data_JPW # _chem_comp.id JPW _chem_comp.name "(4-azanylcyclohexyl)methyl ~{N}-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]carbamate" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C13 H21 N3 O4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2019-03-15 _chem_comp.pdbx_modified_date 2019-08-02 _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 283.324 _chem_comp.one_letter_code ? _chem_comp.three_letter_code JPW _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 6R1W _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 JPW C4 C1 C 0 1 N N N N N N 25.890 -13.799 6.380 -3.220 0.574 0.071 C4 JPW 1 JPW C5 C2 C 0 1 N N N N N N 25.416 -14.168 7.776 -4.338 1.138 -0.810 C5 JPW 2 JPW C6 C3 C 0 1 N N N N N N 26.283 -13.485 8.823 -5.695 0.813 -0.183 C6 JPW 3 JPW C11 C4 C 0 1 N N N N N N 24.440 -14.626 -2.184 5.557 -0.392 0.075 C11 JPW 4 JPW C7 C5 C 0 1 N N N N N N 27.728 -13.339 8.357 -5.853 -0.705 -0.068 C7 JPW 5 JPW C8 C6 C 0 1 N N N N N N 28.142 -14.418 7.367 -4.736 -1.269 0.813 C8 JPW 6 JPW C9 C7 C 0 1 N N N N N N 27.258 -14.420 6.127 -3.379 -0.943 0.186 C9 JPW 7 JPW C10 C8 C 0 1 N N N N N N 23.714 -14.640 0.170 3.317 -0.592 -0.615 C10 JPW 8 JPW C12 C9 C 0 1 N N N N N N 25.786 -14.095 -1.803 5.241 0.754 0.999 C12 JPW 9 JPW C13 C10 C 0 1 N N N N N N 26.178 -14.430 -0.358 3.796 0.622 1.489 C13 JPW 10 JPW N1 N1 N 0 1 N N N N N N 25.313 -14.566 1.990 1.495 0.309 0.711 N1 JPW 11 JPW N2 N2 N 0 1 N N N N N N 27.992 -11.969 7.804 -7.156 -1.017 0.535 N2 JPW 12 JPW C3 C11 C 0 1 N N N N N N 24.902 -14.171 5.302 -1.863 0.900 -0.557 C3 JPW 13 JPW N3 N3 N 0 1 N N N N N N 23.544 -14.856 -1.168 4.601 -0.978 -0.661 N3 JPW 14 JPW C1 C12 C 0 1 N N S N N N 25.050 -14.112 0.625 2.872 0.543 0.269 C1 JPW 15 JPW C2 C13 C 0 1 N N N N N N 25.356 -13.702 3.004 0.463 0.684 -0.070 C2 JPW 16 JPW O1 O1 O 0 1 N N N N N N 25.659 -14.404 4.098 -0.802 0.469 0.336 O1 JPW 17 JPW O2 O2 O 0 1 N N N N N N 25.207 -12.494 2.907 0.675 1.217 -1.142 O2 JPW 18 JPW O3 O3 O 0 1 N N N N N N 22.794 -14.874 0.928 2.498 -1.169 -1.298 O3 JPW 19 JPW O4 O4 O 0 1 N N N N N N 24.081 -14.827 -3.329 6.699 -0.791 -0.008 O4 JPW 20 JPW H1 H1 H 0 1 N N N N N N 26.015 -12.706 6.353 -3.279 1.022 1.063 H1 JPW 21 JPW H2 H2 H 0 1 N N N N N N 24.372 -13.846 7.902 -4.225 2.219 -0.892 H2 JPW 22 JPW H3 H3 H 0 1 N N N N N N 25.481 -15.258 7.905 -4.279 0.691 -1.802 H3 JPW 23 JPW H4 H4 H 0 1 N N N N N N 25.872 -12.485 9.028 -5.753 1.260 0.810 H4 JPW 24 JPW H5 H5 H 0 1 N N N N N N 26.266 -14.084 9.745 -6.490 1.214 -0.810 H5 JPW 25 JPW H6 H6 H 0 1 N N N N N N 28.364 -13.459 9.246 -5.794 -1.152 -1.060 H6 JPW 26 JPW H7 H7 H 0 1 N N N N N N 28.067 -15.399 7.859 -4.794 -0.821 1.805 H7 JPW 27 JPW H8 H8 H 0 1 N N N N N N 29.183 -14.239 7.061 -4.848 -2.350 0.895 H8 JPW 28 JPW H9 H9 H 0 1 N N N N N N 27.117 -15.460 5.797 -3.320 -1.391 -0.807 H9 JPW 29 JPW H10 H10 H 0 1 N N N N N N 27.763 -13.849 5.334 -2.583 -1.345 0.813 H10 JPW 30 JPW H11 H11 H 0 1 N N N N N N 26.538 -14.529 -2.479 5.919 0.732 1.852 H11 JPW 31 JPW H12 H12 H 0 1 N N N N N N 25.776 -13.001 -1.919 5.360 1.697 0.463 H12 JPW 32 JPW H13 H13 H 0 1 N N N N N N 26.415 -15.502 -0.293 3.693 -0.284 2.085 H13 JPW 33 JPW H14 H14 H 0 1 N N N N N N 27.066 -13.841 -0.084 3.532 1.492 2.091 H14 JPW 34 JPW H15 H15 H 0 1 N N N N N N 25.463 -15.539 2.165 1.326 -0.116 1.566 H15 JPW 35 JPW H16 H16 H 0 1 N N N N N N 27.712 -11.280 8.472 -7.284 -2.014 0.621 H16 JPW 36 JPW H17 H17 H 0 1 N N N N N N 28.968 -11.870 7.612 -7.260 -0.560 1.428 H17 JPW 37 JPW H19 H19 H 0 1 N N N N N N 24.187 -13.350 5.146 -1.770 0.379 -1.510 H19 JPW 38 JPW H20 H20 H 0 1 N N N N N N 24.357 -15.083 5.588 -1.787 1.974 -0.720 H20 JPW 39 JPW H21 H21 H 0 1 N N N N N N 22.657 -15.228 -1.442 4.847 -1.708 -1.250 H21 JPW 40 JPW H22 H22 H 0 1 N N N N N N 24.963 -13.016 0.657 2.923 1.479 -0.288 H22 JPW 41 # 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 JPW O4 C11 DOUB N N 1 JPW C11 C12 SING N N 2 JPW C11 N3 SING N N 3 JPW C12 C13 SING N N 4 JPW N3 C10 SING N N 5 JPW C13 C1 SING N N 6 JPW C10 C1 SING N N 7 JPW C10 O3 DOUB N N 8 JPW C1 N1 SING N N 9 JPW N1 C2 SING N N 10 JPW O2 C2 DOUB N N 11 JPW C2 O1 SING N N 12 JPW O1 C3 SING N N 13 JPW C3 C4 SING N N 14 JPW C9 C4 SING N N 15 JPW C9 C8 SING N N 16 JPW C4 C5 SING N N 17 JPW C8 C7 SING N N 18 JPW C5 C6 SING N N 19 JPW N2 C7 SING N N 20 JPW C7 C6 SING N N 21 JPW C4 H1 SING N N 22 JPW C5 H2 SING N N 23 JPW C5 H3 SING N N 24 JPW C6 H4 SING N N 25 JPW C6 H5 SING N N 26 JPW C7 H6 SING N N 27 JPW C8 H7 SING N N 28 JPW C8 H8 SING N N 29 JPW C9 H9 SING N N 30 JPW C9 H10 SING N N 31 JPW C12 H11 SING N N 32 JPW C12 H12 SING N N 33 JPW C13 H13 SING N N 34 JPW C13 H14 SING N N 35 JPW N1 H15 SING N N 36 JPW N2 H16 SING N N 37 JPW N2 H17 SING N N 38 JPW C3 H19 SING N N 39 JPW C3 H20 SING N N 40 JPW N3 H21 SING N N 41 JPW C1 H22 SING N N 42 # 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 JPW InChI InChI 1.03 InChI=1S/C13H21N3O4/c14-9-3-1-8(2-4-9)7-20-13(19)15-10-5-6-11(17)16-12(10)18/h8-10H,1-7,14H2,(H,15,19)(H,16,17,18)/t8-,9-,10-/m0/s1 JPW InChIKey InChI 1.03 HEPIPPZEYDEJHT-GUBZILKMSA-N JPW SMILES_CANONICAL CACTVS 3.385 N[C@H]1CC[C@@H](CC1)COC(=O)N[C@H]2CCC(=O)NC2=O JPW SMILES CACTVS 3.385 N[CH]1CC[CH](CC1)COC(=O)N[CH]2CCC(=O)NC2=O JPW SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 C1CC(=O)NC(=O)[C@H]1NC(=O)OCC2CCC(CC2)N JPW SMILES "OpenEye OEToolkits" 2.0.7 C1CC(CCC1COC(=O)NC2CCC(=O)NC2=O)N # _pdbx_chem_comp_identifier.comp_id JPW _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 "(4-azanylcyclohexyl)methyl ~{N}-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]carbamate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site JPW 'Create component' 2019-03-15 RCSB JPW 'Initial release' 2019-08-07 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 JPW C4 C -3.506 -0.382 1 JPW C5 C -3.504 -1.882 2 JPW C6 C -4.801 -2.635 3 JPW C11 C 5.582 1.886 4 JPW C7 C -6.102 -1.887 5 JPW C8 C -6.105 -0.387 6 JPW C9 C -4.807 0.365 7 JPW C10 C 4.288 -0.367 8 JPW C12 C 4.282 2.634 9 JPW C13 C 2.984 1.881 10 JPW N1 N 1.690 -0.372 11 JPW N2 N -7.399 -2.640 12 JPW C3 C -2.209 0.371 13 JPW N3 N 5.585 0.386 14 JPW C1 C 2.987 0.381 15 JPW C2 C 0.389 0.376 16 JPW O1 O -0.909 -0.377 17 JPW O2 O 0.386 1.876 18 JPW O3 O 4.291 -1.866 19 JPW O4 O 6.880 2.639 20 # 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 JPW O4 C11 DOUBLE NONE 1 JPW C11 C12 SINGLE NONE 2 JPW C11 N3 SINGLE NONE 3 JPW C12 C13 SINGLE NONE 4 JPW N3 C10 SINGLE NONE 5 JPW C13 C1 SINGLE NONE 6 JPW C10 C1 SINGLE NONE 7 JPW C10 O3 DOUBLE NONE 8 JPW C1 N1 SINGLE BEGINWEDGE 9 JPW N1 C2 SINGLE NONE 10 JPW O2 C2 DOUBLE NONE 11 JPW C2 O1 SINGLE NONE 12 JPW O1 C3 SINGLE NONE 13 JPW C4 C3 SINGLE BEGINWEDGE 14 JPW C9 C4 SINGLE NONE 15 JPW C9 C8 SINGLE NONE 16 JPW C4 C5 SINGLE NONE 17 JPW C8 C7 SINGLE NONE 18 JPW C5 C6 SINGLE NONE 19 JPW C7 N2 SINGLE BEGINDASH 20 JPW C7 C6 SINGLE NONE 21 # 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 JPW MurckoScaffold S1 scaffold 'O=C1CC[C@H](NC(=O)OCC2CCCCC2)C(=O)N1' InChI=1S/C13H20N2O4/c16-11-7-6-10(12(17)15-11)14-13(18)19-8-9-4-2-1-3-5-9/h9-10H,1-8H2,(H,14,18)(H,15,16,17)/t10-/m0/s1 PKZQZULJQGYYFK-JTQLQIEISA-N JPW amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N JPW cyclohexane F2 fragment C1CCCCC1 InChI=1S/C6H12/c1-2-4-6-5-3-1/h1-6H2 XDTMQSROBMDMFD-UHFFFAOYSA-N JPW peptide F3 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-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 JPW C4 S1 1 JPW C5 S1 1 JPW C6 S1 1 JPW C11 S1 1 JPW C7 S1 1 JPW C8 S1 1 JPW C9 S1 1 JPW C10 S1 1 JPW C12 S1 1 JPW C13 S1 1 JPW N1 S1 1 JPW C3 S1 1 JPW N3 S1 1 JPW C1 S1 1 JPW C2 S1 1 JPW O1 S1 1 JPW O2 S1 1 JPW O3 S1 1 JPW O4 S1 1 JPW N3 F1 1 JPW C11 F1 1 JPW O4 F1 1 JPW C12 F1 1 JPW N3 F1 2 JPW C10 F1 2 JPW O3 F1 2 JPW C1 F1 2 JPW C4 F2 1 JPW C9 F2 1 JPW C8 F2 1 JPW C7 F2 1 JPW C6 F2 1 JPW C5 F2 1 JPW O3 F3 1 JPW C10 F3 1 JPW C1 F3 1 JPW N1 F3 1 # _pdbe_chem_comp_rdkit_properties.comp_id JPW _pdbe_chem_comp_rdkit_properties.exactmw 283.153 _pdbe_chem_comp_rdkit_properties.amw 283.328 _pdbe_chem_comp_rdkit_properties.lipinskiHBA 7 _pdbe_chem_comp_rdkit_properties.lipinskiHBD 4 _pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4 _pdbe_chem_comp_rdkit_properties.NumHBD 3 _pdbe_chem_comp_rdkit_properties.NumHBA 5 _pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 20 _pdbe_chem_comp_rdkit_properties.NumAtoms 41 _pdbe_chem_comp_rdkit_properties.NumHeteroatoms 7 _pdbe_chem_comp_rdkit_properties.NumAmideBonds 3 _pdbe_chem_comp_rdkit_properties.FractionCSP3 0.769 _pdbe_chem_comp_rdkit_properties.NumRings 2 _pdbe_chem_comp_rdkit_properties.NumAromaticRings 0 _pdbe_chem_comp_rdkit_properties.NumAliphaticRings 2 _pdbe_chem_comp_rdkit_properties.NumSaturatedRings 2 _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 1 _pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0 _pdbe_chem_comp_rdkit_properties.labuteASA 146.881 _pdbe_chem_comp_rdkit_properties.tpsa 110.520 _pdbe_chem_comp_rdkit_properties.CrippenClogP 0.035 _pdbe_chem_comp_rdkit_properties.CrippenMR 70.589 _pdbe_chem_comp_rdkit_properties.chi0v 9.475 _pdbe_chem_comp_rdkit_properties.chi1v 4.889 _pdbe_chem_comp_rdkit_properties.chi2v 1.749 _pdbe_chem_comp_rdkit_properties.chi3v 1.749 _pdbe_chem_comp_rdkit_properties.chi4v 0.981 _pdbe_chem_comp_rdkit_properties.chi0n 30.475 _pdbe_chem_comp_rdkit_properties.chi1n 15.178 _pdbe_chem_comp_rdkit_properties.chi2n 1.749 _pdbe_chem_comp_rdkit_properties.chi3n 1.749 _pdbe_chem_comp_rdkit_properties.chi4n 0.981 _pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.630 _pdbe_chem_comp_rdkit_properties.kappa1 3.401 _pdbe_chem_comp_rdkit_properties.kappa2 6.694 _pdbe_chem_comp_rdkit_properties.kappa3 4.193 _pdbe_chem_comp_rdkit_properties.Phi 1.138 # _pdbe_chem_comp_external_mappings.comp_id JPW _pdbe_chem_comp_external_mappings.source UniChem _pdbe_chem_comp_external_mappings.resource PDBe _pdbe_chem_comp_external_mappings.resource_id JPW # 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 JPW C4 -1.933 0.628 -0.639 ETKDGv3 1 JPW C5 -3.333 1.278 -0.811 ETKDGv3 2 JPW C6 -4.434 0.230 -1.020 ETKDGv3 3 JPW C11 5.810 0.045 1.564 ETKDGv3 4 JPW C7 -4.542 -0.745 0.180 ETKDGv3 5 JPW C8 -3.198 -0.930 0.932 ETKDGv3 6 JPW C9 -2.006 -0.793 -0.020 ETKDGv3 7 JPW C10 4.851 -0.088 -0.733 ETKDGv3 8 JPW C12 4.544 0.664 2.080 ETKDGv3 9 JPW C13 3.343 0.201 1.250 ETKDGv3 10 JPW N1 2.422 -0.061 -1.008 ETKDGv3 11 JPW N2 -5.595 -0.303 1.097 ETKDGv3 12 JPW C3 -1.168 0.601 -1.977 ETKDGv3 13 JPW N3 5.939 -0.286 0.178 ETKDGv3 14 JPW C1 3.545 0.494 -0.247 ETKDGv3 15 JPW C2 1.196 0.654 -1.199 ETKDGv3 16 JPW O1 0.122 0.010 -1.822 ETKDGv3 17 JPW O2 1.088 1.849 -0.810 ETKDGv3 18 JPW O3 5.013 -0.337 -1.958 ETKDGv3 19 JPW O4 6.781 -0.139 2.345 ETKDGv3 20 JPW H1 -1.362 1.274 0.064 ETKDGv3 21 JPW H2 -3.340 1.995 -1.660 ETKDGv3 22 JPW H3 -3.577 1.866 0.101 ETKDGv3 23 JPW H4 -5.406 0.741 -1.193 ETKDGv3 24 JPW H5 -4.203 -0.346 -1.943 ETKDGv3 25 JPW H6 -4.843 -1.735 -0.230 ETKDGv3 26 JPW H7 -3.092 -0.172 1.740 ETKDGv3 27 JPW H8 -3.177 -1.933 1.410 ETKDGv3 28 JPW H9 -2.104 -1.564 -0.817 ETKDGv3 29 JPW H10 -1.066 -1.005 0.535 ETKDGv3 30 JPW H11 4.634 1.770 2.027 ETKDGv3 31 JPW H12 4.388 0.374 3.141 ETKDGv3 32 JPW H13 2.431 0.725 1.610 ETKDGv3 33 JPW H14 3.191 -0.891 1.402 ETKDGv3 34 JPW H15 2.446 -1.068 -1.287 ETKDGv3 35 JPW H16 -5.682 -1.003 1.870 ETKDGv3 36 JPW H17 -5.318 0.609 1.530 ETKDGv3 37 JPW H19 -1.061 1.630 -2.385 ETKDGv3 38 JPW H20 -1.741 0.005 -2.719 ETKDGv3 39 JPW H21 6.839 -0.682 -0.175 ETKDGv3 40 JPW H22 3.597 1.594 -0.400 ETKDGv3 41 #