data_YT1 # _chem_comp.id YT1 _chem_comp.name PB28 _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C24 H38 N2 O" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "1-cyclohexyl-4-{3-[(1R)-5-methoxy-1,2,3,4-tetrahydronaphthalen-1-yl]propyl}piperazine" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2021-03-31 _chem_comp.pdbx_modified_date 2021-12-10 _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 370.571 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YT1 _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 7M93 _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 YT1 C4 C1 C 0 1 N N N -5.593 -30.120 33.564 3.850 -2.474 0.734 C4 YT1 1 YT1 C14 C2 C 0 1 N N N -0.444 -18.507 29.406 -8.433 0.550 0.167 C14 YT1 2 YT1 C5 C3 C 0 1 N N N -5.168 -29.087 32.532 2.690 -1.634 0.189 C5 YT1 3 YT1 C6 C4 C 0 1 N N R -3.734 -29.330 32.063 2.872 -0.194 0.666 C6 YT1 4 YT1 C11 C5 C 0 1 N N N -0.870 -23.173 31.004 -4.283 1.555 0.367 C11 YT1 5 YT1 C7 C6 C 0 1 N N N -3.434 -28.385 30.888 1.853 0.703 -0.039 C7 YT1 6 YT1 C8 C7 C 0 1 N N N -3.272 -26.921 31.277 0.440 0.309 0.394 C8 YT1 7 YT1 C9 C8 C 0 1 N N N -3.239 -25.949 30.111 -0.571 1.286 -0.210 C9 YT1 8 YT1 C10 C9 C 0 1 N N N -1.336 -24.559 30.611 -2.899 1.950 -0.153 C10 YT1 9 YT1 C12 C10 C 0 1 N N N -0.731 -20.858 30.212 -6.026 -0.119 0.208 C12 YT1 10 YT1 C13 C11 C 0 1 N N N -1.248 -19.794 29.253 -7.019 0.944 -0.266 C13 YT1 11 YT1 N1 N1 N 0 1 N N N -1.299 -22.199 29.994 -4.669 0.259 -0.209 N1 YT1 12 YT1 C3 C12 C 0 1 N N N -5.601 -31.494 32.945 5.129 -2.056 0.011 C3 YT1 13 YT1 N N2 N 0 1 N N N -2.797 -24.603 30.495 -1.928 0.908 0.207 N YT1 14 YT1 C C13 C 0 1 N N N -4.680 -35.420 32.062 8.863 -0.291 -0.770 C YT1 15 YT1 O O1 O 0 1 N N N -4.941 -34.045 32.332 7.592 -0.885 -0.501 O YT1 16 YT1 C1 C14 C 0 1 Y N N -4.062 -33.127 31.832 6.566 -0.043 -0.212 C1 YT1 17 YT1 C15 C15 C 0 1 N N N -0.476 -18.008 30.839 -8.798 -0.802 -0.450 C15 YT1 18 YT1 C16 C16 C 0 1 N N N 0.019 -19.077 31.797 -7.805 -1.864 0.024 C16 YT1 19 YT1 C17 C17 C 0 1 N N N -0.788 -20.362 31.650 -6.391 -1.470 -0.410 C17 YT1 20 YT1 C18 C18 C 0 1 N N N -2.764 -22.215 29.917 -3.698 -0.784 0.151 C18 YT1 21 YT1 C19 C19 C 0 1 N N N -3.240 -23.600 29.517 -2.313 -0.388 -0.369 C19 YT1 22 YT1 C2 C20 C 0 1 Y N N -4.353 -31.794 32.145 5.300 -0.561 0.060 C2 YT1 23 YT1 C20 C21 C 0 1 Y N N -3.493 -30.779 31.692 4.262 0.295 0.355 C20 YT1 24 YT1 C21 C22 C 0 1 Y N N -2.383 -31.122 30.928 4.485 1.666 0.375 C21 YT1 25 YT1 C22 C23 C 0 1 Y N N -2.115 -32.444 30.623 5.736 2.181 0.105 C22 YT1 26 YT1 C23 C24 C 0 1 Y N N -2.948 -33.453 31.074 6.781 1.326 -0.189 C23 YT1 27 YT1 H1 H1 H 0 1 N N N -4.887 -30.104 34.407 3.960 -2.299 1.805 H1 YT1 28 YT1 H2 H2 H 0 1 N N N -6.603 -29.878 33.927 3.655 -3.531 0.553 H2 YT1 29 YT1 H3 H3 H 0 1 N N N 0.600 -18.699 29.116 -8.472 0.475 1.254 H3 YT1 30 YT1 H4 H4 H 0 1 N N N -0.872 -17.736 28.748 -9.141 1.307 -0.170 H4 YT1 31 YT1 H5 H5 H 0 1 N N N -5.234 -28.085 32.980 2.695 -1.663 -0.900 H5 YT1 32 YT1 H6 H6 H 0 1 N N N -5.843 -29.147 31.666 1.744 -2.028 0.562 H6 YT1 33 YT1 H7 H7 H 0 1 N N N -3.056 -29.069 32.889 2.707 -0.149 1.742 H7 YT1 34 YT1 H8 H8 H 0 1 N N N 0.228 -23.164 31.077 -4.254 1.476 1.454 H8 YT1 35 YT1 H9 H9 H 0 1 N N N -1.305 -22.904 31.978 -5.011 2.313 0.076 H9 YT1 36 YT1 H10 H10 H 0 1 N N N -4.262 -28.459 30.168 2.038 1.743 0.229 H10 YT1 37 YT1 H11 H11 H 0 1 N N N -2.501 -28.718 30.409 1.948 0.583 -1.118 H11 YT1 38 YT1 H12 H12 H 0 1 N N N -2.329 -26.818 31.834 0.221 -0.701 0.047 H12 YT1 39 YT1 H13 H13 H 0 1 N N N -4.115 -26.645 31.928 0.371 0.341 1.482 H13 YT1 40 YT1 H14 H14 H 0 1 N N N -4.251 -25.877 29.687 -0.352 2.296 0.138 H14 YT1 41 YT1 H15 H15 H 0 1 N N N -2.549 -26.340 29.349 -0.502 1.254 -1.297 H15 YT1 42 YT1 H16 H16 H 0 1 N N N -1.013 -25.279 31.377 -2.934 2.056 -1.237 H16 YT1 43 YT1 H17 H17 H 0 1 N N N -0.889 -24.829 29.643 -2.599 2.898 0.295 H17 YT1 44 YT1 H18 H18 H 0 1 N N N 0.341 -20.951 29.984 -6.065 -0.194 1.294 H18 YT1 45 YT1 H19 H19 H 0 1 N N N -2.306 -19.589 29.474 -6.981 1.018 -1.353 H19 YT1 46 YT1 H20 H20 H 0 1 N N N -1.154 -20.160 28.220 -6.759 1.906 0.174 H20 YT1 47 YT1 H22 H22 H 0 1 N N N -6.472 -31.572 32.277 5.985 -2.532 0.491 H22 YT1 48 YT1 H23 H23 H 0 1 N N N -5.688 -32.239 33.749 5.076 -2.378 -1.029 H23 YT1 49 YT1 H25 H25 H 0 1 N N N -5.464 -36.040 32.522 8.779 0.374 -1.630 H25 YT1 50 YT1 H26 H26 H 0 1 N N N -4.674 -35.585 30.974 9.189 0.279 0.100 H26 YT1 51 YT1 H27 H27 H 0 1 N N N -3.701 -35.696 32.481 9.592 -1.073 -0.986 H27 YT1 52 YT1 H28 H28 H 0 1 N N N 0.168 -17.121 30.926 -9.805 -1.082 -0.141 H28 YT1 53 YT1 H29 H29 H 0 1 N N N -1.509 -17.738 31.103 -8.759 -0.727 -1.537 H29 YT1 54 YT1 H30 H30 H 0 1 N N N 1.076 -19.290 31.582 -7.843 -1.939 1.111 H30 YT1 55 YT1 H31 H31 H 0 1 N N N -0.078 -18.708 32.829 -8.065 -2.827 -0.416 H31 YT1 56 YT1 H32 H32 H 0 1 N N N -1.835 -20.167 31.926 -6.352 -1.395 -1.497 H32 YT1 57 YT1 H33 H33 H 0 1 N N N -0.371 -21.131 32.316 -5.683 -2.227 -0.072 H33 YT1 58 YT1 H34 H34 H 0 1 N N N -3.099 -21.483 29.168 -3.662 -0.889 1.235 H34 YT1 59 YT1 H35 H35 H 0 1 N N N -3.185 -21.953 30.899 -3.999 -1.731 -0.297 H35 YT1 60 YT1 H36 H36 H 0 1 N N N -4.339 -23.604 29.468 -2.341 -0.309 -1.456 H36 YT1 61 YT1 H37 H37 H 0 1 N N N -2.828 -23.852 28.529 -1.585 -1.146 -0.078 H37 YT1 62 YT1 H38 H38 H 0 1 N N N -1.722 -30.347 30.569 3.670 2.337 0.605 H38 YT1 63 YT1 H39 H39 H 0 1 N N N -1.248 -32.691 30.028 5.898 3.248 0.123 H39 YT1 64 YT1 H40 H40 H 0 1 N N N -2.732 -34.485 30.838 7.764 1.723 -0.399 H40 YT1 65 # # 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 YT1 C13 C14 SING N N 1 YT1 C13 C12 SING N N 2 YT1 C14 C15 SING N N 3 YT1 C19 C18 SING N N 4 YT1 C19 N SING N N 5 YT1 C18 N1 SING N N 6 YT1 N1 C12 SING N N 7 YT1 N1 C11 SING N N 8 YT1 C9 N SING N N 9 YT1 C9 C8 SING N N 10 YT1 C12 C17 SING N N 11 YT1 N C10 SING N N 12 YT1 C10 C11 SING N N 13 YT1 C22 C21 DOUB Y N 14 YT1 C22 C23 SING Y N 15 YT1 C15 C16 SING N N 16 YT1 C7 C8 SING N N 17 YT1 C7 C6 SING N N 18 YT1 C21 C20 SING Y N 19 YT1 C23 C1 DOUB Y N 20 YT1 C17 C16 SING N N 21 YT1 C20 C6 SING N N 22 YT1 C20 C2 DOUB Y N 23 YT1 C1 C2 SING Y N 24 YT1 C1 O SING N N 25 YT1 C O SING N N 26 YT1 C6 C5 SING N N 27 YT1 C2 C3 SING N N 28 YT1 C5 C4 SING N N 29 YT1 C3 C4 SING N N 30 YT1 C4 H1 SING N N 31 YT1 C4 H2 SING N N 32 YT1 C14 H3 SING N N 33 YT1 C14 H4 SING N N 34 YT1 C5 H5 SING N N 35 YT1 C5 H6 SING N N 36 YT1 C6 H7 SING N N 37 YT1 C11 H8 SING N N 38 YT1 C11 H9 SING N N 39 YT1 C7 H10 SING N N 40 YT1 C7 H11 SING N N 41 YT1 C8 H12 SING N N 42 YT1 C8 H13 SING N N 43 YT1 C9 H14 SING N N 44 YT1 C9 H15 SING N N 45 YT1 C10 H16 SING N N 46 YT1 C10 H17 SING N N 47 YT1 C12 H18 SING N N 48 YT1 C13 H19 SING N N 49 YT1 C13 H20 SING N N 50 YT1 C3 H22 SING N N 51 YT1 C3 H23 SING N N 52 YT1 C H25 SING N N 53 YT1 C H26 SING N N 54 YT1 C H27 SING N N 55 YT1 C15 H28 SING N N 56 YT1 C15 H29 SING N N 57 YT1 C16 H30 SING N N 58 YT1 C16 H31 SING N N 59 YT1 C17 H32 SING N N 60 YT1 C17 H33 SING N N 61 YT1 C18 H34 SING N N 62 YT1 C18 H35 SING N N 63 YT1 C19 H36 SING N N 64 YT1 C19 H37 SING N N 65 YT1 C21 H38 SING N N 66 YT1 C22 H39 SING N N 67 YT1 C23 H40 SING N N 68 # # 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 YT1 SMILES ACDLabs 12.01 "COc1cccc2c1CCCC2CCCN1CCN(CC1)C1CCCCC1" YT1 InChI InChI 1.03 "InChI=1S/C24H38N2O/c1-27-24-14-6-12-22-20(8-5-13-23(22)24)9-7-15-25-16-18-26(19-17-25)21-10-3-2-4-11-21/h6,12,14,20-21H,2-5,7-11,13,15-19H2,1H3/t20-/m1/s1" YT1 InChIKey InChI 1.03 PHRCDWVPTULQMT-HXUWFJFHSA-N YT1 SMILES_CANONICAL CACTVS 3.385 "COc1cccc2[C@@H](CCCN3CCN(CC3)C4CCCCC4)CCCc12" YT1 SMILES CACTVS 3.385 "COc1cccc2[CH](CCCN3CCN(CC3)C4CCCCC4)CCCc12" YT1 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "COc1cccc2c1CCC[C@@H]2CCCN3CCN(CC3)C4CCCCC4" YT1 SMILES "OpenEye OEToolkits" 2.0.7 "COc1cccc2c1CCCC2CCCN3CCN(CC3)C4CCCCC4" # # 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 YT1 "SYSTEMATIC NAME" ACDLabs 12.01 "1-cyclohexyl-4-{3-[(1R)-5-methoxy-1,2,3,4-tetrahydronaphthalen-1-yl]propyl}piperazine" YT1 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "1-cyclohexyl-4-[3-[(1~{R})-5-methoxy-1,2,3,4-tetrahydronaphthalen-1-yl]propyl]piperazine" # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id YT1 _pdbx_chem_comp_synonyms.name "1-cyclohexyl-4-{3-[(1R)-5-methoxy-1,2,3,4-tetrahydronaphthalen-1-yl]propyl}piperazine" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site YT1 "Create component" 2021-03-31 RCSB YT1 "Modify name" 2021-04-02 RCSB YT1 "Initial release" 2021-12-15 RCSB ##