data_218
#
_chem_comp.id 218
_chem_comp.name 1-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-(2-HYDROXYETHYL)-2-METHYLPYRIDINIUM
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C14 H19 N4 O"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 1
_chem_comp.pdbx_initial_date 2006-07-24
_chem_comp.pdbx_modified_date 2011-06-04
_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 259.327
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 218
_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 2HOP
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
#
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
218 CM2 CM2 C 0 1 N N N N N N -12.219 16.596 54.436 4.890 1.745 1.286 CM2 218 1
218 C2A C2A C 0 1 Y N N N N N -10.964 15.812 54.157 3.753 1.101 0.536 C2A 218 2
218 N1A N1A N 0 1 Y N N N N N -9.779 16.459 54.115 2.863 1.869 -0.060 N1A 218 3
218 C6A C6A C 0 1 Y N N N N N -8.606 15.800 53.872 1.847 1.343 -0.730 C6A 218 4
218 C5A C5A C 0 1 Y N N N N N -8.604 14.396 53.647 1.725 -0.031 -0.800 C5A 218 5
218 C7A C7A C 0 1 N N N N N N -7.308 13.640 53.382 0.585 -0.667 -1.552 C7A 218 6
218 N3 N3 N 1 1 Y N N N N N -6.061 14.412 53.010 -0.504 -0.974 -0.621 N3 218 7
218 C2 C2 C 0 1 Y N N N N N -5.748 14.546 51.667 -0.584 -2.184 -0.102 C2 218 8
218 C1 C1 C 0 1 Y N N N N N -4.603 15.237 51.238 -1.596 -2.509 0.780 C1 218 9
218 C6 C6 C 0 1 Y N N N N N -3.737 15.812 52.213 -2.534 -1.545 1.117 C6 218 10
218 C5 C5 C 0 1 Y N N N N N -4.017 15.699 53.614 -2.418 -0.285 0.551 C5 218 11
218 CM6 CM6 C 0 1 N N N N N N -3.041 16.327 54.608 -3.412 0.797 0.887 CM6 218 12
218 CM7 CM7 C 0 1 N N N N N N -1.791 15.399 54.752 -4.513 0.825 -0.176 CM7 218 13
218 OM7 OM7 O 0 1 N N N N N N -2.126 14.083 55.242 -5.456 1.851 0.142 OM7 218 14
218 C4 C4 C 0 1 Y N N N N N -5.222 14.976 54.026 -1.375 -0.031 -0.320 C4 218 15
218 CM4 CM4 C 0 1 N N N N N N -5.560 14.830 55.540 -1.238 1.336 -0.940 CM4 218 16
218 C4A C4A C 0 1 Y N N N N N -9.880 13.733 53.696 2.685 -0.815 -0.157 C4A 218 17
218 N4A N4A N 0 1 N N N N N N -9.965 12.371 53.489 2.607 -2.197 -0.199 N4A 218 18
218 N3A N3A N 0 1 Y N N N N N -11.021 14.468 53.948 3.678 -0.213 0.491 N3A 218 19
218 HM21 1HM2 H 0 0 N N N N N N -13.093 16.020 54.099 4.596 1.907 2.323 HM21 218 20
218 HM22 2HM2 H 0 0 N N N N N N -12.180 17.554 53.896 5.763 1.092 1.253 HM22 218 21
218 HM23 3HM2 H 0 0 N N N N N N -12.300 16.787 55.516 5.135 2.702 0.824 HM23 218 22
218 H6A H6A H 0 1 N N N N N N -7.676 16.349 53.851 1.123 1.982 -1.215 H6A 218 23
218 H7A1 1H7A H 0 0 N N N N N N -7.528 13.042 52.485 0.226 0.020 -2.318 H7A1 218 24
218 H7A2 2H7A H 0 0 N N N N N N -7.071 13.099 54.310 0.930 -1.588 -2.024 H7A2 218 25
218 H2 H2 H 0 1 N N N N N N -6.403 14.107 50.929 0.151 -2.929 -0.370 H2 218 26
218 H1 H1 H 0 1 N N N N N N -4.382 15.331 50.185 -1.657 -3.502 1.201 H1 218 27
218 H6 H6 H 0 1 N N N N N N -2.853 16.343 51.890 -3.337 -1.771 1.803 H6 218 28
218 HM61 1HM6 H 0 0 N N N N N N -3.531 16.443 55.586 -3.854 0.594 1.862 HM61 218 29
218 HM62 2HM6 H 0 0 N N N N N N -2.727 17.316 54.242 -2.905 1.762 0.911 HM62 218 30
218 HM71 1HM7 H 0 0 N N N N N N -1.113 15.864 55.482 -4.071 1.028 -1.152 HM71 218 31
218 HM72 2HM7 H 0 0 N N N N N N -1.322 15.292 53.763 -5.019 -0.139 -0.200 HM72 218 32
218 HOM7 HOM7 H 0 0 N N N N N N -2.200 13.481 54.510 -6.130 1.835 -0.551 HOM7 218 33
218 HM41 1HM4 H 0 0 N N N N N N -6.127 13.901 55.701 -0.542 1.933 -0.352 HM41 218 34
218 HM42 2HM4 H 0 0 N N N N N N -6.164 15.690 55.865 -0.862 1.236 -1.958 HM42 218 35
218 HM43 3HM4 H 0 0 N N N N N N -4.628 14.796 56.123 -2.212 1.825 -0.958 HM43 218 36
218 H4A1 1H4A H 0 0 N N N N N N -9.171 11.922 53.898 1.881 -2.628 -0.677 H4A1 218 37
218 H4A2 2H4A H 0 0 N N N N N N -9.986 12.183 52.507 3.278 -2.735 0.251 H4A2 218 38
#
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
218 CM2 C2A SING N N 1
218 CM2 HM21 SING N N 2
218 CM2 HM22 SING N N 3
218 CM2 HM23 SING N N 4
218 C2A N1A SING Y N 5
218 C2A N3A DOUB Y N 6
218 N1A C6A DOUB Y N 7
218 C6A C5A SING Y N 8
218 C6A H6A SING N N 9
218 C5A C7A SING N N 10
218 C5A C4A DOUB Y N 11
218 C7A N3 SING N N 12
218 C7A H7A1 SING N N 13
218 C7A H7A2 SING N N 14
218 N3 C2 SING Y N 15
218 N3 C4 DOUB Y N 16
218 C2 C1 DOUB Y N 17
218 C2 H2 SING N N 18
218 C1 C6 SING Y N 19
218 C1 H1 SING N N 20
218 C6 C5 DOUB Y N 21
218 C6 H6 SING N N 22
218 C5 CM6 SING N N 23
218 C5 C4 SING Y N 24
218 CM6 CM7 SING N N 25
218 CM6 HM61 SING N N 26
218 CM6 HM62 SING N N 27
218 CM7 OM7 SING N N 28
218 CM7 HM71 SING N N 29
218 CM7 HM72 SING N N 30
218 OM7 HOM7 SING N N 31
218 C4 CM4 SING N N 32
218 CM4 HM41 SING N N 33
218 CM4 HM42 SING N N 34
218 CM4 HM43 SING N N 35
218 C4A N4A SING N N 36
218 C4A N3A SING Y N 37
218 N4A H4A1 SING N N 38
218 N4A H4A2 SING N N 39
#
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
218 SMILES ACDLabs 10.04 n1c(N)c(cnc1C)C[n+]2cccc(c2C)CCO
218 SMILES_CANONICAL CACTVS 3.341 Cc1ncc(C[n+]2cccc(CCO)c2C)c(N)n1
218 SMILES CACTVS 3.341 Cc1ncc(C[n+]2cccc(CCO)c2C)c(N)n1
218 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 Cc1c(ccc[n+]1Cc2cnc(nc2N)C)CCO
218 SMILES "OpenEye OEToolkits" 1.5.0 Cc1c(ccc[n+]1Cc2cnc(nc2N)C)CCO
218 InChI InChI 1.03 InChI=1S/C14H19N4O/c1-10-12(5-7-19)4-3-6-18(10)9-13-8-16-11(2)17-14(13)15/h3-4,6,8,19H,5,7,9H2,1-2H3,(H2,15,16,17)/q+1
218 InChIKey InChI 1.03 PZWYDZMWPANLMB-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
218 "SYSTEMATIC NAME" ACDLabs 10.04 1-[(4-amino-2-methylpyrimidin-5-yl)methyl]-3-(2-hydroxyethyl)-2-methylpyridinium
218 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 2-[1-[(4-amino-2-methyl-pyrimidin-5-yl)methyl]-2-methyl-pyridin-1-ium-3-yl]ethanol
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
218 'Create component' 2006-07-24 RCSB
218 'Modify descriptor' 2011-06-04 RCSB
#
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
218 CM2 C 9.495 -4.875 1
218 C2A C 8.196 -4.125 2
218 N1A N 8.196 -2.625 3
218 C6A C 6.897 -1.875 4
218 C5A C 5.598 -2.625 5
218 C7A C 4.299 -1.875 6
218 N3 N 4.299 -0.375 7
218 C2 C 3.000 0.375 8
218 C1 C 3.000 1.875 9
218 C6 C 4.299 2.625 10
218 C5 C 5.598 1.875 11
218 CM6 C 6.897 2.625 12
218 CM7 C 6.897 4.125 13
218 OM7 O 8.196 4.875 14
218 C4 C 5.598 0.375 15
218 CM4 C 6.897 -0.375 16
218 C4A C 5.598 -4.125 17
218 N4A N 4.299 -4.875 18
218 N3A N 6.897 -4.875 19
#
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
218 CM2 C2A SINGLE NONE 1
218 C2A N1A DOUBLE NONE 2
218 C2A N3A SINGLE NONE 3
218 N1A C6A SINGLE NONE 4
218 C6A C5A DOUBLE NONE 5
218 C5A C7A SINGLE NONE 6
218 C5A C4A SINGLE NONE 7
218 C7A N3 SINGLE NONE 8
218 N3 C2 DOUBLE NONE 9
218 N3 C4 SINGLE NONE 10
218 C2 C1 SINGLE NONE 11
218 C1 C6 DOUBLE NONE 12
218 C6 C5 SINGLE NONE 13
218 C5 CM6 SINGLE NONE 14
218 C5 C4 DOUBLE NONE 15
218 CM6 CM7 SINGLE NONE 16
218 CM7 OM7 SINGLE NONE 17
218 C4 CM4 SINGLE NONE 18
218 C4A N4A SINGLE NONE 19
218 C4A N3A DOUBLE NONE 20
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
218 MurckoScaffold S1 scaffold 'c1cc[n+](Cc2cncnc2)cc1' InChI=1S/C10H10N3/c1-2-4-13(5-3-1)8-10-6-11-9-12-7-10/h1-7,9H,8H2/q+1 VMHCEVFBSUAPPD-UHFFFAOYSA-N
218 pyridine F1 fragment c1ccncc1 InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H JUJWROOIHBZHMG-UHFFFAOYSA-N
218 pyrimidine F2 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-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
218 C2A S1 1
218 N1A S1 1
218 C6A S1 1
218 C5A S1 1
218 C7A S1 1
218 N3 S1 1
218 C2 S1 1
218 C1 S1 1
218 C6 S1 1
218 C5 S1 1
218 C4 S1 1
218 C4A S1 1
218 N3A S1 1
218 C2 F1 1
218 C1 F1 1
218 C6 F1 1
218 C5 F1 1
218 C4 F1 1
218 N3 F1 1
218 C5A F2 1
218 C6A F2 1
218 N1A F2 1
218 C2A F2 1
218 N3A F2 1
218 C4A F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 218
_pdbe_chem_comp_rdkit_properties.exactmw 259.155
_pdbe_chem_comp_rdkit_properties.amw 259.333
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 8
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 19
_pdbe_chem_comp_rdkit_properties.NumAtoms 38
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.357
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 2
_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 139.213
_pdbe_chem_comp_rdkit_properties.tpsa 75.910
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.053
_pdbe_chem_comp_rdkit_properties.CrippenMR 70.559
_pdbe_chem_comp_rdkit_properties.chi0v 9.197
_pdbe_chem_comp_rdkit_properties.chi1v 4.743
_pdbe_chem_comp_rdkit_properties.chi2v 1.924
_pdbe_chem_comp_rdkit_properties.chi3v 1.924
_pdbe_chem_comp_rdkit_properties.chi4v 1.125
_pdbe_chem_comp_rdkit_properties.chi0n 28.197
_pdbe_chem_comp_rdkit_properties.chi1n 14.046
_pdbe_chem_comp_rdkit_properties.chi2n 1.924
_pdbe_chem_comp_rdkit_properties.chi3n 1.924
_pdbe_chem_comp_rdkit_properties.chi4n 1.125
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.010
_pdbe_chem_comp_rdkit_properties.kappa1 3.175
_pdbe_chem_comp_rdkit_properties.kappa2 5.753
_pdbe_chem_comp_rdkit_properties.kappa3 3.058
_pdbe_chem_comp_rdkit_properties.Phi 0.961
#
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
218 UniChem ChEBI 72290
218 UniChem ZINC ZINC000000902189
218 UniChem fdasrs C8K5X0362H
218 UniChem Nikkaji J500.183H
218 UniChem 'EPA CompTox Dashboard' DTXSID20204528
218 UniChem BRENDA 196584
218 UniChem BRENDA 44751
218 UniChem BRENDA 5609
218 UniChem Rhea 72290
218 UniChem 'Probes And Drugs' PD043760
218 UniChem PubChem 10803
#
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
218 CM2 3.773 -2.282 -2.487 ETKDGv3 1
218 C2A 3.156 -1.280 -1.569 ETKDGv3 2
218 N1A 3.129 -0.023 -1.901 ETKDGv3 3
218 C6A 2.569 0.962 -1.021 ETKDGv3 4
218 C5A 2.048 0.601 0.164 ETKDGv3 5
218 C7A 1.378 1.636 1.047 ETKDGv3 6
218 N3 -0.032 1.289 1.338 ETKDGv3 7
218 C2 -0.386 1.146 2.593 ETKDGv3 8
218 C1 -1.730 0.689 2.958 ETKDGv3 9
218 C6 -2.614 0.430 2.003 ETKDGv3 10
218 C5 -2.274 0.666 0.584 ETKDGv3 11
218 CM6 -3.339 0.329 -0.443 ETKDGv3 12
218 CM7 -3.049 -1.013 -1.122 ETKDGv3 13
218 OM7 -4.058 -1.315 -2.048 ETKDGv3 14
218 C4 -1.029 1.137 0.273 ETKDGv3 15
218 CM4 -0.659 1.464 -1.160 ETKDGv3 16
218 C4A 2.163 -0.834 0.558 ETKDGv3 17
218 N4A 1.774 -1.292 1.854 ETKDGv3 18
218 N3A 2.677 -1.688 -0.280 ETKDGv3 19
218 HM21 3.358 -3.291 -2.282 ETKDGv3 20
218 HM22 4.871 -2.301 -2.328 ETKDGv3 21
218 HM23 3.560 -2.017 -3.544 ETKDGv3 22
218 H6A 2.541 1.994 -1.349 ETKDGv3 23
218 H7A1 1.416 2.650 0.594 ETKDGv3 24
218 H7A2 1.986 1.718 1.975 ETKDGv3 25
218 H2 0.320 1.306 3.400 ETKDGv3 26
218 H1 -1.987 0.534 3.998 ETKDGv3 27
218 H6 -3.596 0.063 2.279 ETKDGv3 28
218 HM61 -4.330 0.259 0.056 ETKDGv3 29
218 HM62 -3.457 1.132 -1.197 ETKDGv3 30
218 HM71 -2.972 -1.821 -0.358 ETKDGv3 31
218 HM72 -2.083 -0.964 -1.664 ETKDGv3 32
218 HOM7 -4.839 -1.632 -1.524 ETKDGv3 33
218 HM41 0.067 2.298 -1.199 ETKDGv3 34
218 HM42 -0.221 0.570 -1.649 ETKDGv3 35
218 HM43 -1.515 1.822 -1.759 ETKDGv3 36
218 H4A1 1.782 -2.313 2.072 ETKDGv3 37
218 H4A2 1.602 -0.629 2.639 ETKDGv3 38
#