data_S3J
#
_chem_comp.id S3J
_chem_comp.name "2-(4-phenylpiperidin-1-yl)ethanoic acid"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C13 H17 N O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2020-03-04
_chem_comp.pdbx_modified_date 2020-04-17
_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 219.280
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code S3J
_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 5RAS
_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
S3J C4 C1 C 0 1 N N N N N N -1.684 65.154 68.106 0.955 0.634 -0.384 C4 S3J 1
S3J C5 C2 C 0 1 Y N N N N N -2.003 63.963 69.007 2.369 0.161 -0.168 C5 S3J 2
S3J C6 C3 C 0 1 Y N N N N N -3.235 63.820 69.737 2.633 -0.828 0.761 C6 S3J 3
S3J C7 C4 C 0 1 Y N N N N N -3.467 62.658 70.498 3.930 -1.262 0.959 C7 S3J 4
S3J C8 C5 C 0 1 Y N N N N N -2.515 61.643 70.548 4.964 -0.708 0.227 C8 S3J 5
S3J C10 C6 C 0 1 Y N N N N N -1.060 62.924 69.100 3.402 0.711 -0.904 C10 S3J 6
S3J N N1 N 0 1 N N N N N N -1.431 68.059 67.443 -1.847 0.468 0.294 N S3J 7
S3J C C7 C 0 1 N N N N N N -2.920 66.080 67.834 0.082 -0.544 -0.825 C S3J 8
S3J O O1 O 0 1 N N N N N N -2.101 71.284 65.881 -3.520 -1.524 -0.039 O S3J 9
S3J C1 C8 C 0 1 N N N N N N -2.551 67.192 66.849 -1.364 -0.071 -0.984 C1 S3J 10
S3J C11 C9 C 0 1 N N N N N N -1.040 69.209 66.478 -3.275 0.805 0.218 C11 S3J 11
S3J C12 C10 C 0 1 N N N N N N -2.040 70.435 66.746 -4.079 -0.455 0.027 C12 S3J 12
S3J C2 C11 C 0 1 N N N N N N -0.185 67.216 67.832 -1.054 1.630 0.714 C2 S3J 13
S3J C3 C12 C 0 1 N N N N N N -0.532 65.989 68.716 0.402 1.207 0.924 C3 S3J 14
S3J C9 C13 C 0 1 Y N N N N N -1.315 61.788 69.853 4.700 0.280 -0.702 C9 S3J 15
S3J O1 O2 O 0 1 N N N N N N -2.653 70.360 67.865 -5.416 -0.390 -0.071 O1 S3J 16
S3J H1 H1 H 0 1 N N N N N N -1.341 64.765 67.136 0.942 1.406 -1.154 H1 S3J 17
S3J H2 H2 H 0 1 N N N N N N -3.979 64.602 69.701 1.825 -1.261 1.333 H2 S3J 18
S3J H3 H3 H 0 1 N N N N N N -4.391 62.553 71.047 4.136 -2.034 1.686 H3 S3J 19
S3J H4 H4 H 0 1 N N N N N N -2.705 60.748 71.122 5.977 -1.047 0.382 H4 S3J 20
S3J H5 H5 H 0 1 N N N N N N -0.120 63.012 68.575 3.195 1.481 -1.633 H5 S3J 21
S3J H7 H7 H 0 1 N N N N N N -3.250 66.531 68.782 0.445 -0.930 -1.778 H7 S3J 22
S3J H8 H8 H 0 1 N N N N N N -3.737 65.478 67.410 0.127 -1.332 -0.073 H8 S3J 23
S3J H9 H9 H 0 1 N N N N N N -3.435 67.818 66.656 -1.991 -0.910 -1.284 H9 S3J 24
S3J H10 H10 H 0 1 N N N N N N -2.206 66.745 65.905 -1.410 0.707 -1.746 H10 S3J 25
S3J H11 H11 H 0 1 N N N N N N -1.133 68.871 65.435 -3.583 1.296 1.141 H11 S3J 26
S3J H12 H12 H 0 1 N N N N N N -0.003 69.523 66.670 -3.445 1.476 -0.624 H12 S3J 27
S3J H13 H13 H 0 1 N N N N N N 0.297 66.858 66.910 -1.102 2.400 -0.056 H13 S3J 28
S3J H14 H14 H 0 1 N N N N N N 0.514 67.860 68.386 -1.455 2.026 1.648 H14 S3J 29
S3J H15 H15 H 0 1 N N N N N N 0.360 65.352 68.809 0.451 0.448 1.704 H15 S3J 30
S3J H16 H16 H 0 1 N N N N N N -0.836 66.342 69.713 0.993 2.073 1.220 H16 S3J 31
S3J H17 H17 H 0 1 N N N N N N -0.574 61.004 69.902 5.507 0.710 -1.277 H17 S3J 32
S3J H18 H18 H 0 1 N N N N N N -3.222 71.114 67.966 -5.889 -1.225 -0.192 H18 S3J 33
#
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
S3J O C12 DOUB N N 1
S3J C11 C12 SING N N 2
S3J C11 N SING N N 3
S3J C12 O1 SING N N 4
S3J C1 N SING N N 5
S3J C1 C SING N N 6
S3J N C2 SING N N 7
S3J C2 C3 SING N N 8
S3J C C4 SING N N 9
S3J C4 C3 SING N N 10
S3J C4 C5 SING N N 11
S3J C5 C10 DOUB Y N 12
S3J C5 C6 SING Y N 13
S3J C10 C9 SING Y N 14
S3J C6 C7 DOUB Y N 15
S3J C9 C8 DOUB Y N 16
S3J C7 C8 SING Y N 17
S3J C4 H1 SING N N 18
S3J C6 H2 SING N N 19
S3J C7 H3 SING N N 20
S3J C8 H4 SING N N 21
S3J C10 H5 SING N N 22
S3J C H7 SING N N 23
S3J C H8 SING N N 24
S3J C1 H9 SING N N 25
S3J C1 H10 SING N N 26
S3J C11 H11 SING N N 27
S3J C11 H12 SING N N 28
S3J C2 H13 SING N N 29
S3J C2 H14 SING N N 30
S3J C3 H15 SING N N 31
S3J C3 H16 SING N N 32
S3J C9 H17 SING N N 33
S3J O1 H18 SING N N 34
#
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
S3J InChI InChI 1.03 InChI=1S/C13H17NO2/c15-13(16)10-14-8-6-12(7-9-14)11-4-2-1-3-5-11/h1-5,12H,6-10H2,(H,15,16)
S3J InChIKey InChI 1.03 OAMRZYKCPQKDBJ-UHFFFAOYSA-N
S3J SMILES_CANONICAL CACTVS 3.385 OC(=O)CN1CCC(CC1)c2ccccc2
S3J SMILES CACTVS 3.385 OC(=O)CN1CCC(CC1)c2ccccc2
S3J SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 c1ccc(cc1)C2CCN(CC2)CC(=O)O
S3J SMILES "OpenEye OEToolkits" 2.0.6 c1ccc(cc1)C2CCN(CC2)CC(=O)O
#
_pdbx_chem_comp_identifier.comp_id S3J
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.6
_pdbx_chem_comp_identifier.identifier "2-(4-phenylpiperidin-1-yl)ethanoic acid"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
S3J 'Create component' 2020-03-04 RCSB
S3J 'Modify model coordinates code' 2020-03-06 RCSB
S3J 'Initial release' 2020-04-22 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
S3J C4 C 5.598 1.357 1
S3J C5 C 5.598 2.857 2
S3J C6 C 4.299 3.607 3
S3J C7 C 4.299 5.107 4
S3J C8 C 5.598 5.857 5
S3J C10 C 6.897 3.607 6
S3J N N 5.598 -1.643 7
S3J C C 4.299 0.608 8
S3J O O 4.299 -5.393 9
S3J C1 C 4.299 -0.892 10
S3J C11 C 5.598 -3.143 11
S3J C12 C 4.299 -3.893 12
S3J C2 C 6.897 -0.892 13
S3J C3 C 6.897 0.608 14
S3J C9 C 6.897 5.107 15
S3J O1 O 3.000 -3.143 16
#
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
S3J O C12 DOUBLE NONE 1
S3J C11 C12 SINGLE NONE 2
S3J C11 N SINGLE NONE 3
S3J C12 O1 SINGLE NONE 4
S3J C1 N SINGLE NONE 5
S3J C1 C SINGLE NONE 6
S3J N C2 SINGLE NONE 7
S3J C2 C3 SINGLE NONE 8
S3J C C4 SINGLE NONE 9
S3J C4 C3 SINGLE NONE 10
S3J C4 C5 SINGLE NONE 11
S3J C5 C10 SINGLE NONE 12
S3J C5 C6 DOUBLE NONE 13
S3J C10 C9 DOUBLE NONE 14
S3J C6 C7 SINGLE NONE 15
S3J C9 C8 SINGLE NONE 16
S3J C7 C8 DOUBLE NONE 17
#
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
S3J MurckoScaffold S1 scaffold c1ccc(C2CCNCC2)cc1 InChI=1S/C11H15N/c1-2-4-10(5-3-1)11-6-8-12-9-7-11/h1-5,11-12H,6-9H2 UTBULQCHEUWJNV-UHFFFAOYSA-N
S3J peptide F1 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
S3J phenyl F2 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
S3J Z287148438 F3 fragment O=C(O)CN1CCC(c2ccccc2)CC1 InChI=1S/C13H17NO2/c15-13(16)10-14-8-6-12(7-9-14)11-4-2-1-3-5-11/h1-5,12H,6-10H2,(H,15,16) OAMRZYKCPQKDBJ-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
S3J C4 S1 1
S3J C5 S1 1
S3J C6 S1 1
S3J C7 S1 1
S3J C8 S1 1
S3J C10 S1 1
S3J N S1 1
S3J C S1 1
S3J C1 S1 1
S3J C2 S1 1
S3J C3 S1 1
S3J C9 S1 1
S3J O F1 1
S3J C12 F1 1
S3J C11 F1 1
S3J N F1 1
S3J C5 F2 1
S3J C10 F2 1
S3J C9 F2 1
S3J C8 F2 1
S3J C7 F2 1
S3J C6 F2 1
S3J O1 F3 1
S3J C12 F3 1
S3J O F3 1
S3J C11 F3 1
S3J N F3 1
S3J C1 F3 1
S3J C F3 1
S3J C4 F3 1
S3J C3 F3 1
S3J C2 F3 1
S3J C5 F3 1
S3J C10 F3 1
S3J C9 F3 1
S3J C8 F3 1
S3J C7 F3 1
S3J C6 F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id S3J
_pdbe_chem_comp_rdkit_properties.exactmw 219.126
_pdbe_chem_comp_rdkit_properties.amw 219.284
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 3
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 16
_pdbe_chem_comp_rdkit_properties.NumAtoms 33
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 3
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.462
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_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 119.667
_pdbe_chem_comp_rdkit_properties.tpsa 40.540
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.896
_pdbe_chem_comp_rdkit_properties.CrippenMR 62.227
_pdbe_chem_comp_rdkit_properties.chi0v 7.764
_pdbe_chem_comp_rdkit_properties.chi1v 4.079
_pdbe_chem_comp_rdkit_properties.chi2v 1.539
_pdbe_chem_comp_rdkit_properties.chi3v 1.539
_pdbe_chem_comp_rdkit_properties.chi4v 0.930
_pdbe_chem_comp_rdkit_properties.chi0n 24.764
_pdbe_chem_comp_rdkit_properties.chi1n 12.487
_pdbe_chem_comp_rdkit_properties.chi2n 1.539
_pdbe_chem_comp_rdkit_properties.chi3n 1.539
_pdbe_chem_comp_rdkit_properties.chi4n 0.930
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.350
_pdbe_chem_comp_rdkit_properties.kappa1 2.561
_pdbe_chem_comp_rdkit_properties.kappa2 5.122
_pdbe_chem_comp_rdkit_properties.kappa3 2.826
_pdbe_chem_comp_rdkit_properties.Phi 0.820
#
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
S3J UniChem ChEMBL CHEMBL3464675
S3J UniChem PDBe S3J
S3J UniChem ZINC ZINC000000808022
S3J UniChem SureChEMBL SCHEMBL7202138
S3J UniChem PubChem 1089052
S3J UniChem ACTor 799266-57-2
S3J UniChem 'EPA CompTox Dashboard' DTXSID40360195
S3J UniChem eMolecules 1497037
S3J UniChem PubChem 6965287
S3J UniChem Mcule MCULE-1367592199
#
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
S3J C4 -0.594 -0.336 -0.069 ETKDGv3 1
S3J C5 -2.095 -0.125 -0.134 ETKDGv3 2
S3J C6 -2.907 -1.115 -0.558 ETKDGv3 3
S3J C7 -4.369 -0.909 -0.623 ETKDGv3 4
S3J C8 -4.898 0.266 -0.265 ETKDGv3 5
S3J C10 -2.697 1.179 0.258 ETKDGv3 6
S3J N 2.116 -0.379 0.101 ETKDGv3 7
S3J C 0.149 0.579 -1.068 ETKDGv3 8
S3J O 4.139 -2.010 -1.371 ETKDGv3 9
S3J C1 1.632 0.769 -0.693 ETKDGv3 10
S3J C11 3.584 -0.345 0.252 ETKDGv3 11
S3J C12 4.248 -0.809 -1.007 ETKDGv3 12
S3J C2 1.464 -0.404 1.432 ETKDGv3 13
S3J C3 -0.057 -0.133 1.358 ETKDGv3 14
S3J C9 -4.022 1.360 0.196 ETKDGv3 15
S3J O1 4.973 0.091 -1.783 ETKDGv3 16
S3J H1 -0.359 -1.390 -0.349 ETKDGv3 17
S3J H2 -2.505 -2.075 -0.856 ETKDGv3 18
S3J H3 -5.010 -1.712 -0.963 ETKDGv3 19
S3J H4 -5.969 0.417 -0.313 ETKDGv3 20
S3J H5 -2.068 1.994 0.592 ETKDGv3 21
S3J H7 0.079 0.125 -2.081 ETKDGv3 22
S3J H8 -0.326 1.582 -1.123 ETKDGv3 23
S3J H9 2.217 0.875 -1.632 ETKDGv3 24
S3J H10 1.753 1.714 -0.115 ETKDGv3 25
S3J H11 3.909 -1.029 1.067 ETKDGv3 26
S3J H12 3.936 0.678 0.516 ETKDGv3 27
S3J H13 1.928 0.344 2.115 ETKDGv3 28
S3J H14 1.619 -1.410 1.882 ETKDGv3 29
S3J H15 -0.590 -0.808 2.063 ETKDGv3 30
S3J H16 -0.248 0.912 1.685 ETKDGv3 31
S3J H17 -4.454 2.311 0.481 ETKDGv3 32
S3J H18 5.421 -0.207 -2.641 ETKDGv3 33
#