data_NNK
#
_chem_comp.id NNK
_chem_comp.name 4-(aminomethyl)-1-methylpyridinium
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C7 H11 N2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 1
_chem_comp.pdbx_initial_date 2011-03-17
_chem_comp.pdbx_modified_date 2012-07-17
_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 123.176
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code NNK
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 3QTV
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBJ
#
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
NNK N16 N16 N 0 1 N N N N N N 15.905 -10.482 20.594 3.117 0.009 -0.789 N16 NNK 1
NNK C17 C17 C 0 1 N N N N N N 14.542 -10.229 20.099 2.441 0.029 0.516 C17 NNK 2
NNK C18 C18 C 0 1 Y N N N N N 13.536 -10.459 21.209 0.949 0.017 0.309 C18 NNK 3
NNK C22 C22 C 0 1 Y N N N N N 13.203 -9.442 22.100 0.252 -1.179 0.232 C22 NNK 4
NNK C23 C23 C 0 1 Y N N N N N 12.279 -9.697 23.109 -1.116 -1.151 0.042 C23 NNK 5
NNK N24 N24 N 1 1 Y N N N N N 11.719 -10.910 23.244 -1.758 -0.004 -0.067 N24 NNK 6
NNK C25 C25 C 0 1 N N N N N N 10.747 -11.145 24.319 -3.210 -0.015 -0.268 C25 NNK 7
NNK C26 C26 C 0 1 Y N N N N N 12.035 -11.908 22.401 -1.129 1.152 0.001 C26 NNK 8
NNK C27 C27 C 0 1 Y N N N N N 12.946 -11.704 21.373 0.239 1.202 0.196 C27 NNK 9
NNK HN16 HN16 H 0 0 N N N N N N 16.562 -10.328 19.856 4.120 0.016 -0.677 HN16 NNK 10
NNK HN1A HN1A H 0 0 N N N N N N 16.105 -9.862 21.352 2.820 -0.784 -1.338 HN1A NNK 11
NNK H17 H17 H 0 1 N N N N N N 14.469 -9.188 19.752 2.735 -0.850 1.090 H17 NNK 12
NNK H17A H17A H 0 0 N N N N N N 14.326 -10.913 19.265 2.726 0.930 1.059 H17A NNK 13
NNK H22 H22 H 0 1 N N N N N N 13.657 -8.466 22.009 0.773 -2.122 0.319 H22 NNK 14
NNK H23 H23 H 0 1 N N N N N N 12.008 -8.907 23.794 -1.666 -2.078 -0.019 H23 NNK 15
NNK H25 H25 H 0 1 N N N N N N 10.397 -12.187 24.276 -3.711 -0.001 0.700 H25 NNK 16
NNK H25A H25A H 0 0 N N N N N N 11.225 -10.959 25.292 -3.504 0.863 -0.842 H25A NNK 17
NNK H25B H25B H 0 0 N N N N N N 9.891 -10.465 24.194 -3.494 -0.917 -0.811 H25B NNK 18
NNK H26 H26 H 0 1 N N N N N N 11.576 -12.878 22.524 -1.688 2.071 -0.093 H26 NNK 19
NNK H27 H27 H 0 1 N N N N N N 13.195 -12.513 20.702 0.748 2.153 0.255 H27 NNK 20
#
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
NNK N16 C17 SING N N 1
NNK C17 C18 SING N N 2
NNK C18 C22 DOUB Y N 3
NNK C18 C27 SING Y N 4
NNK C22 C23 SING Y N 5
NNK C23 N24 DOUB Y N 6
NNK N24 C25 SING N N 7
NNK N24 C26 SING Y N 8
NNK C26 C27 DOUB Y N 9
NNK N16 HN16 SING N N 10
NNK N16 HN1A SING N N 11
NNK C17 H17 SING N N 12
NNK C17 H17A SING N N 13
NNK C22 H22 SING N N 14
NNK C23 H23 SING N N 15
NNK C25 H25 SING N N 16
NNK C25 H25A SING N N 17
NNK C25 H25B SING N N 18
NNK C26 H26 SING N N 19
NNK C27 H27 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
NNK SMILES ACDLabs 12.01 NCc1cc[n+](cc1)C
NNK SMILES_CANONICAL CACTVS 3.370 C[n+]1ccc(CN)cc1
NNK SMILES CACTVS 3.370 C[n+]1ccc(CN)cc1
NNK SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 C[n+]1ccc(cc1)CN
NNK SMILES "OpenEye OEToolkits" 1.7.0 C[n+]1ccc(cc1)CN
NNK InChI InChI 1.03 InChI=1S/C7H11N2/c1-9-4-2-7(6-8)3-5-9/h2-5H,6,8H2,1H3/q+1
NNK InChIKey InChI 1.03 BBCRICAXKQUDPF-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
NNK "SYSTEMATIC NAME" ACDLabs 12.01 4-(aminomethyl)-1-methylpyridinium
NNK "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 (1-methylpyridin-1-ium-4-yl)methanamine
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
NNK 'Create component' 2011-03-17 PDBJ
NNK 'Modify aromatic_flag' 2011-06-04 RCSB
NNK 'Modify descriptor' 2011-06-04 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2023.03.3 'Core functionality.'
pdbeccdutils 0.8.4 '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
NNK N16 N 5.598 2.910 1
NNK C17 C 4.299 2.160 2
NNK C18 C 4.299 0.660 3
NNK C22 C 3.000 -0.090 4
NNK C23 C 3.000 -1.590 5
NNK N24 N 4.299 -2.340 6
NNK C25 C 4.299 -3.840 7
NNK C26 C 5.598 -1.590 8
NNK C27 C 5.598 -0.090 9
#
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
NNK N16 C17 SINGLE NONE 1
NNK C17 C18 SINGLE NONE 2
NNK C18 C22 DOUBLE NONE 3
NNK C18 C27 SINGLE NONE 4
NNK C22 C23 SINGLE NONE 5
NNK C23 N24 DOUBLE NONE 6
NNK N24 C25 SINGLE NONE 7
NNK N24 C26 SINGLE NONE 8
NNK C26 C27 DOUBLE NONE 9
#
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
NNK MurckoScaffold S1 scaffold 'c1cc[nH+]cc1' InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H/p+1 JUJWROOIHBZHMG-UHFFFAOYSA-O
NNK pyridine F1 fragment c1ccncc1 InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H JUJWROOIHBZHMG-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
NNK C18 S1 1
NNK C22 S1 1
NNK C23 S1 1
NNK N24 S1 1
NNK C26 S1 1
NNK C27 S1 1
NNK C23 F1 1
NNK C22 F1 1
NNK C18 F1 1
NNK C27 F1 1
NNK C26 F1 1
NNK N24 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id NNK
_pdbe_chem_comp_rdkit_properties.exactmw 123.092
_pdbe_chem_comp_rdkit_properties.amw 123.179
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 2
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 3
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 1
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 9
_pdbe_chem_comp_rdkit_properties.NumAtoms 20
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 2
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.286
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_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 70.502
_pdbe_chem_comp_rdkit_properties.tpsa 29.900
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.085
_pdbe_chem_comp_rdkit_properties.CrippenMR 35.243
_pdbe_chem_comp_rdkit_properties.chi0v 4.394
_pdbe_chem_comp_rdkit_properties.chi1v 2.144
_pdbe_chem_comp_rdkit_properties.chi2v 0.697
_pdbe_chem_comp_rdkit_properties.chi3v 0.697
_pdbe_chem_comp_rdkit_properties.chi4v 0.339
_pdbe_chem_comp_rdkit_properties.chi0n 15.394
_pdbe_chem_comp_rdkit_properties.chi1n 7.539
_pdbe_chem_comp_rdkit_properties.chi2n 0.697
_pdbe_chem_comp_rdkit_properties.chi3n 0.697
_pdbe_chem_comp_rdkit_properties.chi4n 0.339
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.890
_pdbe_chem_comp_rdkit_properties.kappa1 1.123
_pdbe_chem_comp_rdkit_properties.kappa2 2.597
_pdbe_chem_comp_rdkit_properties.kappa3 1.504
_pdbe_chem_comp_rdkit_properties.Phi 0.324
#
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
NNK UniChem PDBe NNK
NNK UniChem ZINC ZINC000044249405
NNK UniChem SureChEMBL SCHEMBL10762406
NNK UniChem PubChem 20185407
NNK UniChem Nikkaji J2.719.239D
#
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
NNK N16 -3.191 -0.305 -0.936 ETKDGv3 1
NNK C17 -2.535 -0.382 0.367 ETKDGv3 2
NNK C18 -1.046 -0.197 0.235 ETKDGv3 3
NNK C22 -0.239 -1.244 0.011 ETKDGv3 4
NNK C23 1.212 -1.027 -0.148 ETKDGv3 5
NNK N24 1.713 0.182 -0.106 ETKDGv3 6
NNK C25 3.158 0.379 -0.232 ETKDGv3 7
NNK C26 0.857 1.322 0.133 ETKDGv3 8
NNK C27 -0.461 1.161 0.291 ETKDGv3 9
NNK HN16 -2.973 0.622 -1.369 ETKDGv3 10
NNK HN1A -2.794 -1.047 -1.557 ETKDGv3 11
NNK H17 -2.955 0.401 1.034 ETKDGv3 12
NNK H17A -2.764 -1.365 0.836 ETKDGv3 13
NNK H22 -0.637 -2.249 -0.055 ETKDGv3 14
NNK H23 1.853 -1.887 -0.304 ETKDGv3 15
NNK H25 3.579 -0.292 -1.012 ETKDGv3 16
NNK H25A 3.650 0.163 0.740 ETKDGv3 17
NNK H25B 3.390 1.425 -0.527 ETKDGv3 18
NNK H26 1.278 2.319 0.184 ETKDGv3 19
NNK H27 -1.095 2.022 0.462 ETKDGv3 20
#