data_E5R # _chem_comp.id E5R _chem_comp.name (3R)-3-[[(3R)-3-methylpiperidin-1-yl]methyl]-6,8-bis(oxidanyl)-3,4-dihydroisochromen-1-one _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C16 H21 N O4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2019-10-21 _chem_comp.pdbx_modified_date 2021-05-14 _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 291.342 _chem_comp.one_letter_code ? _chem_comp.three_letter_code E5R _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 6L4Q _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 E5R N N1 N 0 1 N N N N N N -4.923 16.925 26.614 2.770 0.542 -0.505 N E5R 1 E5R C C1 C 0 1 Y N N N N N -10.042 16.574 22.812 -3.380 -1.172 -0.021 C E5R 2 E5R O O1 O 0 1 N N N N N N -9.886 15.546 21.937 -3.424 -2.521 -0.159 O E5R 3 E5R C1 C2 C 0 1 Y N N N N N -11.302 17.130 22.961 -4.519 -0.470 0.334 C1 E5R 4 E5R C10 C3 C 0 1 N N N N N N -3.512 15.342 28.587 5.455 -0.195 0.260 C10 E5R 5 E5R C11 C4 C 0 1 N N R N N N -4.900 14.949 28.113 4.231 -0.641 1.066 C11 E5R 6 E5R C12 C5 C 0 1 N N N N N N -5.685 14.212 29.193 4.611 -0.771 2.542 C12 E5R 7 E5R C13 C6 C 0 1 N N N N N N -5.637 16.201 27.665 3.120 0.401 0.914 C13 E5R 8 E5R C14 C7 C 0 1 Y N N N N N -8.944 17.063 23.553 -2.179 -0.481 -0.232 C14 E5R 9 E5R C15 C8 C 0 1 N N N N N N -7.632 16.436 23.427 -0.952 -1.213 -0.600 C15 E5R 10 E5R C2 C9 C 0 1 Y N N N N N -11.488 18.182 23.845 -4.466 0.909 0.478 C2 E5R 11 E5R C3 C10 C 0 1 Y N N N N N -10.423 18.683 24.578 -3.274 1.594 0.266 C3 E5R 12 E5R C4 C11 C 0 1 Y N N N N N -9.151 18.136 24.441 -2.133 0.909 -0.089 C4 E5R 13 E5R C5 C12 C 0 1 N N N N N N -7.965 18.670 25.208 -0.850 1.661 -0.326 C5 E5R 14 E5R C6 C13 C 0 1 N N R N N N -6.966 17.566 25.461 0.349 0.722 -0.186 C6 E5R 15 E5R C7 C14 C 0 1 N N N N N N -5.695 18.071 26.120 1.613 1.431 -0.676 C7 E5R 16 E5R C8 C15 C 0 1 N N N N N N -3.612 17.354 27.110 3.917 1.014 -1.291 C8 E5R 17 E5R C9 C16 C 0 1 N N N N N N -2.776 16.169 27.540 5.052 -0.009 -1.205 C9 E5R 18 E5R O1 O2 O 0 1 N N N N N N -12.731 18.728 23.996 -5.584 1.594 0.827 O1 E5R 19 E5R O2 O3 O 0 1 N N N N N N -6.631 16.895 24.203 0.119 -0.474 -0.987 O2 E5R 20 E5R O3 O4 O 0 1 N N N N N N -7.380 15.534 22.669 -0.902 -2.427 -0.559 O3 E5R 21 E5R H2 H2 H 0 1 N N N N N N -8.981 15.257 21.946 -3.645 -2.818 -1.052 H2 E5R 22 E5R H3 H3 H 0 1 N N N N N N -12.135 16.746 22.391 -5.449 -0.995 0.498 H3 E5R 23 E5R H4 H4 H 0 1 N N N N N N -2.933 14.430 28.793 5.829 0.748 0.658 H4 E5R 24 E5R H5 H5 H 0 1 N N N N N N -3.604 15.934 29.510 6.234 -0.955 0.331 H5 E5R 25 E5R H6 H6 H 0 1 N N N N N N -4.794 14.280 27.246 3.881 -1.603 0.694 H6 E5R 26 E5R H7 H7 H 0 1 N N N N N N -5.132 13.312 29.499 4.960 0.193 2.914 H7 E5R 27 E5R H8 H8 H 0 1 N N N N N N -5.821 14.872 30.062 3.740 -1.088 3.115 H8 E5R 28 E5R H9 H9 H 0 1 N N N N N N -6.669 13.920 28.797 5.405 -1.510 2.649 H9 E5R 29 E5R H10 H10 H 0 1 N N N N N N -5.760 16.867 28.532 3.467 1.360 1.300 H10 E5R 30 E5R H11 H11 H 0 1 N N N N N N -6.627 15.910 27.283 2.243 0.080 1.475 H11 E5R 31 E5R H12 H12 H 0 1 N N N N N N -10.582 19.504 25.261 -3.243 2.668 0.380 H12 E5R 32 E5R H13 H13 H 0 1 N N N N N N -7.484 19.468 24.623 -0.860 2.086 -1.330 H13 E5R 33 E5R H14 H14 H 0 1 N N N N N N -8.308 19.077 26.171 -0.764 2.467 0.403 H14 E5R 34 E5R H15 H15 H 0 1 N N N N N N -7.431 16.834 26.137 0.471 0.442 0.861 H15 E5R 35 E5R H16 H16 H 0 1 N N N N N N -5.096 18.630 25.386 1.766 2.342 -0.097 H16 E5R 36 E5R H17 H17 H 0 1 N N N N N N -5.953 18.731 26.961 1.502 1.684 -1.730 H17 E5R 37 E5R H18 H18 H 0 1 N N N N N N -3.085 17.894 26.310 3.618 1.138 -2.332 H18 E5R 38 E5R H19 H19 H 0 1 N N N N N N -3.755 18.023 27.971 4.259 1.970 -0.895 H19 E5R 39 E5R H20 H20 H 0 1 N N N N N N -2.566 15.538 26.664 5.908 0.349 -1.776 H20 E5R 40 E5R H21 H21 H 0 1 N N N N N N -1.829 16.531 27.966 4.714 -0.962 -1.613 H21 E5R 41 E5R H22 H22 H 0 1 N N N N N N -12.693 19.433 24.632 -5.701 1.695 1.782 H22 E5R 42 # 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 E5R O C SING N N 1 E5R O3 C15 DOUB N N 2 E5R C C1 DOUB Y N 3 E5R C C14 SING Y N 4 E5R C1 C2 SING Y N 5 E5R C15 C14 SING N N 6 E5R C15 O2 SING N N 7 E5R C14 C4 DOUB Y N 8 E5R C2 O1 SING N N 9 E5R C2 C3 DOUB Y N 10 E5R O2 C6 SING N N 11 E5R C4 C3 SING Y N 12 E5R C4 C5 SING N N 13 E5R C5 C6 SING N N 14 E5R C6 C7 SING N N 15 E5R C7 N SING N N 16 E5R N C8 SING N N 17 E5R N C13 SING N N 18 E5R C8 C9 SING N N 19 E5R C9 C10 SING N N 20 E5R C13 C11 SING N N 21 E5R C11 C10 SING N N 22 E5R C11 C12 SING N N 23 E5R O H2 SING N N 24 E5R C1 H3 SING N N 25 E5R C10 H4 SING N N 26 E5R C10 H5 SING N N 27 E5R C11 H6 SING N N 28 E5R C12 H7 SING N N 29 E5R C12 H8 SING N N 30 E5R C12 H9 SING N N 31 E5R C13 H10 SING N N 32 E5R C13 H11 SING N N 33 E5R C3 H12 SING N N 34 E5R C5 H13 SING N N 35 E5R C5 H14 SING N N 36 E5R C6 H15 SING N N 37 E5R C7 H16 SING N N 38 E5R C7 H17 SING N N 39 E5R C8 H18 SING N N 40 E5R C8 H19 SING N N 41 E5R C9 H20 SING N N 42 E5R C9 H21 SING N N 43 E5R O1 H22 SING N N 44 # 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 E5R InChI InChI 1.03 InChI=1S/C16H21NO4/c1-10-3-2-4-17(8-10)9-13-6-11-5-12(18)7-14(19)15(11)16(20)21-13/h5,7,10,13,18-19H,2-4,6,8-9H2,1H3/t10-,13-/m1/s1 E5R InChIKey InChI 1.03 ZNIKUZOBPQNYBK-ZWNOBZJWSA-N E5R SMILES_CANONICAL CACTVS 3.385 C[C@@H]1CCCN(C1)C[C@H]2Cc3cc(O)cc(O)c3C(=O)O2 E5R SMILES CACTVS 3.385 C[CH]1CCCN(C1)C[CH]2Cc3cc(O)cc(O)c3C(=O)O2 E5R SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 C[C@@H]1CCCN(C1)C[C@H]2Cc3cc(cc(c3C(=O)O2)O)O E5R SMILES "OpenEye OEToolkits" 2.0.7 CC1CCCN(C1)CC2Cc3cc(cc(c3C(=O)O2)O)O # _pdbx_chem_comp_identifier.comp_id E5R _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~{R})-3-[[(3~{R})-3-methylpiperidin-1-yl]methyl]-6,8-bis(oxidanyl)-3,4-dihydroisochromen-1-one # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site E5R 'Create component' 2019-10-21 PDBJ E5R 'Initial release' 2021-05-19 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 E5R N N 12.999 1.737 1 E5R C C 6.463 -0.565 2 E5R O O 6.480 -2.065 3 E5R C1 C 5.103 0.206 4 E5R C10 C 15.598 0.237 5 E5R C11 C 14.298 -0.513 6 E5R C12 C 14.298 -2.013 7 E5R C13 C 12.999 0.237 8 E5R C14 C 7.803 0.237 9 E5R C15 C 9.102 -0.513 10 E5R C2 C 5.103 1.768 11 E5R C3 C 6.463 2.539 12 E5R C4 C 7.803 1.737 13 E5R C5 C 9.102 2.487 14 E5R C6 C 10.402 1.737 15 E5R C7 C 11.700 2.487 16 E5R C8 C 14.298 2.487 17 E5R C9 C 15.598 1.737 18 E5R O1 O 3.807 2.523 19 E5R O2 O 10.402 0.237 20 E5R O3 O 9.102 -2.013 21 # 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 E5R O C SINGLE NONE 1 E5R O3 C15 DOUBLE NONE 2 E5R C C1 DOUBLE NONE 3 E5R C C14 SINGLE NONE 4 E5R C1 C2 SINGLE NONE 5 E5R C15 C14 SINGLE NONE 6 E5R C15 O2 SINGLE NONE 7 E5R C14 C4 DOUBLE NONE 8 E5R C2 O1 SINGLE NONE 9 E5R C2 C3 DOUBLE NONE 10 E5R O2 C6 SINGLE NONE 11 E5R C4 C3 SINGLE NONE 12 E5R C4 C5 SINGLE NONE 13 E5R C5 C6 SINGLE NONE 14 E5R C6 C7 SINGLE BEGINDASH 15 E5R C7 N SINGLE NONE 16 E5R N C8 SINGLE NONE 17 E5R N C13 SINGLE NONE 18 E5R C8 C9 SINGLE NONE 19 E5R C9 C10 SINGLE NONE 20 E5R C13 C11 SINGLE NONE 21 E5R C11 C10 SINGLE NONE 22 E5R C11 C12 SINGLE BEGINWEDGE 23 # 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 E5R MurckoScaffold S1 scaffold 'O=C1O[C@@H](CN2CCCCC2)Cc2ccccc21' InChI=1S/C15H19NO2/c17-15-14-7-3-2-6-12(14)10-13(18-15)11-16-8-4-1-5-9-16/h2-3,6-7,13H,1,4-5,8-11H2/t13-/m1/s1 KMTOMFCKXFFZFZ-CYBMUJFWSA-N E5R phenyl F1 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N E5R Z419084966 F2 fragment NCC(O)Cc1ccccc1 InChI=1S/C9H13NO/c10-7-9(11)6-8-4-2-1-3-5-8/h1-5,9,11H,6-7,10H2 JIIXMZQZEAAIJX-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 E5R N S1 1 E5R C S1 1 E5R C1 S1 1 E5R C10 S1 1 E5R C11 S1 1 E5R C13 S1 1 E5R C14 S1 1 E5R C15 S1 1 E5R C2 S1 1 E5R C3 S1 1 E5R C4 S1 1 E5R C5 S1 1 E5R C6 S1 1 E5R C7 S1 1 E5R C8 S1 1 E5R C9 S1 1 E5R O2 S1 1 E5R O3 S1 1 E5R C F1 1 E5R C1 F1 1 E5R C2 F1 1 E5R C3 F1 1 E5R C4 F1 1 E5R C14 F1 1 E5R N F2 1 E5R C7 F2 1 E5R C6 F2 1 E5R O2 F2 1 E5R C5 F2 1 E5R C4 F2 1 E5R C14 F2 1 E5R C F2 1 E5R C1 F2 1 E5R C2 F2 1 E5R C3 F2 1 # _pdbe_chem_comp_rdkit_properties.comp_id E5R _pdbe_chem_comp_rdkit_properties.exactmw 291.147 _pdbe_chem_comp_rdkit_properties.amw 291.347 _pdbe_chem_comp_rdkit_properties.lipinskiHBA 5 _pdbe_chem_comp_rdkit_properties.lipinskiHBD 2 _pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5 _pdbe_chem_comp_rdkit_properties.NumHBD 2 _pdbe_chem_comp_rdkit_properties.NumHBA 5 _pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 21 _pdbe_chem_comp_rdkit_properties.NumAtoms 42 _pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5 _pdbe_chem_comp_rdkit_properties.NumAmideBonds 0 _pdbe_chem_comp_rdkit_properties.FractionCSP3 0.562 _pdbe_chem_comp_rdkit_properties.NumRings 3 _pdbe_chem_comp_rdkit_properties.NumAromaticRings 1 _pdbe_chem_comp_rdkit_properties.NumAliphaticRings 2 _pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1 _pdbe_chem_comp_rdkit_properties.NumHeterocycles 2 _pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0 _pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1 _pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 2 _pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0 _pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0 _pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 2 _pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0 _pdbe_chem_comp_rdkit_properties.labuteASA 153.370 _pdbe_chem_comp_rdkit_properties.tpsa 70 _pdbe_chem_comp_rdkit_properties.CrippenClogP 0.877 _pdbe_chem_comp_rdkit_properties.CrippenMR 75.765 _pdbe_chem_comp_rdkit_properties.chi0v 10.080 _pdbe_chem_comp_rdkit_properties.chi1v 5.441 _pdbe_chem_comp_rdkit_properties.chi2v 2.372 _pdbe_chem_comp_rdkit_properties.chi3v 2.372 _pdbe_chem_comp_rdkit_properties.chi4v 1.580 _pdbe_chem_comp_rdkit_properties.chi0n 31.080 _pdbe_chem_comp_rdkit_properties.chi1n 15.758 _pdbe_chem_comp_rdkit_properties.chi2n 2.372 _pdbe_chem_comp_rdkit_properties.chi3n 2.372 _pdbe_chem_comp_rdkit_properties.chi4n 1.580 _pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.750 _pdbe_chem_comp_rdkit_properties.kappa1 3.592 _pdbe_chem_comp_rdkit_properties.kappa2 5.561 _pdbe_chem_comp_rdkit_properties.kappa3 2.975 _pdbe_chem_comp_rdkit_properties.Phi 0.951 # 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 E5R UniChem PDBe E5R E5R UniChem PubChem 155908652 # 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 E5R N -1.271 -0.605 -0.181 ETKDGv3 1 E5R C 4.060 0.090 1.440 ETKDGv3 2 E5R O 4.693 -0.515 2.526 ETKDGv3 3 E5R C1 4.280 1.396 1.236 ETKDGv3 4 E5R C10 -3.348 0.907 -1.125 ETKDGv3 5 E5R C11 -2.906 1.187 0.331 ETKDGv3 6 E5R C12 -4.111 1.457 1.241 ETKDGv3 7 E5R C13 -2.042 0.037 0.901 ETKDGv3 8 E5R C14 3.123 -0.652 0.532 ETKDGv3 9 E5R C15 2.929 -2.123 0.593 ETKDGv3 10 E5R C2 3.558 2.128 0.175 ETKDGv3 11 E5R C3 2.671 1.486 -0.590 ETKDGv3 12 E5R C4 2.426 0.038 -0.403 ETKDGv3 13 E5R C5 1.483 -0.671 -1.350 ETKDGv3 14 E5R C6 0.825 -1.893 -0.677 ETKDGv3 15 E5R C7 -0.227 -1.492 0.380 ETKDGv3 16 E5R C8 -2.171 -1.341 -1.107 ETKDGv3 17 E5R C9 -3.494 -0.593 -1.383 ETKDGv3 18 E5R O1 3.790 3.486 -0.026 ETKDGv3 19 E5R O2 1.834 -2.696 -0.062 ETKDGv3 20 E5R O3 3.769 -2.875 1.150 ETKDGv3 21 E5R H2 4.451 -1.433 2.871 ETKDGv3 22 E5R H3 4.959 1.936 1.884 ETKDGv3 23 E5R H4 -2.580 1.310 -1.823 ETKDGv3 24 E5R H5 -4.304 1.424 -1.362 ETKDGv3 25 E5R H6 -2.286 2.112 0.319 ETKDGv3 26 E5R H7 -4.671 2.346 0.880 ETKDGv3 27 E5R H8 -3.768 1.662 2.278 ETKDGv3 28 E5R H9 -4.797 0.583 1.254 ETKDGv3 29 E5R H10 -1.361 0.473 1.666 ETKDGv3 30 E5R H11 -2.676 -0.723 1.414 ETKDGv3 31 E5R H12 2.139 2.027 -1.364 ETKDGv3 32 E5R H13 2.071 -1.017 -2.227 ETKDGv3 33 E5R H14 0.707 0.029 -1.727 ETKDGv3 34 E5R H15 0.334 -2.511 -1.458 ETKDGv3 35 E5R H16 -0.682 -2.409 0.819 ETKDGv3 36 E5R H17 0.308 -0.976 1.208 ETKDGv3 37 E5R H18 -1.649 -1.469 -2.079 ETKDGv3 38 E5R H19 -2.415 -2.354 -0.715 ETKDGv3 39 E5R H20 -3.811 -0.763 -2.435 ETKDGv3 40 E5R H21 -4.294 -0.997 -0.724 ETKDGv3 41 E5R H22 4.456 3.995 0.543 ETKDGv3 42 #