well as other cardiovascular and neurological disorders. Acetylcholine is one of the major neurotransmitters and requires choline for its synthesis. Adequate acetylcholine levels in the brain are believed to be protective against certain types of dementia, including Alzheimer's disease."
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
CHT Bilineurine DrugBank ?
CHT 'Choline ion' DrugBank ?
CHT N-trimethylethanolamine DrugBank ?
CHT N,N,N-trimethylethanol-ammonium DrugBank ?
CHT trimethylethanolamine DrugBank ?
CHT 'Vitamin J' DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id CHT
_pdbe_chem_comp_drugbank_classification.drugbank_id DB00122
_pdbe_chem_comp_drugbank_classification.parent Cholines
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Organonitrogen compounds'
_pdbe_chem_comp_drugbank_classification.superclass 'Organic nitrogen compounds'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as cholines. These are organic compounds containing a N,N,N-trimethylethanolammonium cation.'
#
loop_
_pdbe_chem_comp_drugbank_targets.comp_id
_pdbe_chem_comp_drugbank_targets.drugbank_id
_pdbe_chem_comp_drugbank_targets.name
_pdbe_chem_comp_drugbank_targets.organism
_pdbe_chem_comp_drugbank_targets.uniprot_id
_pdbe_chem_comp_drugbank_targets.pharmacologically_active
_pdbe_chem_comp_drugbank_targets.ordinal
CHT DB00122 'Neuronal acetylcholine receptor subunit alpha-2' Humans Q15822 yes 1
CHT DB00122 'Neuronal acetylcholine receptor subunit alpha-7' Humans P36544 unknown 2
CHT DB00122 'Choline-phosphate cytidylyltransferase B' Humans Q9Y5K3 unknown 3
CHT DB00122 Acetylcholinesterase Humans P22303 unknown 4
CHT DB00122 'Choline-phosphate cytidylyltransferase A' Humans P49585 unknown 5
CHT DB00122 'Phospholipase D2' Humans O14939 unknown 6
CHT DB00122 Cholinesterase Humans P06276 unknown 7
CHT DB00122 'Phospholipase D1' Humans Q13393 unknown 8
CHT DB00122 'Phosphoethanolamine/phosphocholine phosphatase' Humans Q8TCT1 unknown 9
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
CHT C4 C 6.897 0.000 1
CHT C5 C 5.598 0.750 2
CHT C6 C 3.000 -0.750 3
CHT C7 C 3.549 1.299 4
CHT C8 C 5.049 -1.299 5
CHT O6 O 8.196 0.750 6
CHT N1 N 4.299 0.000 7
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
CHT C4 C5 SINGLE NONE 1
CHT C4 O6 SINGLE NONE 2
CHT C5 N1 SINGLE NONE 3
CHT C6 N1 SINGLE NONE 4
CHT C7 N1 SINGLE NONE 5
CHT C8 N1 SINGLE NONE 6
#
#
#
_pdbe_chem_comp_rdkit_properties.comp_id CHT
_pdbe_chem_comp_rdkit_properties.exactmw 104.107
_pdbe_chem_comp_rdkit_properties.amw 104.173
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 2
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 6
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 1
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 7
_pdbe_chem_comp_rdkit_properties.NumAtoms 21
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 2
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 1
_pdbe_chem_comp_rdkit_properties.NumRings 0
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 64.719
_pdbe_chem_comp_rdkit_properties.tpsa 20.230
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.315
_pdbe_chem_comp_rdkit_properties.CrippenMR 29.985
_pdbe_chem_comp_rdkit_properties.chi0v 3.355
_pdbe_chem_comp_rdkit_properties.chi1v 1.349
_pdbe_chem_comp_rdkit_properties.chi2v 0.213
_pdbe_chem_comp_rdkit_properties.chi3v 0.213
_pdbe_chem_comp_rdkit_properties.chi4v 0.068
_pdbe_chem_comp_rdkit_properties.chi0n 17.355
_pdbe_chem_comp_rdkit_properties.chi1n 8.257
_pdbe_chem_comp_rdkit_properties.chi2n 0.213
_pdbe_chem_comp_rdkit_properties.chi3n 0.213
_pdbe_chem_comp_rdkit_properties.chi4n 0.068
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.080
_pdbe_chem_comp_rdkit_properties.kappa1 0.611
_pdbe_chem_comp_rdkit_properties.kappa2 2.285
_pdbe_chem_comp_rdkit_properties.kappa3 5.920
_pdbe_chem_comp_rdkit_properties.Phi 0.199
#
loop_
_pdbe_chem_comp_external_mappings.comp_id
_pdbe_chem_comp_external_mappings.source
_pdbe_chem_comp_external_mappings.resource
_pdbe_chem_comp_external_mappings.resource_id
CHT UniChem DrugBank DB00122
CHT UniChem 'Guide to Pharmacology' 4551
CHT UniChem 'KEGG LIGAND' C00114
CHT UniChem ChEBI 15354
CHT UniChem ZINC ZINC000003079337
CHT UniChem eMolecules 1012302
CHT UniChem fdasrs N91BDP6H0X
CHT UniChem PharmGKB PA448976
CHT UniChem HMDB HMDB0000097
CHT UniChem PubChem 305
CHT UniChem NMRShiftDB 10017762
CHT UniChem ACTor 139741-81-4
CHT UniChem ACTor 5413-08-1
CHT UniChem Recon chol
CHT UniChem Nikkaji J4.822D
CHT UniChem BindingDb 50026220
CHT UniChem 'EPA CompTox Dashboard' DTXSID8043789
CHT UniChem DrugCentral 3097
CHT UniChem MetaboLights MTBLC15354
CHT UniChem BRENDA 149
CHT UniChem BRENDA 265917
CHT UniChem BRENDA 30682
CHT UniChem Rhea 15354
CHT UniChem ChemicalBook CB1139255
CHT UniChem ChemicalBook CB91178266
CHT UniChem DailyMed CHOLINE
CHT UniChem ClinicalTrials CHOLINE
CHT UniChem ClinicalTrials METHYL-D9-CHOLINE
CHT UniChem rxnorm CHOLINE
CHT UniChem 'Probes And Drugs' PD010230
CHT UniChem CCDC CHOCHL
CHT UniChem Mcule MCULE-7712564949
CHT UniChem SureChEMBL SCHEMBL3142
#
loop_
_pdbe_chem_comp_rdkit_conformer.comp_id
_pdbe_chem_comp_rdkit_conformer.atom_id
_pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit
_pdbe_chem_comp_rdkit_conformer.rdkit_method
_pdbe_chem_comp_rdkit_conformer.rdkit_ordinal
CHT C4 1.904 -0.334 -0.063 ETKDGv3 1
CHT C5 0.736 0.520 0.469 ETKDGv3 2
CHT C6 -0.949 -1.272 0.432 ETKDGv3 3
CHT C7 -0.737 0.208 -1.476 ETKDGv3 4
CHT C8 -1.613 1.032 0.605 ETKDGv3 5
CHT O6 3.106 0.163 0.456 ETKDGv3 6
CHT N1 -0.623 0.109 -0.001 ETKDGv3 7
CHT HC41 1.948 -0.285 -1.172 ETKDGv3 8
CHT HC42 1.789 -1.392 0.256 ETKDGv3 9
CHT HC51 0.778 0.488 1.582 ETKDGv3 10
CHT HC52 0.934 1.577 0.177 ETKDGv3 11
CHT H61 -0.782 -1.398 1.525 ETKDGv3 12
CHT H62 -2.013 -1.518 0.216 ETKDGv3 13
CHT H63 -0.335 -2.026 -0.106 ETKDGv3 14
CHT H71 -0.408 1.208 -1.836 ETKDGv3 15
CHT H72 -0.126 -0.567 -1.988 ETKDGv3 16
CHT H73 -1.788 0.052 -1.808 ETKDGv3 17
CHT H81 -1.577 0.986 1.717 ETKDGv3 18
CHT H82 -1.419 2.085 0.299 ETKDGv3 19
CHT H83 -2.651 0.777 0.292 ETKDGv3 20
CHT HO6 3.826 -0.413 0.089 ETKDGv3 21
#