data_LDV # _chem_comp.id LDV _chem_comp.name 3-[(4-methylpiperidin-1-yl)methyl]-1H-indole _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C15 H20 N2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2019-02-22 _chem_comp.pdbx_modified_date 2019-05-03 _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 228.333 _chem_comp.one_letter_code ? _chem_comp.three_letter_code LDV _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 5QOM _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 LDV N1 N1 N 0 1 N N N N N N -54.279 19.053 85.437 -1.399 0.219 0.465 N1 LDV 1 LDV C4 C1 C 0 1 N N N N N N -54.963 17.728 85.615 -2.546 0.877 1.103 C4 LDV 2 LDV C5 C2 C 0 1 N N N N N N -53.840 19.137 84.006 -1.837 -0.856 -0.435 C5 LDV 3 LDV C6 C3 C 0 1 N N N N N N -55.067 19.172 83.105 -2.700 -0.268 -1.553 C6 LDV 4 LDV C7 C4 C 0 1 N N N N N N -53.158 19.273 86.435 -0.455 -0.287 1.470 C7 LDV 5 LDV C8 C5 C 0 1 Y N N N N N -52.337 20.522 86.251 0.814 -0.731 0.790 C8 LDV 6 LDV C10 C6 C 0 1 Y N N N N N -50.755 22.162 86.549 2.868 -0.725 -0.232 C10 LDV 7 LDV C13 C7 C 0 1 Y N N N N N -49.656 21.212 88.859 3.294 2.018 -0.144 C13 LDV 8 LDV C15 C8 C 0 1 Y N N N N N -49.705 22.876 87.118 4.038 -0.184 -0.755 C15 LDV 9 LDV C1 C9 C 0 1 N N N N N N -55.029 16.745 82.523 -4.766 -0.586 -0.181 C1 LDV 10 LDV C11 C10 C 0 1 Y N N N N N -51.267 20.971 87.103 1.909 0.132 0.339 C11 LDV 11 LDV C12 C11 C 0 1 Y N N N N N -50.682 20.495 88.280 2.138 1.508 0.376 C12 LDV 12 LDV C14 C12 C 0 1 Y N N N N N -49.161 22.376 88.276 4.244 1.177 -0.708 C14 LDV 13 LDV C2 C13 C 0 1 N N N N N N -55.817 17.865 83.192 -3.914 0.434 -0.938 C2 LDV 14 LDV C3 C14 C 0 1 N N N N N N -56.148 17.580 84.655 -3.431 1.517 0.031 C3 LDV 15 LDV C9 C15 C 0 1 Y N N N N N -52.425 21.450 85.259 1.158 -1.993 0.486 C9 LDV 16 LDV N2 N2 N 0 1 Y N N N N N -51.481 22.421 85.427 2.381 -2.008 -0.126 N2 LDV 17 LDV H2 H2 H 0 1 N N N N N N -55.328 17.649 86.650 -3.125 0.139 1.659 H2 LDV 18 LDV H3 H3 H 0 1 N N N N N N -54.240 16.922 85.419 -2.189 1.648 1.786 H3 LDV 19 LDV H4 H4 H 0 1 N N N N N N -53.227 18.258 83.758 -0.964 -1.344 -0.869 H4 LDV 20 LDV H5 H5 H 0 1 N N N N N N -53.248 20.052 83.856 -2.419 -1.586 0.128 H5 LDV 21 LDV H6 H6 H 0 1 N N N N N N -54.749 19.340 82.065 -2.115 0.452 -2.125 H6 LDV 22 LDV H7 H7 H 0 1 N N N N N N -55.728 19.992 83.423 -3.038 -1.068 -2.211 H7 LDV 23 LDV H8 H8 H 0 1 N N N N N N -53.606 19.311 87.439 -0.227 0.504 2.185 H8 LDV 24 LDV H9 H9 H 0 1 N N N N N N -52.477 18.412 86.370 -0.902 -1.132 1.994 H9 LDV 25 LDV H10 H10 H 0 1 N N N N N N -49.226 20.863 89.786 3.470 3.083 -0.115 H10 LDV 26 LDV H11 H11 H 0 1 N N N N N N -49.333 23.785 86.668 4.784 -0.830 -1.196 H11 LDV 27 LDV H12 H12 H 0 1 N N N N N N -55.593 15.804 82.598 -4.170 -1.041 0.611 H12 LDV 28 LDV H13 H13 H 0 1 N N N N N N -54.868 16.992 81.463 -5.630 -0.086 0.257 H13 LDV 29 LDV H14 H14 H 0 1 N N N N N N -54.057 16.631 83.025 -5.105 -1.360 -0.870 H14 LDV 30 LDV H15 H15 H 0 1 N N N N N N -51.029 19.577 88.730 1.403 2.168 0.813 H15 LDV 31 LDV H16 H16 H 0 1 N N N N N N -48.336 22.894 88.742 5.153 1.595 -1.115 H16 LDV 32 LDV H17 H17 H 0 1 N N N N N N -56.766 17.980 82.648 -4.510 0.891 -1.728 H17 LDV 33 LDV H18 H18 H 0 1 N N N N N N -56.936 18.279 84.971 -4.291 1.992 0.504 H18 LDV 34 LDV H19 H19 H 0 1 N N N N N N -56.522 16.548 84.728 -2.857 2.265 -0.516 H19 LDV 35 LDV H20 H20 H 0 1 N N N N N N -53.142 21.422 84.452 0.557 -2.866 0.693 H20 LDV 36 LDV H21 H21 H 0 1 N N N N N N -51.344 23.203 84.819 2.839 -2.805 -0.437 H21 LDV 37 # 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 LDV C1 C2 SING N N 1 LDV C6 C2 SING N N 2 LDV C6 C5 SING N N 3 LDV C2 C3 SING N N 4 LDV C5 N1 SING N N 5 LDV C3 C4 SING N N 6 LDV C9 N2 SING Y N 7 LDV C9 C8 DOUB Y N 8 LDV N2 C10 SING Y N 9 LDV N1 C4 SING N N 10 LDV N1 C7 SING N N 11 LDV C8 C7 SING N N 12 LDV C8 C11 SING Y N 13 LDV C10 C11 DOUB Y N 14 LDV C10 C15 SING Y N 15 LDV C11 C12 SING Y N 16 LDV C15 C14 DOUB Y N 17 LDV C14 C13 SING Y N 18 LDV C12 C13 DOUB Y N 19 LDV C4 H2 SING N N 20 LDV C4 H3 SING N N 21 LDV C5 H4 SING N N 22 LDV C5 H5 SING N N 23 LDV C6 H6 SING N N 24 LDV C6 H7 SING N N 25 LDV C7 H8 SING N N 26 LDV C7 H9 SING N N 27 LDV C13 H10 SING N N 28 LDV C15 H11 SING N N 29 LDV C1 H12 SING N N 30 LDV C1 H13 SING N N 31 LDV C1 H14 SING N N 32 LDV C12 H15 SING N N 33 LDV C14 H16 SING N N 34 LDV C2 H17 SING N N 35 LDV C3 H18 SING N N 36 LDV C3 H19 SING N N 37 LDV C9 H20 SING N N 38 LDV N2 H21 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 LDV SMILES ACDLabs 12.01 N1(CCC(CC1)C)Cc3c2c(cccc2)nc3 LDV InChI InChI 1.03 InChI=1S/C15H20N2/c1-12-6-8-17(9-7-12)11-13-10-16-15-5-3-2-4-14(13)15/h2-5,10,12,16H,6-9,11H2,1H3 LDV InChIKey InChI 1.03 DGCGMYNLCDVYMB-UHFFFAOYSA-N LDV SMILES_CANONICAL CACTVS 3.385 CC1CCN(CC1)Cc2c[nH]c3ccccc23 LDV SMILES CACTVS 3.385 CC1CCN(CC1)Cc2c[nH]c3ccccc23 LDV SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 CC1CCN(CC1)Cc2c[nH]c3c2cccc3 LDV SMILES "OpenEye OEToolkits" 2.0.6 CC1CCN(CC1)Cc2c[nH]c3c2cccc3 # 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 LDV "SYSTEMATIC NAME" ACDLabs 12.01 3-[(4-methylpiperidin-1-yl)methyl]-1H-indole LDV "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 3-[(4-methylpiperidin-1-yl)methyl]-1~{H}-indole # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site LDV 'Create component' 2019-02-22 RCSB LDV 'Initial release' 2019-05-08 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 LDV N1 N 8.951 1.649 1 LDV C4 C 9.417 3.075 2 LDV C5 C 9.953 0.533 3 LDV C6 C 11.421 0.842 4 LDV C7 C 7.483 1.340 5 LDV C8 C 7.018 -0.086 6 LDV C10 C 5.598 -2.043 7 LDV C13 C 3.000 -0.543 8 LDV C15 C 4.299 -2.793 9 LDV C1 C 13.354 2.577 10 LDV C11 C 5.598 -0.543 11 LDV C12 C 4.299 0.207 12 LDV C14 C 3.000 -2.043 13 LDV C2 C 11.887 2.268 14 LDV C3 C 10.885 3.384 15 LDV C9 C 7.893 -1.293 16 LDV N2 N 7.018 -2.500 17 # 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 LDV C1 C2 SINGLE NONE 1 LDV C6 C2 SINGLE NONE 2 LDV C6 C5 SINGLE NONE 3 LDV C2 C3 SINGLE NONE 4 LDV C5 N1 SINGLE NONE 5 LDV C3 C4 SINGLE NONE 6 LDV C9 N2 SINGLE NONE 7 LDV C9 C8 DOUBLE NONE 8 LDV N2 C10 SINGLE NONE 9 LDV N1 C4 SINGLE NONE 10 LDV N1 C7 SINGLE NONE 11 LDV C8 C7 SINGLE NONE 12 LDV C8 C11 SINGLE NONE 13 LDV C10 C11 SINGLE NONE 14 LDV C10 C15 DOUBLE NONE 15 LDV C11 C12 DOUBLE NONE 16 LDV C15 C14 SINGLE NONE 17 LDV C14 C13 DOUBLE NONE 18 LDV C12 C13 SINGLE NONE 19 # 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 LDV MurckoScaffold S1 scaffold 'c1ccc2c(CN3CCCCC3)c[nH]c2c1' InChI=1S/C14H18N2/c1-4-8-16(9-5-1)11-12-10-15-14-7-3-2-6-13(12)14/h2-3,6-7,10,15H,1,4-5,8-9,11H2 HPKXPFRRVVWAPD-UHFFFAOYSA-N LDV indole F1 fragment 'c1ccc2[nH]ccc2c1' InChI=1S/C8H7N/c1-2-4-8-7(3-1)5-6-9-8/h1-6,9H SIKJAQJRHWYJAI-UHFFFAOYSA-N LDV phenyl F2 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N LDV pyrrole F3 fragment 'c1cc[nH]c1' InChI=1S/C4H5N/c1-2-4-5-3-1/h1-5H KAESVJOAVNADME-UHFFFAOYSA-N LDV Z2856434912 F4 fragment 'CC1CCN(Cc2c[nH]c3ccccc23)CC1' InChI=1S/C15H20N2/c1-12-6-8-17(9-7-12)11-13-10-16-15-5-3-2-4-14(13)15/h2-5,10,12,16H,6-9,11H2,1H3 DGCGMYNLCDVYMB-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 LDV N1 S1 1 LDV C4 S1 1 LDV C5 S1 1 LDV C6 S1 1 LDV C7 S1 1 LDV C8 S1 1 LDV C10 S1 1 LDV C13 S1 1 LDV C15 S1 1 LDV C11 S1 1 LDV C12 S1 1 LDV C14 S1 1 LDV C2 S1 1 LDV C3 S1 1 LDV C9 S1 1 LDV N2 S1 1 LDV C10 F1 1 LDV C11 F1 1 LDV C8 F1 1 LDV C9 F1 1 LDV N2 F1 1 LDV C12 F1 1 LDV C13 F1 1 LDV C14 F1 1 LDV C15 F1 1 LDV C10 F2 1 LDV C11 F2 1 LDV C12 F2 1 LDV C13 F2 1 LDV C14 F2 1 LDV C15 F2 1 LDV C10 F3 1 LDV C11 F3 1 LDV C8 F3 1 LDV C9 F3 1 LDV N2 F3 1 LDV C1 F4 1 LDV C2 F4 1 LDV C6 F4 1 LDV C5 F4 1 LDV N1 F4 1 LDV C7 F4 1 LDV C8 F4 1 LDV C9 F4 1 LDV N2 F4 1 LDV C10 F4 1 LDV C15 F4 1 LDV C14 F4 1 LDV C13 F4 1 LDV C12 F4 1 LDV C11 F4 1 LDV C4 F4 1 LDV C3 F4 1 # _pdbe_chem_comp_rdkit_properties.comp_id LDV _pdbe_chem_comp_rdkit_properties.exactmw 228.163 _pdbe_chem_comp_rdkit_properties.amw 228.339 _pdbe_chem_comp_rdkit_properties.lipinskiHBA 2 _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 1 _pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 17 _pdbe_chem_comp_rdkit_properties.NumAtoms 37 _pdbe_chem_comp_rdkit_properties.NumHeteroatoms 2 _pdbe_chem_comp_rdkit_properties.NumAmideBonds 0 _pdbe_chem_comp_rdkit_properties.FractionCSP3 0.467 _pdbe_chem_comp_rdkit_properties.NumRings 3 _pdbe_chem_comp_rdkit_properties.NumAromaticRings 2 _pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1 _pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1 _pdbe_chem_comp_rdkit_properties.NumHeterocycles 2 _pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1 _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 130.788 _pdbe_chem_comp_rdkit_properties.tpsa 19.030 _pdbe_chem_comp_rdkit_properties.CrippenClogP 2.917 _pdbe_chem_comp_rdkit_properties.CrippenMR 69.502 _pdbe_chem_comp_rdkit_properties.chi0v 8.394 _pdbe_chem_comp_rdkit_properties.chi1v 4.618 _pdbe_chem_comp_rdkit_properties.chi2v 2.006 _pdbe_chem_comp_rdkit_properties.chi3v 2.006 _pdbe_chem_comp_rdkit_properties.chi4v 1.270 _pdbe_chem_comp_rdkit_properties.chi0n 28.394 _pdbe_chem_comp_rdkit_properties.chi1n 14.565 _pdbe_chem_comp_rdkit_properties.chi2n 2.006 _pdbe_chem_comp_rdkit_properties.chi3n 2.006 _pdbe_chem_comp_rdkit_properties.chi4n 1.270 _pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.280 _pdbe_chem_comp_rdkit_properties.kappa1 2.394 _pdbe_chem_comp_rdkit_properties.kappa2 4.534 _pdbe_chem_comp_rdkit_properties.kappa3 2.225 _pdbe_chem_comp_rdkit_properties.Phi 0.639 # 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 LDV UniChem ChEMBL CHEMBL57478 LDV UniChem PDBe LDV LDV UniChem ZINC ZINC000000142608 LDV UniChem eMolecules 1061616 LDV UniChem 'PubChem TPHARMA' 14798110 LDV UniChem ACTor 21000-95-3 LDV UniChem Nikkaji J62.682A LDV UniChem BindingDb 50050469 LDV UniChem 'EPA CompTox Dashboard' DTXSID30175210 LDV UniChem SureChEMBL SCHEMBL13504100 LDV UniChem PubChem 30438 LDV UniChem Mcule MCULE-4620579742 # 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 LDV N1 -0.705 -0.982 1.528 ETKDGv3 1 LDV C4 -0.975 0.468 1.361 ETKDGv3 2 LDV C5 -1.532 -1.882 0.690 ETKDGv3 3 LDV C6 -2.932 -1.302 0.471 ETKDGv3 4 LDV C7 0.731 -1.344 1.536 ETKDGv3 5 LDV C8 1.456 -0.983 0.261 ETKDGv3 6 LDV C10 2.732 0.093 -1.339 ETKDGv3 7 LDV C13 3.467 2.303 0.191 ETKDGv3 8 LDV C15 3.534 1.001 -1.900 ETKDGv3 9 LDV C1 -4.085 0.901 -0.002 ETKDGv3 10 LDV C11 2.243 0.226 0.008 ETKDGv3 11 LDV C12 2.592 1.256 0.786 ETKDGv3 12 LDV C14 3.910 2.184 -1.080 ETKDGv3 13 LDV C2 -2.857 0.033 -0.307 ETKDGv3 14 LDV C3 -1.541 0.803 -0.027 ETKDGv3 15 LDV C9 1.525 -1.747 -0.841 ETKDGv3 16 LDV N2 2.290 -1.136 -1.887 ETKDGv3 17 LDV H2 -1.716 0.776 2.129 ETKDGv3 18 LDV H3 -0.072 1.081 1.550 ETKDGv3 19 LDV H4 -1.626 -2.866 1.198 ETKDGv3 20 LDV H5 -1.071 -2.050 -0.304 ETKDGv3 21 LDV H6 -3.408 -1.154 1.466 ETKDGv3 22 LDV H7 -3.553 -2.030 -0.095 ETKDGv3 23 LDV H8 0.841 -2.435 1.723 ETKDGv3 24 LDV H9 1.227 -0.840 2.393 ETKDGv3 25 LDV H10 3.754 3.161 0.785 ETKDGv3 26 LDV H11 3.908 0.874 -2.907 ETKDGv3 27 LDV H12 -4.090 1.213 1.064 ETKDGv3 28 LDV H13 -4.081 1.809 -0.642 ETKDGv3 29 LDV H14 -5.016 0.333 -0.215 ETKDGv3 30 LDV H15 2.267 1.327 1.814 ETKDGv3 31 LDV H16 4.551 2.946 -1.504 ETKDGv3 32 LDV H17 -2.882 -0.201 -1.395 ETKDGv3 33 LDV H18 -1.690 1.901 -0.113 ETKDGv3 34 LDV H19 -0.784 0.523 -0.792 ETKDGv3 35 LDV H20 1.075 -2.727 -0.936 ETKDGv3 36 LDV H21 2.513 -1.534 -2.825 ETKDGv3 37 #