data_YPB # _chem_comp.id YPB _chem_comp.name "(4bS)-1-ethyl-7,20-dimethyl-4b,10,11,21-tetrahydro-2H,17H-dibenzo[12',13':5',6'][1,4,8]trioxacyclotridecino[11',10':4,5]pyrido[2,3-d]pyrimidine-2,4,19(1H,3H)-trione" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C27 H27 N3 O6" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms JJ-II-363A _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-12-08 _chem_comp.pdbx_modified_date 2024-12-13 _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 489.520 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YPB _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 8V9F _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _chem_comp.pdbx_pcm ? # 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_n_terminal_atom_flag _chem_comp_atom.pdbx_backbone_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 YPB C15 C1 C 0 1 N N N N N N 11.758 -3.539 2.480 4.742 3.722 -0.806 C15 YPB 1 YPB C17 C2 C 0 1 Y N N N N N 8.870 -5.199 -2.320 2.068 -1.956 -0.625 C17 YPB 2 YPB C20 C3 C 0 1 Y N N N N N 8.969 -5.790 -4.967 -0.127 -3.609 -0.529 C20 YPB 3 YPB C21 C4 C 0 1 Y N N N N N 9.530 -6.670 -4.012 -0.209 -2.328 0.009 C21 YPB 4 YPB C24 C5 C 0 1 N N N N N N 9.960 -9.985 -5.464 -3.733 -1.750 -0.201 C24 YPB 5 YPB C26 C6 C 0 1 Y N N N N N 9.131 -11.584 -3.893 -4.711 0.313 0.475 C26 YPB 6 YPB C28 C7 C 0 1 N N N N N N 7.677 -10.658 -2.102 -3.058 1.381 -1.091 C28 YPB 7 YPB C01 C8 C 0 1 N N N N N N 7.912 -7.105 1.644 -0.080 2.418 -2.015 C01 YPB 8 YPB C02 C9 C 0 1 N N N N N N 9.023 -6.988 0.606 0.715 1.594 -1.038 C02 YPB 9 YPB C03 C10 C 0 1 N N N N N N 9.152 -7.727 -0.531 0.146 0.859 -0.077 C03 YPB 10 YPB C04 C11 C 0 1 N N S N N N 10.139 -7.285 -1.566 0.964 -0.163 0.678 C04 YPB 11 YPB C05 C12 C 0 1 N N N N N N 11.280 -6.586 -0.932 2.414 0.257 0.724 C05 YPB 12 YPB C06 C13 C 0 1 N N N N N N 11.247 -6.098 0.329 2.915 1.071 -0.253 C06 YPB 13 YPB C09 C14 C 0 1 N N N N N N 13.460 -5.182 0.175 5.046 0.923 0.748 C09 YPB 14 YPB C11 C15 C 0 1 N N N N N N 12.479 -6.397 -1.694 3.254 -0.186 1.755 C11 YPB 15 YPB C14 C16 C 0 1 N N N N N N 12.311 -4.912 2.292 4.835 2.263 -1.256 C14 YPB 16 YPB C16 C17 C 0 1 Y N N N N N 9.520 -6.376 -2.658 0.910 -1.508 0.001 C16 YPB 17 YPB C18 C18 C 0 1 Y N N N N N 8.312 -4.332 -3.245 2.140 -3.222 -1.166 C18 YPB 18 YPB C19 C19 C 0 1 Y N N N N N 8.348 -4.599 -4.576 1.040 -4.056 -1.117 C19 YPB 19 YPB C23 C20 C 0 1 N N N N N N 9.775 -8.417 -5.580 -2.567 -2.673 0.158 C23 YPB 20 YPB C27 C21 C 0 1 Y N N N N N 8.490 -11.749 -2.708 -4.396 1.341 -0.400 C27 YPB 21 YPB C30 C22 C 0 1 N N N N N N 8.084 -8.623 -0.904 -1.187 1.033 0.336 C30 YPB 22 YPB C32 C23 C 0 1 Y N N N N N 8.644 -12.985 -2.058 -5.320 2.341 -0.646 C32 YPB 23 YPB C33 C24 C 0 1 Y N N N N N 9.411 -14.005 -2.592 -6.557 2.312 -0.031 C33 YPB 24 YPB C34 C25 C 0 1 Y N N N N N 10.046 -13.820 -3.814 -6.873 1.287 0.841 C34 YPB 25 YPB C35 C26 C 0 1 Y N N N N N 9.906 -12.593 -4.473 -5.953 0.289 1.095 C35 YPB 26 YPB C36 C27 C 0 1 N N N N N N 7.761 -3.687 -5.544 1.112 -5.443 -1.701 C36 YPB 27 YPB N07 N1 N 0 1 N N N N N N 10.095 -6.270 1.071 2.079 1.579 -1.211 N07 YPB 28 YPB N08 N2 N 0 1 N N N N N N 12.303 -5.429 0.910 4.249 1.397 -0.229 N08 YPB 29 YPB N10 N3 N 0 1 N N N N N N 13.533 -5.693 -1.074 4.558 0.156 1.739 N10 YPB 30 YPB O12 O1 O 0 1 N N N N N N 12.694 -6.810 -2.835 2.815 -0.875 2.658 O12 YPB 31 YPB O13 O2 O 0 1 N N N N N N 14.382 -4.548 0.655 6.232 1.199 0.732 O13 YPB 32 YPB O22 O3 O 0 1 N N N N N N 10.145 -7.875 -4.348 -1.407 -1.916 0.503 O22 YPB 33 YPB O25 O4 O 0 1 N N N N N N 8.979 -10.412 -4.571 -3.818 -0.678 0.735 O25 YPB 34 YPB O29 O5 O 0 1 N N N N N N 8.529 -9.574 -1.744 -2.057 1.891 -0.215 O29 YPB 35 YPB O31 O6 O 0 1 N N N N N N 6.887 -8.604 -0.598 -1.579 0.363 1.291 O31 YPB 36 YPB H153 H1 H 0 0 N N N N N N 11.816 -3.262 3.543 5.285 3.850 0.130 H153 YPB 37 YPB H151 H2 H 0 0 N N N N N N 12.342 -2.824 1.883 5.179 4.366 -1.570 H151 YPB 38 YPB H152 H3 H 0 0 N N N N N N 10.708 -3.519 2.152 3.696 3.991 -0.659 H152 YPB 39 YPB H171 H4 H 0 0 N N N N N N 8.794 -4.943 -1.274 2.936 -1.317 -0.681 H171 YPB 40 YPB H201 H5 H 0 0 N N N N N N 9.021 -6.042 -6.016 -0.971 -4.281 -0.476 H201 YPB 41 YPB H242 H6 H 0 0 N N N N N N 9.820 -10.462 -6.445 -3.582 -1.350 -1.204 H242 YPB 42 YPB H241 H7 H 0 0 N N N N N N 10.962 -10.226 -5.079 -4.664 -2.321 -0.184 H241 YPB 43 YPB H281 H8 H 0 0 N N N N N N 6.928 -10.311 -2.829 -2.780 0.379 -1.415 H281 YPB 44 YPB H282 H9 H 0 0 N N N N N N 7.167 -11.036 -1.203 -3.129 2.030 -1.966 H282 YPB 45 YPB H013 H10 H 0 0 N N N N N N 8.082 -6.374 2.448 0.596 2.888 -2.730 H013 YPB 46 YPB H011 H11 H 0 0 N N N N N N 6.942 -6.905 1.166 -0.782 1.776 -2.547 H011 YPB 47 YPB H012 H12 H 0 0 N N N N N N 7.910 -8.121 2.066 -0.631 3.189 -1.476 H012 YPB 48 YPB H041 H15 H 0 0 N N N N N N 10.526 -8.183 -2.070 0.585 -0.245 1.690 H041 YPB 49 YPB H142 H16 H 0 0 N N N N N N 11.719 -5.601 2.913 4.293 2.136 -2.193 H142 YPB 50 YPB H141 H17 H 0 0 N N N N N N 13.353 -4.906 2.643 5.882 1.994 -1.403 H141 YPB 51 YPB H181 H18 H 0 0 N N N N N N 7.838 -3.425 -2.900 3.054 -3.562 -1.629 H181 YPB 52 YPB H232 H19 H 0 0 N N N N N N 10.418 -8.018 -6.378 -2.849 -3.305 1.000 H232 YPB 53 YPB H231 H20 H 0 0 N N N N N N 8.725 -8.175 -5.800 -2.357 -3.305 -0.708 H231 YPB 54 YPB H321 H21 H 0 0 N N N N N N 8.148 -13.144 -1.112 -5.073 3.146 -1.323 H321 YPB 55 YPB H331 H22 H 0 0 N N N N N N 9.516 -14.940 -2.062 -7.277 3.093 -0.229 H331 YPB 56 YPB H341 H23 H 0 0 N N N N N N 10.639 -14.611 -4.249 -7.839 1.266 1.322 H341 YPB 57 YPB H351 H24 H 0 0 N N N N N N 10.393 -12.427 -5.423 -6.201 -0.512 1.776 H351 YPB 58 YPB H363 H25 H 0 0 N N N N N N 6.708 -3.957 -5.711 0.812 -5.413 -2.748 H363 YPB 59 YPB H361 H26 H 0 0 N N N N N N 7.820 -2.658 -5.160 2.134 -5.816 -1.626 H361 YPB 60 YPB H362 H27 H 0 0 N N N N N N 8.312 -3.756 -6.494 0.443 -6.104 -1.150 H362 YPB 61 YPB H071 H28 H 0 0 N N N N N N 10.041 -5.856 1.980 2.423 1.920 -2.049 H071 YPB 62 YPB H101 H29 H 0 0 N N N N N N 14.381 -5.565 -1.588 5.147 -0.157 2.443 H101 YPB 63 # 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 YPB C23 C24 SING N N 1 YPB C23 O22 SING N N 2 YPB C36 C19 SING N N 3 YPB C24 O25 SING N N 4 YPB C20 C19 DOUB Y N 5 YPB C20 C21 SING Y N 6 YPB C19 C18 SING Y N 7 YPB O25 C26 SING N N 8 YPB C35 C26 DOUB Y N 9 YPB C35 C34 SING Y N 10 YPB O22 C21 SING N N 11 YPB C21 C16 DOUB Y N 12 YPB C26 C27 SING Y N 13 YPB C34 C33 DOUB Y N 14 YPB C18 C17 DOUB Y N 15 YPB O12 C11 DOUB N N 16 YPB C27 C28 SING N N 17 YPB C27 C32 DOUB Y N 18 YPB C16 C17 SING Y N 19 YPB C16 C04 SING N N 20 YPB C33 C32 SING Y N 21 YPB C28 O29 SING N N 22 YPB O29 C30 SING N N 23 YPB C11 N10 SING N N 24 YPB C11 C05 SING N N 25 YPB C04 C05 SING N N 26 YPB C04 C03 SING N N 27 YPB N10 C09 SING N N 28 YPB C05 C06 DOUB N N 29 YPB C30 O31 DOUB N N 30 YPB C30 C03 SING N N 31 YPB C03 C02 DOUB N N 32 YPB C09 O13 DOUB N N 33 YPB C09 N08 SING N N 34 YPB C06 N08 SING N N 35 YPB C06 N07 SING N N 36 YPB C02 N07 SING N N 37 YPB C02 C01 SING N N 38 YPB N08 C14 SING N N 39 YPB C14 C15 SING N N 40 YPB C15 H153 SING N N 41 YPB C15 H151 SING N N 42 YPB C15 H152 SING N N 43 YPB C17 H171 SING N N 44 YPB C20 H201 SING N N 45 YPB C24 H242 SING N N 46 YPB C24 H241 SING N N 47 YPB C28 H281 SING N N 48 YPB C28 H282 SING N N 49 YPB C01 H013 SING N N 50 YPB C01 H011 SING N N 51 YPB C01 H012 SING N N 52 YPB C04 H041 SING N N 53 YPB C14 H142 SING N N 54 YPB C14 H141 SING N N 55 YPB C18 H181 SING N N 56 YPB C23 H232 SING N N 57 YPB C23 H231 SING N N 58 YPB C32 H321 SING N N 59 YPB C33 H331 SING N N 60 YPB C34 H341 SING N N 61 YPB C35 H351 SING N N 62 YPB C36 H363 SING N N 63 YPB C36 H361 SING N N 64 YPB C36 H362 SING N N 65 YPB N07 H071 SING N N 66 YPB N10 H101 SING N N 67 # 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 YPB SMILES ACDLabs 12.01 "Cc1ccc2c(OCCOc3ccccc3COC(=O)C3=C(C)NC=4N(CC)C(=O)NC(=O)C=4C32)c1" YPB InChI InChI 1.06 "InChI=1S/C27H27N3O6/c1-4-30-24-23(25(31)29-27(30)33)22-18-10-9-15(2)13-20(18)35-12-11-34-19-8-6-5-7-17(19)14-36-26(32)21(22)16(3)28-24/h5-10,13,22,28H,4,11-12,14H2,1-3H3,(H,29,31,33)/t22-/m1/s1" YPB InChIKey InChI 1.06 ILMBIUFRDHNTSS-JOCHJYFZSA-N YPB SMILES_CANONICAL CACTVS 3.385 "CCN1C(=O)NC(=O)C2=C1NC(=C3[C@H]2c4ccc(C)cc4OCCOc5ccccc5COC3=O)C" YPB SMILES CACTVS 3.385 "CCN1C(=O)NC(=O)C2=C1NC(=C3[CH]2c4ccc(C)cc4OCCOc5ccccc5COC3=O)C" YPB SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CCN1C2=C([C@@H]3c4ccc(cc4OCCOc5ccccc5COC(=O)C3=C(N2)C)C)C(=O)NC1=O" YPB SMILES "OpenEye OEToolkits" 2.0.7 "CCN1C2=C(C3c4ccc(cc4OCCOc5ccccc5COC(=O)C3=C(N2)C)C)C(=O)NC1=O" # _pdbx_chem_comp_identifier.comp_id YPB _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program ACDLabs _pdbx_chem_comp_identifier.program_version 12.01 _pdbx_chem_comp_identifier.identifier "(4bS)-1-ethyl-7,20-dimethyl-4b,10,11,21-tetrahydro-2H,17H-dibenzo[12',13':5',6'][1,4,8]trioxacyclotridecino[11',10':4,5]pyrido[2,3-d]pyrimidine-2,4,19(1H,3H)-trione" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site YPB "Create component" 2023-12-08 RCSB YPB "Initial release" 2024-12-18 RCSB # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id YPB _pdbx_chem_comp_synonyms.name JJ-II-363A _pdbx_chem_comp_synonyms.provenance AUTHOR _pdbx_chem_comp_synonyms.type ? #