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         ? 
# 
