data_D9Y # _chem_comp.id D9Y _chem_comp.name "1-cyclohexyl-3-[(1S,2S,3S,4R,5R)-3-hydroxy-4-(piperidin-1-yl)-6,8-dioxabicyclo[3.2.1]octan-2-yl]urea" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C18 H31 N3 O4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-10-23 _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 353.456 _chem_comp.one_letter_code ? _chem_comp.three_letter_code D9Y _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 5QBP _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.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 D9Y O3 O1 O 0 1 N N N -4.217 3.386 8.166 3.405 1.743 1.603 O3 D9Y 1 D9Y C4 C1 C 0 1 N N N -3.421 7.579 6.459 -4.448 -0.882 0.808 C4 D9Y 2 D9Y C5 C2 C 0 1 N N N -4.072 8.902 6.077 -5.915 -0.450 0.756 C5 D9Y 3 D9Y C6 C3 C 0 1 N N N -2.212 5.663 8.677 -1.184 0.788 0.552 C6 D9Y 4 D9Y N1 N1 N 0 1 N N N -1.605 4.474 8.778 0.108 0.407 0.598 N1 D9Y 5 D9Y C7 C4 C 0 1 N N S -2.225 3.446 9.591 1.163 1.411 0.756 C7 D9Y 6 D9Y C8 C5 C 0 1 N N S -1.308 2.449 10.285 1.474 2.052 -0.607 C8 D9Y 7 D9Y N2 N2 N 0 1 N N N -4.753 0.616 8.584 2.097 -1.328 0.011 N2 D9Y 8 D9Y C9 C6 C 0 1 N N N -1.794 2.083 11.681 2.822 2.800 -0.478 C9 D9Y 9 D9Y C10 C7 C 0 1 N N R -2.636 0.671 10.115 3.128 0.597 -1.112 C10 D9Y 10 D9Y C11 C8 C 0 1 N N R -3.836 1.459 9.500 3.003 -0.188 0.203 C11 D9Y 11 D9Y C12 C9 C 0 1 N N S -3.163 2.603 8.726 2.438 0.742 1.282 C12 D9Y 12 D9Y C13 C10 C 0 1 N N N -5.026 -0.750 9.153 2.090 -2.199 1.193 C13 D9Y 13 D9Y C14 C11 C 0 1 N N N -6.235 -1.368 8.491 1.031 -3.291 1.017 C14 D9Y 14 D9Y C15 C12 C 0 1 N N N -6.244 -1.109 6.998 1.349 -4.106 -0.239 C15 D9Y 15 D9Y O O2 O 0 1 N N N -3.065 6.034 9.484 -1.474 1.965 0.642 O D9Y 16 D9Y N N3 N 0 1 N N N -1.672 6.496 7.772 -2.154 -0.137 0.407 N D9Y 17 D9Y C3 C13 C 0 1 N N N -2.295 7.784 7.465 -3.558 0.277 0.357 C3 D9Y 18 D9Y C2 C14 C 0 1 N N N -1.276 8.773 6.936 -3.923 0.672 -1.076 C2 D9Y 19 D9Y C1 C15 C 0 1 N N N -1.940 10.093 6.549 -5.390 1.104 -1.128 C1 D9Y 20 D9Y C C16 C 0 1 N N N -3.050 9.876 5.541 -6.280 -0.055 -0.677 C D9Y 21 D9Y O1 O3 O 0 1 N N N -2.567 0.882 11.503 3.821 1.829 -0.837 O1 D9Y 22 D9Y O2 O4 O 0 1 N N N -1.424 1.179 9.605 1.796 0.975 -1.522 O2 D9Y 23 D9Y C17 C17 C 0 1 N N N -4.319 0.495 7.152 2.446 -2.080 -1.201 C17 D9Y 24 D9Y C16 C18 C 0 1 N N N -4.860 -0.763 6.498 1.398 -3.168 -1.448 C16 D9Y 25 D9Y H1 H1 H 0 1 N N N -3.847 4.110 7.675 3.114 2.368 2.281 H1 D9Y 26 D9Y H2 H2 H 0 1 N N N -4.182 6.920 6.903 -4.188 -1.164 1.829 H2 D9Y 27 D9Y H3 H3 H 0 1 N N N -3.011 7.107 5.554 -4.297 -1.735 0.147 H3 D9Y 28 D9Y H4 H4 H 0 1 N N N -4.551 9.337 6.967 -6.549 -1.276 1.078 H4 D9Y 29 D9Y H5 H5 H 0 1 N N N -4.833 8.718 5.304 -6.066 0.403 1.418 H5 D9Y 30 D9Y H6 H6 H 0 1 N N N -0.743 4.299 8.303 0.340 -0.532 0.527 H6 D9Y 31 D9Y H7 H7 H 0 1 N N N -2.836 3.933 10.366 0.835 2.180 1.456 H7 D9Y 32 D9Y H8 H8 H 0 1 N N N -0.271 2.816 10.310 0.668 2.695 -0.961 H8 D9Y 33 D9Y H10 H10 H 0 1 N N N -0.941 1.898 12.351 2.852 3.646 -1.165 H10 D9Y 34 D9Y H11 H11 H 0 1 N N N -2.419 2.887 12.096 2.971 3.139 0.547 H11 D9Y 35 D9Y H12 H12 H 0 1 N N N -2.750 -0.397 9.879 3.634 0.021 -1.887 H12 D9Y 36 D9Y H13 H13 H 0 1 N N N -4.438 1.882 10.317 3.985 -0.549 0.507 H13 D9Y 37 D9Y H14 H14 H 0 1 N N N -2.569 2.158 7.914 2.203 0.163 2.175 H14 D9Y 38 D9Y H15 H15 H 0 1 N N N -5.211 -0.661 10.234 3.070 -2.660 1.310 H15 D9Y 39 D9Y H16 H16 H 0 1 N N N -4.151 -1.394 8.982 1.858 -1.608 2.079 H16 D9Y 40 D9Y H17 H17 H 0 1 N N N -7.145 -0.937 8.934 1.037 -3.947 1.888 H17 D9Y 41 D9Y H18 H18 H 0 1 N N N -6.222 -2.454 8.665 0.048 -2.831 0.914 H18 D9Y 42 D9Y H19 H19 H 0 1 N N N -6.924 -0.271 6.783 2.315 -4.597 -0.120 H19 D9Y 43 D9Y H20 H20 H 0 1 N N N -6.598 -2.012 6.479 0.574 -4.858 -0.391 H20 D9Y 44 D9Y H21 H21 H 0 1 N N N -0.831 6.232 7.300 -1.922 -1.076 0.335 H21 D9Y 45 D9Y H22 H22 H 0 1 N N N -2.730 8.198 8.386 -3.710 1.130 1.018 H22 D9Y 46 D9Y H23 H23 H 0 1 N N N -0.786 8.344 6.050 -3.289 1.498 -1.398 H23 D9Y 47 D9Y H24 H24 H 0 1 N N N -0.523 8.964 7.715 -3.772 -0.181 -1.737 H24 D9Y 48 D9Y H25 H25 H 0 1 N N N -1.183 10.760 6.110 -5.541 1.957 -0.466 H25 D9Y 49 D9Y H26 H26 H 0 1 N N N -2.362 10.560 7.451 -5.649 1.386 -2.148 H26 D9Y 50 D9Y H27 H27 H 0 1 N N N -2.621 9.474 4.611 -6.128 -0.908 -1.338 H27 D9Y 51 D9Y H28 H28 H 0 1 N N N -3.542 10.838 5.332 -7.324 0.252 -0.714 H28 D9Y 52 D9Y H29 H29 H 0 1 N N N -3.220 0.470 7.115 2.473 -1.402 -2.054 H29 D9Y 53 D9Y H30 H30 H 0 1 N N N -4.685 1.370 6.595 3.425 -2.542 -1.073 H30 D9Y 54 D9Y H31 H31 H 0 1 N N N -4.182 -1.600 6.722 1.666 -3.736 -2.339 H31 D9Y 55 D9Y H32 H32 H 0 1 N N N -4.904 -0.607 5.410 0.421 -2.706 -1.590 H32 D9Y 56 # # 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 D9Y C C5 SING N N 1 D9Y C C1 SING N N 2 D9Y C5 C4 SING N N 3 D9Y C4 C3 SING N N 4 D9Y C16 C15 SING N N 5 D9Y C16 C17 SING N N 6 D9Y C1 C2 SING N N 7 D9Y C2 C3 SING N N 8 D9Y C15 C14 SING N N 9 D9Y C17 N2 SING N N 10 D9Y C3 N SING N N 11 D9Y N C6 SING N N 12 D9Y O3 C12 SING N N 13 D9Y C14 C13 SING N N 14 D9Y N2 C13 SING N N 15 D9Y N2 C11 SING N N 16 D9Y C6 N1 SING N N 17 D9Y C6 O DOUB N N 18 D9Y C12 C11 SING N N 19 D9Y C12 C7 SING N N 20 D9Y N1 C7 SING N N 21 D9Y C11 C10 SING N N 22 D9Y C7 C8 SING N N 23 D9Y O2 C10 SING N N 24 D9Y O2 C8 SING N N 25 D9Y C10 O1 SING N N 26 D9Y C8 C9 SING N N 27 D9Y O1 C9 SING N N 28 D9Y O3 H1 SING N N 29 D9Y C4 H2 SING N N 30 D9Y C4 H3 SING N N 31 D9Y C5 H4 SING N N 32 D9Y C5 H5 SING N N 33 D9Y N1 H6 SING N N 34 D9Y C7 H7 SING N N 35 D9Y C8 H8 SING N N 36 D9Y C9 H10 SING N N 37 D9Y C9 H11 SING N N 38 D9Y C10 H12 SING N N 39 D9Y C11 H13 SING N N 40 D9Y C12 H14 SING N N 41 D9Y C13 H15 SING N N 42 D9Y C13 H16 SING N N 43 D9Y C14 H17 SING N N 44 D9Y C14 H18 SING N N 45 D9Y C15 H19 SING N N 46 D9Y C15 H20 SING N N 47 D9Y N H21 SING N N 48 D9Y C3 H22 SING N N 49 D9Y C2 H23 SING N N 50 D9Y C2 H24 SING N N 51 D9Y C1 H25 SING N N 52 D9Y C1 H26 SING N N 53 D9Y C H27 SING N N 54 D9Y C H28 SING N N 55 D9Y C17 H29 SING N N 56 D9Y C17 H30 SING N N 57 D9Y C16 H31 SING N N 58 D9Y C16 H32 SING N N 59 # # 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 D9Y SMILES ACDLabs 12.01 "OC3C(NC(=O)NC1CCCCC1)C4COC(C3N2CCCCC2)O4" D9Y InChI InChI 1.03 "InChI=1S/C18H31N3O4/c22-16-14(20-18(23)19-12-7-3-1-4-8-12)13-11-24-17(25-13)15(16)21-9-5-2-6-10-21/h12-17,22H,1-11H2,(H2,19,20,23)/t13-,14-,15-,16+,17-/m1/s1" D9Y InChIKey InChI 1.03 NLUHIVDPQQPQPD-OVYGPGRDSA-N D9Y SMILES_CANONICAL CACTVS 3.385 "O[C@H]1[C@H](NC(=O)NC2CCCCC2)[C@H]3CO[C@H](O3)[C@@H]1N4CCCCC4" D9Y SMILES CACTVS 3.385 "O[CH]1[CH](NC(=O)NC2CCCCC2)[CH]3CO[CH](O3)[CH]1N4CCCCC4" D9Y SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "C1CCC(CC1)NC(=O)N[C@@H]2[C@H]3CO[C@H](O3)[C@@H]([C@H]2O)N4CCCCC4" D9Y SMILES "OpenEye OEToolkits" 2.0.6 "C1CCC(CC1)NC(=O)NC2C3COC(O3)C(C2O)N4CCCCC4" # # 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 D9Y "SYSTEMATIC NAME" ACDLabs 12.01 "1-cyclohexyl-3-[(1S,2S,3S,4R,5R)-3-hydroxy-4-(piperidin-1-yl)-6,8-dioxabicyclo[3.2.1]octan-2-yl]urea (non-preferred name)" D9Y "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "1-cyclohexyl-3-[(1~{S},2~{S},3~{S},4~{R},5~{R})-3-oxidanyl-4-piperidin-1-yl-6,8-dioxabicyclo[3.2.1]octan-2-yl]urea" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site D9Y "Create component" 2017-10-23 RCSB D9Y "Initial release" 2020-04-22 RCSB ##