data_YB4
# 
_chem_comp.id                                    YB4 
_chem_comp.name                                  "~{N}-(2,6-diethylphenyl)-2-[[4-(4-methylpiperazin-1-yl)-2-(propanoylamino)phenyl]amino]-5,6-dihydropyrimido[4,5-e]indolizine-7-carboxamide" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C35 H42 N8 O2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2021-02-15 
_chem_comp.pdbx_modified_date                    2024-09-27 
_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                        606.760 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YB4 
_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        7LQD 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_chem_comp.pdbx_pcm                              Y 
# 
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 
YB4 C4  C1  C 0 1 Y N N N N N 67.408 64.991 47.431 5.257   1.378  0.586  C4  YB4 1  
YB4 C14 C2  C 0 1 Y N N N N N 69.486 70.864 45.217 0.567   1.988  -0.277 C14 YB4 2  
YB4 C5  C3  C 0 1 Y N N N N N 67.560 66.245 46.916 3.967   0.886  0.653  C5  YB4 3  
YB4 C6  C4  C 0 1 Y N N N N N 67.477 67.374 47.751 3.725   -0.461 0.430  C6  YB4 4  
YB4 C11 C5  C 0 1 N N N N N N 71.036 70.373 43.196 -1.885  2.498  -0.273 C11 YB4 5  
YB4 C7  C6  C 0 1 N N N N N N 72.223 66.758 40.549 -5.820  0.247  -0.055 C7  YB4 6  
YB4 C8  C7  C 0 1 Y N N N N N 71.468 66.830 41.807 -4.444  -0.175 0.258  C8  YB4 7  
YB4 C9  C8  C 0 1 Y N N N N N 71.040 65.736 42.631 -4.035  -1.393 0.973  C9  YB4 8  
YB4 C10 C9  C 0 1 Y N N N N N 70.379 66.245 43.702 -2.691  -1.368 1.037  C10 YB4 9  
YB4 C12 C10 C 0 1 N N N N N N 71.195 69.415 42.025 -3.124  1.777  -0.807 C12 YB4 10 
YB4 C13 C11 C 0 1 Y N N N N N 71.038 67.993 42.444 -3.299  0.481  -0.056 C13 YB4 11 
YB4 N1  N1  N 0 1 Y N N N N N 70.367 67.635 43.608 -2.241  -0.238 0.427  N1  YB4 12 
YB4 N2  N2  N 0 1 N N N N N N 67.633 68.656 47.228 2.415   -0.959 0.498  N2  YB4 13 
YB4 C3  C12 C 0 1 Y N N N N N 67.141 64.788 48.813 6.314   0.524  0.296  C3  YB4 14 
YB4 N3  N3  N 0 1 Y N N N N N 69.002 68.187 45.445 0.108   -0.571 0.468  N3  YB4 15 
YB4 C1  C13 C 0 1 Y N N N N N 67.220 67.195 49.119 4.784   -1.320 0.139  C1  YB4 16 
YB4 C2  C14 C 0 1 Y N N N N N 67.063 65.916 49.644 6.077   -0.826 0.078  C2  YB4 17 
YB4 C15 C15 C 0 1 Y N N N N N 70.099 69.931 44.289 -0.733  1.552  -0.089 C15 YB4 18 
YB4 C16 C16 C 0 1 Y N N N N N 69.816 68.593 44.463 -0.933  0.222  0.278  C16 YB4 19 
YB4 C17 C17 C 0 1 Y N N N N N 68.469 69.108 46.264 1.340   -0.111 0.293  C17 YB4 20 
YB4 N4  N4  N 0 1 Y N N N N N 68.675 70.435 46.177 1.566   1.140  -0.084 N4  YB4 21 
YB4 N5  N5  N 0 1 N N N N N N 67.117 68.326 49.964 4.541   -2.682 -0.086 N5  YB4 22 
YB4 N6  N6  N 0 1 N N N N N N 67.028 63.489 49.328 7.618   1.026  0.224  N6  YB4 23 
YB4 C18 C18 C 0 1 N N N N N N 67.308 62.300 48.505 8.229   0.721  -1.077 C18 YB4 24 
YB4 C19 C19 C 0 1 N N N N N N 66.459 61.107 48.876 9.677   1.215  -1.087 C19 YB4 25 
YB4 N7  N7  N 0 1 N N N N N N 66.556 60.838 50.308 9.700   2.661  -0.824 N7  YB4 26 
YB4 C20 C20 C 0 1 N N N N N N 65.976 61.982 51.008 9.089   2.967  0.477  C20 YB4 27 
YB4 C21 C21 C 0 1 N N N N N N 66.789 63.231 50.759 7.641   2.472  0.487  C21 YB4 28 
YB4 C22 C22 C 0 1 N N N N N N 65.874 59.592 50.662 11.069  3.188  -0.900 C22 YB4 29 
YB4 N8  N8  N 0 1 N N N N N N 72.298 65.549 39.952 -6.863  -0.518 0.326  N8  YB4 30 
YB4 O1  O1  O 0 1 N N N N N N 72.764 67.757 40.093 -6.016  1.285  -0.657 O1  YB4 31 
YB4 C23 C23 C 0 1 Y N N N N N 73.147 65.238 38.854 -8.161  -0.177 -0.067 C23 YB4 32 
YB4 C24 C24 C 0 1 Y N N N N N 74.460 64.840 39.105 -8.711  1.036  0.325  C24 YB4 33 
YB4 C25 C25 C 0 1 Y N N N N N 75.270 64.549 38.007 -9.993  1.370  -0.065 C25 YB4 34 
YB4 C26 C26 C 0 1 Y N N N N N 74.807 64.678 36.717 -10.729 0.498  -0.846 C26 YB4 35 
YB4 C27 C27 C 0 1 Y N N N N N 73.512 65.091 36.495 -10.184 -0.711 -1.238 C27 YB4 36 
YB4 C28 C28 C 0 1 Y N N N N N 72.657 65.391 37.557 -8.900  -1.049 -0.856 C28 YB4 37 
YB4 C29 C29 C 0 1 N N N N N N 74.995 64.679 40.509 -7.910  1.987  1.177  C29 YB4 38 
YB4 C30 C30 C 0 1 N N N N N N 71.242 65.845 37.291 -8.308  -2.366 -1.284 C30 YB4 39 
YB4 C31 C31 C 0 1 N N N N N N 70.206 64.818 37.637 -8.506  -3.400 -0.173 C31 YB4 40 
YB4 C32 C32 C 0 1 N N N N N N 76.191 65.534 40.818 -8.566  3.369  1.153  C32 YB4 41 
YB4 C33 C33 C 0 1 N N N N N N 67.868 68.568 51.058 5.530   -3.580 0.091  C33 YB4 42 
YB4 C34 C34 C 0 1 N N N N N N 67.442 69.781 51.855 5.307   -5.027 -0.269 C34 YB4 43 
YB4 O2  O2  O 0 1 N N N N N N 68.811 67.865 51.382 6.599   -3.225 0.540  O2  YB4 44 
YB4 C35 C35 C 0 1 N N N N N N 67.748 71.085 51.175 6.577   -5.827 0.027  C35 YB4 45 
YB4 H1  H1  H 0 1 N N N N N N 67.492 64.136 46.777 5.443   2.428  0.756  H1  YB4 46 
YB4 H2  H2  H 0 1 N N N N N N 69.692 71.920 45.125 0.764   3.005  -0.582 H2  YB4 47 
YB4 H3  H3  H 0 1 N N N N N N 67.745 66.372 45.860 3.147   1.552  0.879  H3  YB4 48 
YB4 H4  H4  H 0 1 N N N N N N 72.029 70.524 43.645 -1.595  3.279  -0.976 H4  YB4 49 
YB4 H5  H5  H 0 1 N N N N N N 70.664 71.329 42.800 -2.126  2.956  0.687  H5  YB4 50 
YB4 H6  H6  H 0 1 N N N N N N 71.214 64.689 42.433 -4.686  -2.157 1.370  H6  YB4 51 
YB4 H7  H7  H 0 1 N N N N N N 69.934 65.666 44.498 -2.070  -2.122 1.497  H7  YB4 52 
YB4 H8  H8  H 0 1 N N N N N N 72.196 69.549 41.590 -4.003  2.405  -0.661 H8  YB4 53 
YB4 H9  H9  H 0 1 N N N N N N 70.432 69.649 41.268 -2.995  1.569  -1.869 H9  YB4 54 
YB4 H10 H10 H 0 1 N N N N N N 67.034 69.350 47.627 2.262   -1.898 0.689  H10 YB4 55 
YB4 H11 H11 H 0 1 N N N N N N 66.879 65.790 50.701 6.899   -1.489 -0.148 H11 YB4 56 
YB4 H12 H12 H 0 1 N N N N N N 66.424 69.008 49.728 3.662   -2.978 -0.368 H12 YB4 57 
YB4 H13 H13 H 0 1 N N N N N N 68.367 62.029 48.631 8.211   -0.356 -1.243 H13 YB4 58 
YB4 H14 H14 H 0 1 N N N N N N 67.117 62.551 47.451 7.669   1.220  -1.868 H14 YB4 59 
YB4 H15 H15 H 0 1 N N N N N N 65.410 61.314 48.616 10.244  0.696  -0.314 H15 YB4 60 
YB4 H16 H16 H 0 1 N N N N N N 66.808 60.226 48.317 10.123  1.016  -2.061 H16 YB4 61 
YB4 H18 H18 H 0 1 N N N N N N 64.949 62.142 50.648 9.649   2.467  1.268  H18 YB4 62 
YB4 H19 H19 H 0 1 N N N N N N 65.958 61.773 52.088 9.107   4.044  0.643  H19 YB4 63 
YB4 H20 H20 H 0 1 N N N N N N 67.761 63.122 51.262 7.074   2.991  -0.286 H20 YB4 64 
YB4 H21 H21 H 0 1 N N N N N N 66.250 64.090 51.184 7.195   2.672  1.461  H21 YB4 65 
YB4 H22 H22 H 0 1 N N N N N N 65.965 59.418 51.744 11.473  3.007  -1.896 H22 YB4 66 
YB4 H23 H23 H 0 1 N N N N N N 64.811 59.666 50.391 11.057  4.260  -0.702 H23 YB4 67 
YB4 H24 H24 H 0 1 N N N N N N 66.334 58.755 50.116 11.693  2.688  -0.159 H24 YB4 68 
YB4 H25 H25 H 0 1 N N N N N N 71.714 64.819 40.308 -6.712  -1.305 0.873  H25 YB4 69 
YB4 H26 H26 H 0 1 N N N N N N 76.284 64.215 38.173 -10.421 2.314  0.239  H26 YB4 70 
YB4 H27 H27 H 0 1 N N N N N N 75.456 64.456 35.883 -11.731 0.761  -1.149 H27 YB4 71 
YB4 H28 H28 H 0 1 N N N N N N 73.152 65.184 35.481 -10.761 -1.390 -1.848 H28 YB4 72 
YB4 H29 H29 H 0 1 N N N N N N 74.193 64.941 41.215 -7.877  1.618  2.202  H29 YB4 73 
YB4 H30 H30 H 0 1 N N N N N N 75.279 63.626 40.651 -6.895  2.060  0.784  H30 YB4 74 
YB4 H31 H31 H 0 1 N N N N N N 71.049 66.748 37.888 -8.803  -2.710 -2.192 H31 YB4 75 
YB4 H32 H32 H 0 1 N N N N N N 71.149 66.086 36.222 -7.242  -2.240 -1.477 H32 YB4 76 
YB4 H33 H33 H 0 1 N N N N N N 69.205 65.218 37.418 -8.088  -3.017 0.758  H33 YB4 77 
YB4 H34 H34 H 0 1 N N N N N N 70.377 63.910 37.041 -9.571  -3.592 -0.041 H34 YB4 78 
YB4 H35 H35 H 0 1 N N N N N N 70.276 64.573 38.707 -8.001  -4.327 -0.445 H35 YB4 79 
YB4 H36 H36 H 0 1 N N N N N N 76.513 65.355 41.855 -8.670  3.705  0.121  H36 YB4 80 
YB4 H37 H37 H 0 1 N N N N N N 77.011 65.279 40.130 -9.550  3.312  1.617  H37 YB4 81 
YB4 H38 H38 H 0 1 N N N N N N 75.925 66.594 40.695 -7.945  4.076  1.704  H38 YB4 82 
YB4 H39 H39 H 0 1 N N N N N N 66.357 69.723 52.023 4.481   -5.424 0.321  H39 YB4 83 
YB4 H40 H40 H 0 1 N N N N N N 67.965 69.762 52.823 5.067   -5.104 -1.329 H40 YB4 84 
YB4 H41 H41 H 0 1 N N N N N N 67.412 71.918 51.810 6.416   -6.873 -0.233 H41 YB4 85 
YB4 H42 H42 H 0 1 N N N N N N 68.832 71.166 51.008 7.403   -5.429 -0.562 H42 YB4 86 
YB4 H43 H43 H 0 1 N N N N N N 67.224 71.126 50.209 6.817   -5.749 1.088  H43 YB4 87 
# 
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 
YB4 C27 C26 DOUB Y N 1  
YB4 C27 C28 SING Y N 2  
YB4 C26 C25 SING Y N 3  
YB4 C30 C28 SING N N 4  
YB4 C30 C31 SING N N 5  
YB4 C28 C23 DOUB Y N 6  
YB4 C25 C24 DOUB Y N 7  
YB4 C23 C24 SING Y N 8  
YB4 C23 N8  SING N N 9  
YB4 C24 C29 SING N N 10 
YB4 N8  C7  SING N N 11 
YB4 O1  C7  DOUB N N 12 
YB4 C29 C32 SING N N 13 
YB4 C7  C8  SING N N 14 
YB4 C8  C13 DOUB Y N 15 
YB4 C8  C9  SING Y N 16 
YB4 C12 C13 SING N N 17 
YB4 C12 C11 SING N N 18 
YB4 C13 N1  SING Y N 19 
YB4 C9  C10 DOUB Y N 20 
YB4 C11 C15 SING N N 21 
YB4 N1  C10 SING Y N 22 
YB4 N1  C16 SING N N 23 
YB4 C15 C16 DOUB Y N 24 
YB4 C15 C14 SING Y N 25 
YB4 C16 N3  SING Y N 26 
YB4 C14 N4  DOUB Y N 27 
YB4 N3  C17 DOUB Y N 28 
YB4 N4  C17 SING Y N 29 
YB4 C17 N2  SING N N 30 
YB4 C5  C4  DOUB Y N 31 
YB4 C5  C6  SING Y N 32 
YB4 N2  C6  SING N N 33 
YB4 C4  C3  SING Y N 34 
YB4 C6  C1  DOUB Y N 35 
YB4 C18 C19 SING N N 36 
YB4 C18 N6  SING N N 37 
YB4 C3  N6  SING N N 38 
YB4 C3  C2  DOUB Y N 39 
YB4 C19 N7  SING N N 40 
YB4 C1  C2  SING Y N 41 
YB4 C1  N5  SING N N 42 
YB4 N6  C21 SING N N 43 
YB4 N5  C33 SING N N 44 
YB4 N7  C22 SING N N 45 
YB4 N7  C20 SING N N 46 
YB4 C21 C20 SING N N 47 
YB4 C33 O2  DOUB N N 48 
YB4 C33 C34 SING N N 49 
YB4 C35 C34 SING N N 50 
YB4 C4  H1  SING N N 51 
YB4 C14 H2  SING N N 52 
YB4 C5  H3  SING N N 53 
YB4 C11 H4  SING N N 54 
YB4 C11 H5  SING N N 55 
YB4 C9  H6  SING N N 56 
YB4 C10 H7  SING N N 57 
YB4 C12 H8  SING N N 58 
YB4 C12 H9  SING N N 59 
YB4 N2  H10 SING N N 60 
YB4 C2  H11 SING N N 61 
YB4 N5  H12 SING N N 62 
YB4 C18 H13 SING N N 63 
YB4 C18 H14 SING N N 64 
YB4 C19 H15 SING N N 65 
YB4 C19 H16 SING N N 66 
YB4 C20 H18 SING N N 67 
YB4 C20 H19 SING N N 68 
YB4 C21 H20 SING N N 69 
YB4 C21 H21 SING N N 70 
YB4 C22 H22 SING N N 71 
YB4 C22 H23 SING N N 72 
YB4 C22 H24 SING N N 73 
YB4 N8  H25 SING N N 74 
YB4 C25 H26 SING N N 75 
YB4 C26 H27 SING N N 76 
YB4 C27 H28 SING N N 77 
YB4 C29 H29 SING N N 78 
YB4 C29 H30 SING N N 79 
YB4 C30 H31 SING N N 80 
YB4 C30 H32 SING N N 81 
YB4 C31 H33 SING N N 82 
YB4 C31 H34 SING N N 83 
YB4 C31 H35 SING N N 84 
YB4 C32 H36 SING N N 85 
YB4 C32 H37 SING N N 86 
YB4 C32 H38 SING N N 87 
YB4 C34 H39 SING N N 88 
YB4 C34 H40 SING N N 89 
YB4 C35 H41 SING N N 90 
YB4 C35 H42 SING N N 91 
YB4 C35 H43 SING N N 92 
# 
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 
YB4 InChI            InChI                1.03  "InChI=1S/C35H42N8O2/c1-5-23-9-8-10-24(6-2)32(23)39-34(45)27-15-16-43-30(27)14-11-25-22-36-35(40-33(25)43)38-28-13-12-26(21-29(28)37-31(44)7-3)42-19-17-41(4)18-20-42/h8-10,12-13,15-16,21-22H,5-7,11,14,17-20H2,1-4H3,(H,37,44)(H,39,45)(H,36,38,40)" 
YB4 InChIKey         InChI                1.03  OFKCTLDDZSLLFR-UHFFFAOYSA-N                                                                                                                                                                                                                            
YB4 SMILES_CANONICAL CACTVS               3.385 "CCC(=O)Nc1cc(ccc1Nc2ncc3CCc4n(ccc4C(=O)Nc5c(CC)cccc5CC)c3n2)N6CCN(C)CC6"                                                                                                                                                                              
YB4 SMILES           CACTVS               3.385 "CCC(=O)Nc1cc(ccc1Nc2ncc3CCc4n(ccc4C(=O)Nc5c(CC)cccc5CC)c3n2)N6CCN(C)CC6"                                                                                                                                                                              
YB4 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CCc1cccc(c1NC(=O)c2ccn-3c2CCc4c3nc(nc4)Nc5ccc(cc5NC(=O)CC)N6CCN(CC6)C)CC"                                                                                                                                                                             
YB4 SMILES           "OpenEye OEToolkits" 2.0.7 "CCc1cccc(c1NC(=O)c2ccn-3c2CCc4c3nc(nc4)Nc5ccc(cc5NC(=O)CC)N6CCN(CC6)C)CC"                                                                                                                                                                             
# 
_pdbx_chem_comp_identifier.comp_id           YB4 
_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        "~{N}-(2,6-diethylphenyl)-2-[[4-(4-methylpiperazin-1-yl)-2-(propanoylamino)phenyl]amino]-5,6-dihydropyrimido[4,5-e]indolizine-7-carboxamide" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
YB4 "Create component" 2021-02-15 RCSB 
YB4 "Initial release"  2022-02-16 RCSB 
YB4 "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            YB4 
_pdbx_chem_comp_pcm.modified_residue_id                CYS 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Covalent chemical modification" 
_pdbx_chem_comp_pcm.position                           "Amino-acid side chain" 
_pdbx_chem_comp_pcm.polypeptide_position               "Any position" 
_pdbx_chem_comp_pcm.comp_id_linking_atom               C35 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   SG 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
