data_LG5
#
_chem_comp.id LG5
_chem_comp.name 1-METHYL-1,6-DIHYDROPYRIDIN-3-AMINE
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C6 H10 N2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms 1-METHYL-1-LAMBDA-5-PYRIDIN-3-YL-AMINE
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2005-11-10
_chem_comp.pdbx_modified_date 2021-03-01
_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 110.157
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code LG5
_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 2EUO
_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
LG5 C1 C1 C 0 1 N N N N N N -9.295 71.846 16.821 0.058 1.782 0.113 C1 LG5 1
LG5 C2 C2 C 0 1 N N N N N N -8.773 71.946 15.525 1.234 1.044 -0.475 C2 LG5 2
LG5 N3 N3 N 0 1 N N N N N N -7.928 70.978 15.091 1.148 -0.372 -0.097 N3 LG5 3
LG5 C4 C4 C 0 1 N N N N N N -7.629 69.892 15.844 -0.087 -1.016 -0.193 C4 LG5 4
LG5 C5 C5 C 0 1 N N N N N N -8.146 69.768 17.134 -1.205 -0.291 0.019 C5 LG5 5
LG5 C6 C6 C 0 1 N N N N N N -9.000 70.749 17.619 -1.086 1.141 0.337 C6 LG5 6
LG5 C7 C7 C 0 1 N N N N N N -7.317 71.055 13.775 2.335 -1.096 0.367 C7 LG5 7
LG5 N8 N8 N 0 1 N N N N N N -7.841 68.666 17.898 -2.472 -0.898 -0.067 N8 LG5 8
LG5 H1 H1 H 0 1 N N N N N N -9.933 72.629 17.203 0.145 2.832 0.352 H1 LG5 9
LG5 H21 1H2 H 0 1 N N N N N N -8.158 72.858 15.546 2.161 1.469 -0.090 H21 LG5 10
LG5 H22 2H2 H 0 1 N N N N N N -9.633 71.942 14.839 1.215 1.133 -1.562 H22 LG5 11
LG5 H4 H4 H 0 1 N N N N N N -6.988 69.120 15.444 -0.148 -2.069 -0.424 H4 LG5 12
LG5 H6 H6 H 0 1 N N N N N N -9.430 70.660 18.606 -1.929 1.672 0.754 H6 LG5 13
LG5 H71 1H7 H 0 1 N N N N N N -6.673 70.177 13.618 2.416 -1.003 1.450 H71 LG5 14
LG5 H72 2H7 H 0 1 N N N N N N -6.713 71.971 13.705 2.247 -2.148 0.098 H72 LG5 15
LG5 H73 3H7 H 0 1 N N N N N N -8.103 71.074 13.006 3.224 -0.674 -0.102 H73 LG5 16
LG5 HN81 1HN8 H 0 0 N N N N N N -6.971 68.816 18.367 -3.273 -0.372 0.083 HN81 LG5 17
LG5 HN82 2HN8 H 0 0 N N N N N N -7.767 67.861 17.309 -2.544 -1.842 -0.277 HN82 LG5 18
#
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
LG5 C1 C2 SING N N 1
LG5 C1 C6 DOUB N N 2
LG5 C1 H1 SING N N 3
LG5 C2 N3 SING N N 4
LG5 C2 H21 SING N N 5
LG5 C2 H22 SING N N 6
LG5 N3 C4 SING N N 7
LG5 N3 C7 SING N N 8
LG5 C4 C5 DOUB N N 9
LG5 C4 H4 SING N N 10
LG5 C5 C6 SING N N 11
LG5 C5 N8 SING N N 12
LG5 C6 H6 SING N N 13
LG5 C7 H71 SING N N 14
LG5 C7 H72 SING N N 15
LG5 C7 H73 SING N N 16
LG5 N8 HN81 SING N N 17
LG5 N8 HN82 SING N N 18
#
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
LG5 SMILES ACDLabs 10.04 NC=1C=CCN(C=1)C
LG5 SMILES_CANONICAL CACTVS 3.341 CN1CC=CC(=C1)N
LG5 SMILES CACTVS 3.341 CN1CC=CC(=C1)N
LG5 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CN1CC=CC(=C1)N
LG5 SMILES "OpenEye OEToolkits" 1.5.0 CN1CC=CC(=C1)N
LG5 InChI InChI 1.03 InChI=1S/C6H10N2/c1-8-4-2-3-6(7)5-8/h2-3,5H,4,7H2,1H3
LG5 InChIKey InChI 1.03 NJIDBKRVRJXCLL-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
LG5 "SYSTEMATIC NAME" ACDLabs 10.04 1-methyl-1,6-dihydropyridin-3-amine
LG5 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 1-methyl-6H-pyridin-3-amine
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
LG5 'Create component' 2005-11-10 RCSB
LG5 'Modify descriptor' 2011-06-04 RCSB
LG5 'Modify synonyms' 2021-03-01 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id LG5
_pdbx_chem_comp_synonyms.name 1-METHYL-1-LAMBDA-5-PYRIDIN-3-YL-AMINE
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_synonyms.comp_id LG5
_pdbe_chem_comp_synonyms.name 1-METHYL-1-LAMBDA-5-PYRIDIN-3-YL-AMINE
_pdbe_chem_comp_synonyms.provenance wwPDB
_pdbe_chem_comp_synonyms.type ?
#
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
LG5 C1 C 7.702 1.035 1
LG5 C2 C 7.702 -0.465 2
LG5 N3 N 6.404 -1.215 3
LG5 C4 C 5.104 -0.465 4
LG5 C5 C 5.104 1.035 5
LG5 C6 C 6.404 1.785 6
LG5 C7 C 6.404 -2.715 7
LG5 N8 N 3.805 1.785 8
#
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
LG5 C1 C2 SINGLE NONE 1
LG5 C1 C6 DOUBLE NONE 2
LG5 C2 N3 SINGLE NONE 3
LG5 N3 C4 SINGLE NONE 4
LG5 N3 C7 SINGLE NONE 5
LG5 C4 C5 DOUBLE NONE 6
LG5 C5 C6 SINGLE NONE 7
LG5 C5 N8 SINGLE NONE 8
#
_pdbe_chem_comp_substructure.comp_id LG5
_pdbe_chem_comp_substructure.substructure_name MurckoScaffold
_pdbe_chem_comp_substructure.id S1
_pdbe_chem_comp_substructure.substructure_type scaffold
_pdbe_chem_comp_substructure.substructure_smiles C1=CCNC=C1
_pdbe_chem_comp_substructure.substructure_inchis InChI=1S/C5H7N/c1-2-4-6-5-3-1/h1-4,6H,5H2
_pdbe_chem_comp_substructure.substructure_inchikeys MMWRGWQTAMNAFC-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
LG5 C1 S1 1
LG5 C2 S1 1
LG5 N3 S1 1
LG5 C4 S1 1
LG5 C5 S1 1
LG5 C6 S1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id LG5
_pdbe_chem_comp_rdkit_properties.exactmw 110.084
_pdbe_chem_comp_rdkit_properties.amw 110.160
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 2
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 2
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 2
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 8
_pdbe_chem_comp_rdkit_properties.NumAtoms 18
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 2
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.333
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1
_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 63.444
_pdbe_chem_comp_rdkit_properties.tpsa 29.260
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.288
_pdbe_chem_comp_rdkit_properties.CrippenMR 34.040
_pdbe_chem_comp_rdkit_properties.chi0v 3.894
_pdbe_chem_comp_rdkit_properties.chi1v 1.894
_pdbe_chem_comp_rdkit_properties.chi2v 0.566
_pdbe_chem_comp_rdkit_properties.chi3v 0.566
_pdbe_chem_comp_rdkit_properties.chi4v 0.305
_pdbe_chem_comp_rdkit_properties.chi0n 13.894
_pdbe_chem_comp_rdkit_properties.chi1n 6.789
_pdbe_chem_comp_rdkit_properties.chi2n 0.566
_pdbe_chem_comp_rdkit_properties.chi3n 0.566
_pdbe_chem_comp_rdkit_properties.chi4n 0.305
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.920
_pdbe_chem_comp_rdkit_properties.kappa1 0.897
_pdbe_chem_comp_rdkit_properties.kappa2 1.903
_pdbe_chem_comp_rdkit_properties.kappa3 1.026
_pdbe_chem_comp_rdkit_properties.Phi 0.213
#
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
LG5 UniChem PDBe LG5
LG5 UniChem ZINC ZINC000103548388
LG5 UniChem SureChEMBL SCHEMBL16629066
LG5 UniChem PubChem 11840957
#
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
LG5 C1 -0.492 1.640 -0.792 ETKDGv3 1
LG5 C2 0.918 1.116 -0.714 ETKDGv3 2
LG5 N3 1.014 -0.190 -0.042 ETKDGv3 3
LG5 C4 -0.142 -0.870 0.477 ETKDGv3 4
LG5 C5 -1.360 -0.334 0.366 ETKDGv3 5
LG5 C6 -1.532 0.969 -0.295 ETKDGv3 6
LG5 C7 2.322 -0.824 0.108 ETKDGv3 7
LG5 N8 -2.502 -1.021 0.886 ETKDGv3 8
LG5 H1 -0.662 2.596 -1.270 ETKDGv3 9
LG5 H21 1.315 1.025 -1.747 ETKDGv3 10
LG5 H22 1.537 1.856 -0.164 ETKDGv3 11
LG5 H4 -0.021 -1.831 0.964 ETKDGv3 12
LG5 H6 -2.524 1.395 -0.379 ETKDGv3 13
LG5 H71 2.323 -1.808 -0.406 ETKDGv3 14
LG5 H72 2.545 -0.973 1.185 ETKDGv3 15
LG5 H73 3.124 -0.194 -0.335 ETKDGv3 16
LG5 HN81 -3.456 -0.605 0.801 ETKDGv3 17
LG5 HN82 -2.406 -1.948 1.359 ETKDGv3 18
#