data_Y8J
#
_chem_comp.id Y8J
_chem_comp.name 3-butylpyridine
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C9 H13 N"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2021-02-10
_chem_comp.pdbx_modified_date 2021-08-20
_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 135.206
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code Y8J
_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 7LOG
_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
Y8J C10 C1 C 0 1 Y N N N N N -33.762 7.137 5.166 -1.235 1.171 -0.205 C10 Y8J 1
Y8J C01 C2 C 0 1 N N N N N N -33.471 9.270 0.386 4.235 0.007 0.840 C01 Y8J 2
Y8J C02 C3 C 0 1 N N N N N N -32.311 9.064 1.345 3.253 0.001 -0.334 C02 Y8J 3
Y8J C03 C4 C 0 1 N N N N N N -32.683 9.356 2.801 1.820 -0.006 0.200 C03 Y8J 4
Y8J C04 C5 C 0 1 N N N N N N -32.063 8.339 3.757 0.839 -0.011 -0.974 C04 Y8J 5
Y8J C05 C6 C 0 1 Y N N N N N -33.015 7.180 4.002 -0.574 -0.018 -0.448 C05 Y8J 6
Y8J C06 C7 C 0 1 Y N N N N N -33.151 6.165 3.071 -1.226 -1.217 -0.202 C06 Y8J 7
Y8J C07 C8 C 0 1 Y N N N N N -34.034 5.136 3.349 -2.524 -1.174 0.282 C07 Y8J 8
Y8J C08 C9 C 0 1 Y N N N N N -34.749 5.158 4.537 -3.122 0.052 0.501 C08 Y8J 9
Y8J N09 N1 N 0 1 Y N N N N N -34.597 6.142 5.402 -2.471 1.173 0.255 N09 Y8J 10
Y8J H1 H1 H 0 1 N N N N N N -33.660 7.930 5.893 -0.733 2.109 -0.390 H1 Y8J 11
Y8J H2 H2 H 0 1 N N N N N N -33.144 9.046 -0.640 4.069 0.896 1.448 H2 Y8J 12
Y8J H3 H3 H 0 1 N N N N N N -34.298 8.599 0.662 4.078 -0.884 1.449 H3 Y8J 13
Y8J H4 H4 H 0 1 N N N N N N -33.812 10.314 0.442 5.256 0.011 0.460 H4 Y8J 14
Y8J H5 H5 H 0 1 N N N N N N -31.976 8.019 1.271 3.410 0.891 -0.943 H5 Y8J 15
Y8J H6 H6 H 0 1 N N N N N N -31.490 9.734 1.051 3.419 -0.889 -0.941 H6 Y8J 16
Y8J H7 H7 H 0 1 N N N N N N -32.322 10.361 3.066 1.663 -0.896 0.809 H7 Y8J 17
Y8J H8 H8 H 0 1 N N N N N N -33.778 9.320 2.903 1.654 0.884 0.808 H8 Y8J 18
Y8J H9 H9 H 0 1 N N N N N N -31.131 7.954 3.319 0.995 0.879 -1.583 H9 Y8J 19
Y8J H10 H10 H 0 1 N N N N N N -31.841 8.833 4.715 1.004 -0.901 -1.582 H10 Y8J 20
Y8J H11 H11 H 0 1 N N N N N N -32.583 6.176 2.152 -0.734 -2.161 -0.383 H11 Y8J 21
Y8J H12 H12 H 0 1 N N N N N N -34.165 4.325 2.648 -3.062 -2.089 0.484 H12 Y8J 22
Y8J H13 H13 H 0 1 N N N N N N -35.440 4.358 4.757 -4.133 0.094 0.877 H13 Y8J 23
#
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
Y8J C01 C02 SING N N 1
Y8J C02 C03 SING N N 2
Y8J C03 C04 SING N N 3
Y8J C06 C07 DOUB Y N 4
Y8J C06 C05 SING Y N 5
Y8J C07 C08 SING Y N 6
Y8J C04 C05 SING N N 7
Y8J C05 C10 DOUB Y N 8
Y8J C08 N09 DOUB Y N 9
Y8J C10 N09 SING Y N 10
Y8J C10 H1 SING N N 11
Y8J C01 H2 SING N N 12
Y8J C01 H3 SING N N 13
Y8J C01 H4 SING N N 14
Y8J C02 H5 SING N N 15
Y8J C02 H6 SING N N 16
Y8J C03 H7 SING N N 17
Y8J C03 H8 SING N N 18
Y8J C04 H9 SING N N 19
Y8J C04 H10 SING N N 20
Y8J C06 H11 SING N N 21
Y8J C07 H12 SING N N 22
Y8J C08 H13 SING N N 23
#
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
Y8J InChI InChI 1.03 InChI=1S/C9H13N/c1-2-3-5-9-6-4-7-10-8-9/h4,6-8H,2-3,5H2,1H3
Y8J InChIKey InChI 1.03 QSNMFWFDOFQASV-UHFFFAOYSA-N
Y8J SMILES_CANONICAL CACTVS 3.385 CCCCc1cccnc1
Y8J SMILES CACTVS 3.385 CCCCc1cccnc1
Y8J SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 CCCCc1cccnc1
Y8J SMILES "OpenEye OEToolkits" 2.0.7 CCCCc1cccnc1
#
_pdbx_chem_comp_identifier.comp_id Y8J
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.7
_pdbx_chem_comp_identifier.identifier 3-butylpyridine
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
Y8J 'Create component' 2021-02-10 RCSB
Y8J 'Initial release' 2021-08-25 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
Y8J C10 C 6.897 -0.375 1
Y8J C01 C 3.000 3.375 2
Y8J C02 C 3.000 1.875 3
Y8J C03 C 4.299 1.125 4
Y8J C04 C 4.299 -0.375 5
Y8J C05 C 5.598 -1.125 6
Y8J C06 C 5.598 -2.625 7
Y8J C07 C 6.897 -3.375 8
Y8J C08 C 8.196 -2.625 9
Y8J N09 N 8.196 -1.125 10
#
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
Y8J C01 C02 SINGLE NONE 1
Y8J C02 C03 SINGLE NONE 2
Y8J C03 C04 SINGLE NONE 3
Y8J C06 C07 DOUBLE NONE 4
Y8J C06 C05 SINGLE NONE 5
Y8J C07 C08 SINGLE NONE 6
Y8J C04 C05 SINGLE NONE 7
Y8J C05 C10 DOUBLE NONE 8
Y8J C08 N09 DOUBLE NONE 9
Y8J C10 N09 SINGLE NONE 10
#
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
Y8J MurckoScaffold S1 scaffold c1ccncc1 InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H JUJWROOIHBZHMG-UHFFFAOYSA-N
Y8J 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
Y8J C10 S1 1
Y8J C05 S1 1
Y8J C06 S1 1
Y8J C07 S1 1
Y8J C08 S1 1
Y8J N09 S1 1
Y8J C10 F1 1
Y8J C05 F1 1
Y8J C06 F1 1
Y8J C07 F1 1
Y8J C08 F1 1
Y8J N09 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id Y8J
_pdbe_chem_comp_rdkit_properties.exactmw 135.105
_pdbe_chem_comp_rdkit_properties.amw 135.210
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 1
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 0
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 0
_pdbe_chem_comp_rdkit_properties.NumHBA 1
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 10
_pdbe_chem_comp_rdkit_properties.NumAtoms 23
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 1
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.444
_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 80.375
_pdbe_chem_comp_rdkit_properties.tpsa 12.890
_pdbe_chem_comp_rdkit_properties.CrippenClogP 2.369
_pdbe_chem_comp_rdkit_properties.CrippenMR 42.583
_pdbe_chem_comp_rdkit_properties.chi0v 4.947
_pdbe_chem_comp_rdkit_properties.chi1v 2.447
_pdbe_chem_comp_rdkit_properties.chi2v 0.717
_pdbe_chem_comp_rdkit_properties.chi3v 0.717
_pdbe_chem_comp_rdkit_properties.chi4v 0.383
_pdbe_chem_comp_rdkit_properties.chi0n 17.947
_pdbe_chem_comp_rdkit_properties.chi1n 8.947
_pdbe_chem_comp_rdkit_properties.chi2n 0.717
_pdbe_chem_comp_rdkit_properties.chi3n 0.717
_pdbe_chem_comp_rdkit_properties.chi4n 0.383
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.850
_pdbe_chem_comp_rdkit_properties.kappa1 1.239
_pdbe_chem_comp_rdkit_properties.kappa2 4.044
_pdbe_chem_comp_rdkit_properties.kappa3 2.175
_pdbe_chem_comp_rdkit_properties.Phi 0.501
#
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
Y8J UniChem PDBe Y8J
Y8J UniChem ChEBI 173362
Y8J UniChem ZINC ZINC000002034874
Y8J UniChem fdasrs 7I8G7Q77YM
Y8J UniChem HMDB HMDB0032934
Y8J UniChem NMRShiftDB 20207972
Y8J UniChem Nikkaji J45.599G
Y8J UniChem ChemicalBook CB1151336
Y8J UniChem 'EPA CompTox Dashboard' DTXSID9060231
Y8J UniChem eMolecules 496360
Y8J UniChem SureChEMBL SCHEMBL681571
Y8J UniChem 'PubChem TPHARMA' 16901778
Y8J UniChem PubChem 10874
Y8J UniChem ACTor 539-32-2
#
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
Y8J C10 1.927 -1.263 0.348 ETKDGv3 1
Y8J C01 -3.307 0.598 -0.128 ETKDGv3 2
Y8J C02 -2.576 -0.661 -0.593 ETKDGv3 3
Y8J C03 -1.066 -0.441 -0.766 ETKDGv3 4
Y8J C04 -0.337 -0.272 0.574 ETKDGv3 5
Y8J C05 1.148 -0.167 0.356 ETKDGv3 6
Y8J C06 1.769 1.150 0.079 ETKDGv3 7
Y8J C07 3.083 1.235 -0.150 ETKDGv3 8
Y8J C08 3.900 0.006 -0.130 ETKDGv3 9
Y8J N09 3.340 -1.145 0.103 ETKDGv3 10
Y8J H1 1.503 -2.244 0.523 ETKDGv3 11
Y8J H2 -4.402 0.412 -0.135 ETKDGv3 12
Y8J H3 -3.089 1.448 -0.808 ETKDGv3 13
Y8J H4 -3.010 0.865 0.907 ETKDGv3 14
Y8J H5 -3.001 -0.967 -1.574 ETKDGv3 15
Y8J H6 -2.763 -1.489 0.126 ETKDGv3 16
Y8J H7 -0.648 -1.328 -1.292 ETKDGv3 17
Y8J H8 -0.886 0.448 -1.411 ETKDGv3 18
Y8J H9 -0.690 0.648 1.086 ETKDGv3 19
Y8J H10 -0.564 -1.133 1.240 ETKDGv3 20
Y8J H11 1.160 2.046 0.060 ETKDGv3 21
Y8J H12 3.544 2.192 -0.352 ETKDGv3 22
Y8J H13 4.965 0.061 -0.312 ETKDGv3 23
#