data_PC
#
_chem_comp.id PC
_chem_comp.name PHOSPHOCHOLINE
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula 'C5 H15 N O4 P'
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 1
_chem_comp.pdbx_initial_date 1999-07-08
_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 POC
_chem_comp.formula_weight 184.151
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code PC
_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 1B09
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
_chem_comp.pdbx_pcm N
#
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
PC P1 P1 P 0 1 N N N N N N 134.277 187.641 -3.640 1.904 0.025 0.019 P1 PC 1
PC O1 O1 O 0 1 N N N N N N 135.312 187.540 -4.839 2.503 -1.302 0.281 O1 PC 2
PC O3 O3 O 0 1 N N N N N N 135.331 187.391 -2.445 1.872 0.296 -1.567 O3 PC 3
PC O4 O4 O 0 1 N N N N N N 133.973 189.121 -3.313 2.786 1.164 0.740 O4 PC 4
PC O2 O2 O 0 1 N N N N N N 133.170 186.531 -3.291 0.403 0.062 0.601 O2 PC 5
PC C1 C1 C 0 1 N N N N N N 132.849 185.353 -4.052 -0.293 -1.039 0.014 C1 PC 6
PC C2 C2 C 0 1 N N N N N N 131.763 184.466 -3.346 -1.734 -1.063 0.528 C2 PC 7
PC N1 N1 N 1 1 N N N N N N 130.740 183.554 -3.993 -2.459 0.105 0.009 N1 PC 8
PC C3 C3 C 0 1 N N N N N N 130.341 184.080 -5.286 -2.365 0.127 -1.457 C3 PC 9
PC C4 C4 C 0 1 N N N N N N 129.369 183.257 -3.521 -1.865 1.332 0.556 C4 PC 10
PC C5 C5 C 0 1 N N N N N N 131.215 182.170 -3.878 -3.870 0.023 0.408 C5 PC 11
PC HO3 HO3 H 0 1 N N N N N N 134.711 187.451 -1.727 1.475 1.169 -1.694 HO3 PC 12
PC HO4 HO4 H 0 1 N N N N N N 133.353 189.181 -2.595 3.676 1.108 0.364 HO4 PC 13
PC H11 1H1 H 0 1 N N N N N N 132.541 185.616 -5.090 0.204 -1.971 0.285 H11 PC 14
PC H12 2H1 H 0 1 N N N N N N 133.765 184.760 -4.282 -0.296 -0.931 -1.070 H12 PC 15
PC H21 1H2 H 0 1 N N N N N N 132.318 183.829 -2.618 -1.732 -1.034 1.618 H21 PC 16
PC H22 2H2 H 0 1 N N N N N N 131.181 185.160 -2.696 -2.226 -1.975 0.190 H22 PC 17
PC H31 1H3 H 0 1 N N N N N N 129.588 183.409 -5.762 -1.317 0.188 -1.753 H31 PC 18
PC H32 2H3 H 0 1 N N N N N N 129.973 185.130 -5.212 -2.805 -0.783 -1.863 H32 PC 19
PC H33 3H3 H 0 1 N N N N N N 131.218 184.258 -5.950 -2.902 0.994 -1.842 H33 PC 20
PC H41 1H4 H 0 1 N N N N N N 128.616 182.586 -3.997 -2.504 2.182 0.318 H41 PC 21
PC H42 2H4 H 0 1 N N N N N N 129.479 182.895 -2.472 -1.773 1.239 1.638 H42 PC 22
PC H43 3H4 H 0 1 N N N N N N 128.865 184.245 -3.404 -0.879 1.485 0.119 H43 PC 23
PC H51 1H5 H 0 1 N N N N N N 130.462 181.499 -4.354 -4.310 -0.888 0.001 H51 PC 24
PC H52 2H5 H 0 1 N N N N N N 132.238 182.031 -4.297 -3.940 0.006 1.495 H52 PC 25
PC H53 3H5 H 0 1 N N N N N N 131.442 181.880 -2.825 -4.407 0.890 0.022 H53 PC 26
#
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
PC P1 O1 DOUB N N 1
PC P1 O3 SING N N 2
PC P1 O4 SING N N 3
PC P1 O2 SING N N 4
PC O3 HO3 SING N N 5
PC O4 HO4 SING N N 6
PC O2 C1 SING N N 7
PC C1 C2 SING N N 8
PC C1 H11 SING N N 9
PC C1 H12 SING N N 10
PC C2 N1 SING N N 11
PC C2 H21 SING N N 12
PC C2 H22 SING N N 13
PC N1 C3 SING N N 14
PC N1 C4 SING N N 15
PC N1 C5 SING N N 16
PC C3 H31 SING N N 17
PC C3 H32 SING N N 18
PC C3 H33 SING N N 19
PC C4 H41 SING N N 20
PC C4 H42 SING N N 21
PC C4 H43 SING N N 22
PC C5 H51 SING N N 23
PC C5 H52 SING N N 24
PC C5 H53 SING N N 25
#
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
PC SMILES ACDLabs 10.04 'O=P(O)(O)OCC[N+](C)(C)C'
PC SMILES_CANONICAL CACTVS 3.341 'C[N+](C)(C)CCO[P](O)(O)=O'
PC SMILES CACTVS 3.341 'C[N+](C)(C)CCO[P](O)(O)=O'
PC SMILES_CANONICAL 'OpenEye OEToolkits' 1.5.0 'C[N+](C)(C)CCOP(=O)(O)O'
PC SMILES 'OpenEye OEToolkits' 1.5.0 'C[N+](C)(C)CCOP(=O)(O)O'
PC InChI InChI 1.03 'InChI=1S/C5H14NO4P/c1-6(2,3)4-5-10-11(7,8)9/h4-5H2,1-3H3,(H-,7,8,9)/p+1'
PC InChIKey InChI 1.03 YHHSONZFOIEMCP-UHFFFAOYSA-O
#
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
PC 'SYSTEMATIC NAME' ACDLabs 10.04 'N,N,N-trimethyl-2-(phosphonooxy)ethanaminium'
PC 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.5.0 'trimethyl-(2-phosphonooxyethyl)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
PC 'Create component' 1999-07-08 RCSB
PC 'Modify descriptor' 2011-06-04 RCSB
PC 'Modify PCM' 2024-09-27 PDBE
#
_pdbe_chem_comp_drugbank_details.comp_id PC
_pdbe_chem_comp_drugbank_details.drugbank_id DB03945
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name N,N,N-Trimethyl-2-(phosphonooxy)ethanaminium
_pdbe_chem_comp_drugbank_details.description
'Calcium and magnesium salts used therapeutically in hepatobiliary dysfunction.'
_pdbe_chem_comp_drugbank_details.cas_number 3616-04-4
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
PC 'Choline, dihydrogen phosphate (ester) (8CI)' DrugBank ?
PC 'Ethanaminium, N,N,N-trimethyl-2-(phosphonooxy)-' DrugBank ?
PC 'Phosphocholine cation' DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id PC
_pdbe_chem_comp_drugbank_classification.drugbank_id DB03945
_pdbe_chem_comp_drugbank_classification.parent Phosphocholines
_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 phosphocholines. These are compounds containing a [2-(trimethylazaniumyl)ethoxy]phosphonic acid or derivative.'
#
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
PC DB03945 'C-reactive protein' Humans P02741 yes 1
PC DB03945 'Epididymal sperm-binding protein 1' Humans Q96BH3 unknown 2
PC DB03945 'Gamma-hemolysin component B' 'Staphylococcus aureus (strain MW2)' P0A076 unknown 3
#
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
PC P1 P 5.104 -0.403 1
PC O1 O 3.805 -1.153 2
PC O3 O 4.354 0.896 3
PC O4 O 5.854 -1.702 4
PC O2 O 6.404 0.347 5
PC C1 C 7.702 -0.403 6
PC C2 C 9.002 0.347 7
PC N1 N 10.301 -0.403 8
PC C3 C 11.600 -1.153 9
PC C4 C 11.051 0.896 10
PC C5 C 9.551 -1.702 11
#
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
PC P1 O1 DOUBLE NONE 1
PC P1 O3 SINGLE NONE 2
PC P1 O4 SINGLE NONE 3
PC P1 O2 SINGLE NONE 4
PC O2 C1 SINGLE NONE 5
PC C1 C2 SINGLE NONE 6
PC C2 N1 SINGLE NONE 7
PC N1 C3 SINGLE NONE 8
PC N1 C4 SINGLE NONE 9
PC N1 C5 SINGLE NONE 10
#
_pdbe_chem_comp_substructure.comp_id PC
_pdbe_chem_comp_substructure.substructure_name phosphate
_pdbe_chem_comp_substructure.id F1
_pdbe_chem_comp_substructure.substructure_type fragment
_pdbe_chem_comp_substructure.substructure_smiles O=P(O)(O)O
_pdbe_chem_comp_substructure.substructure_inchis InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)
_pdbe_chem_comp_substructure.substructure_inchikeys NBIIXXVUZAFLBC-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
PC O3 F1 1
PC P1 F1 1
PC O1 F1 1
PC O4 F1 1
PC O2 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id PC
_pdbe_chem_comp_rdkit_properties.exactmw 184.073
_pdbe_chem_comp_rdkit_properties.amw 184.152
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 9
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 11
_pdbe_chem_comp_rdkit_properties.NumAtoms 26
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_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 87.668
_pdbe_chem_comp_rdkit_properties.tpsa 66.760
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.198
_pdbe_chem_comp_rdkit_properties.CrippenMR 40.896
_pdbe_chem_comp_rdkit_properties.chi0v 5.922
_pdbe_chem_comp_rdkit_properties.chi1v 3.539
_pdbe_chem_comp_rdkit_properties.chi2v 0.686
_pdbe_chem_comp_rdkit_properties.chi3v 0.686
_pdbe_chem_comp_rdkit_properties.chi4v 0.297
_pdbe_chem_comp_rdkit_properties.chi0n 20.027
_pdbe_chem_comp_rdkit_properties.chi1n 9.395
_pdbe_chem_comp_rdkit_properties.chi2n 0.371
_pdbe_chem_comp_rdkit_properties.chi3n 0.371
_pdbe_chem_comp_rdkit_properties.chi4n 0.145
_pdbe_chem_comp_rdkit_properties.hallKierAlpha 0.070
_pdbe_chem_comp_rdkit_properties.kappa1 1.786
_pdbe_chem_comp_rdkit_properties.kappa2 3.648
_pdbe_chem_comp_rdkit_properties.kappa3 10.070
_pdbe_chem_comp_rdkit_properties.Phi 0.592
#
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
PC UniChem DrugBank DB03945
PC UniChem 'KEGG LIGAND' C00588
PC UniChem ChEBI 18132
PC UniChem ZINC ZINC000001532692
PC UniChem SureChEMBL SCHEMBL8012
PC UniChem HMDB HMDB0001565
PC UniChem NMRShiftDB 60023536
PC UniChem Nikkaji J40.088B
PC UniChem MetaboLights MTBLC18132
PC UniChem BRENDA 1330
PC UniChem BRENDA 1396
PC UniChem BRENDA 20441
PC UniChem BRENDA 31711
PC UniChem BRENDA 33001
PC UniChem BRENDA 748
PC UniChem BRENDA 92912
PC UniChem 'Probes And Drugs' PD006620
PC UniChem Nikkaji J3.416.513K
PC UniChem PubChem 1014
#
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
PC P1 3.428 -0.372 -0.211 ETKDGv3 1
PC O1 3.408 -1.165 -1.499 ETKDGv3 2
PC O3 4.736 -0.882 0.733 ETKDGv3 3
PC O4 3.612 1.274 -0.561 ETKDGv3 4
PC O2 1.983 -0.633 0.658 ETKDGv3 5
PC C1 0.909 -0.117 -0.093 ETKDGv3 6
PC C2 -0.398 -0.377 0.682 ETKDGv3 7
PC N1 -1.646 0.114 0.019 ETKDGv3 8
PC C3 -1.617 1.585 -0.166 ETKDGv3 9
PC C4 -2.792 -0.220 0.901 ETKDGv3 10
PC C5 -1.860 -0.548 -1.290 ETKDGv3 11
PC HO3 4.527 -1.822 0.967 ETKDGv3 12
PC HO4 4.496 1.342 -1.002 ETKDGv3 13
PC H11 0.859 -0.627 -1.079 ETKDGv3 14
PC H12 1.041 0.977 -0.232 ETKDGv3 15
PC H21 -0.470 -1.475 0.858 ETKDGv3 16
PC H22 -0.292 0.095 1.686 ETKDGv3 17
PC H31 -0.878 1.887 -0.939 ETKDGv3 18
PC H32 -2.606 1.965 -0.510 ETKDGv3 19
PC H33 -1.362 2.103 0.786 ETKDGv3 20
PC H41 -3.756 0.121 0.462 ETKDGv3 21
PC H42 -2.686 0.266 1.897 ETKDGv3 22
PC H43 -2.866 -1.320 1.062 ETKDGv3 23
PC H51 -2.864 -0.302 -1.704 ETKDGv3 24
PC H52 -1.117 -0.213 -2.046 ETKDGv3 25
PC H53 -1.790 -1.655 -1.195 ETKDGv3 26
#