data_Y4O
# 
_chem_comp.id                                    Y4O 
_chem_comp.name                                  "3-[4-(dimethylamino)butanoylamino]-~{N}-[3-methyl-4-[(4-pyridin-3-ylpyrimidin-2-yl)amino]phenyl]benzamide" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C29 H31 N7 O2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-11-20 
_chem_comp.pdbx_modified_date                    2023-12-22 
_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                        509.602 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     Y4O 
_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        8X5M 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBJ 
# 
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 
Y4O C1  C1  C 0 1 N N N N N N -19.035 -30.764 16.976 1.636   2.106  0.739  C1  Y4O 1  
Y4O C2  C2  C 0 1 Y N N N N N -17.770 -31.530 16.697 1.636   0.645  0.371  C2  Y4O 2  
Y4O N3  N1  N 0 1 N N N N N N -8.504  -42.474 17.537 -9.564  3.749  0.022  N3  Y4O 3  
Y4O C4  C3  C 0 1 Y N N N N N -15.926 -32.142 15.243 2.820   -1.325 -0.340 C4  Y4O 4  
Y4O N5  N2  N 0 1 Y N N N N N -17.718 -29.353 12.506 5.237   -1.194 0.390  N5  Y4O 5  
Y4O C6  C4  C 0 1 Y N N N N N -16.060 -33.062 17.452 0.457   -1.421 0.059  C6  Y4O 6  
Y4O C7  C5  C 0 1 Y N N N N N -17.233 -32.348 17.668 0.457   -0.074 0.398  C7  Y4O 7  
Y4O C10 C6  C 0 1 Y N N N N N -13.135 -36.298 19.551 -4.385  -1.658 -0.389 C10 Y4O 8  
Y4O C11 C7  C 0 1 Y N N N N N -12.949 -37.349 20.449 -5.575  -2.357 -0.259 C11 Y4O 9  
Y4O C15 C8  C 0 1 N N N N N N -10.979 -38.443 19.362 -6.975  -0.433 -0.288 C15 Y4O 10 
Y4O C16 C9  C 0 1 N N N N N N -9.974  -39.536 19.640 -8.316  0.209  -0.530 C16 Y4O 11 
Y4O C17 C10 C 0 1 N N N N N N -9.813  -40.522 18.478 -8.258  1.683  -0.123 C17 Y4O 12 
Y4O C18 C11 C 0 1 N N N N N N -8.660  -41.518 18.640 -9.620  2.334  -0.368 C18 Y4O 13 
Y4O C19 C12 C 0 1 N N N N N N -7.918  -41.834 16.362 -10.770 4.465  -0.415 C19 Y4O 14 
Y4O C20 C13 C 0 1 N N N N N N -7.691  -43.615 17.942 -9.367  3.888  1.472  C20 Y4O 15 
Y4O C21 C14 C 0 1 Y N N N N N -16.970 -29.894 13.496 5.228   0.101  0.108  C21 Y4O 16 
Y4O C22 C15 C 0 1 Y N N N N N -17.035 -28.682 11.580 6.377   -1.852 0.533  C22 Y4O 17 
Y4O C23 C16 C 0 1 Y N N N N N -15.664 -28.527 11.595 7.573   -1.174 0.385  C23 Y4O 18 
Y4O C24 C17 C 0 1 Y N N N N N -14.978 -29.096 12.656 7.533   0.191  0.088  C24 Y4O 19 
Y4O C25 C18 C 0 1 Y N N N N N -13.494 -29.047 12.797 8.788   0.963  -0.080 C25 Y4O 20 
Y4O C29 C19 C 0 1 Y N N N N N -12.826 -29.769 13.775 8.751   2.348  -0.268 C29 Y4O 21 
Y4O C3  C20 C 0 1 Y N N N N N -17.101 -31.431 15.474 2.820   0.022  -0.000 C3  Y4O 22 
Y4O C5  C21 C 0 1 Y N N N N N -15.412 -32.959 16.224 1.643   -2.045 -0.308 C5  Y4O 23 
Y4O N1  N3  N 0 1 N N N N N N -15.595 -33.901 18.494 -0.738  -2.149 0.087  N1  Y4O 24 
Y4O C8  C22 C 0 1 N N N N N N -14.319 -34.256 18.773 -1.904  -1.543 -0.214 C8  Y4O 25 
Y4O O1  O1  O 0 1 N N N N N N -13.337 -33.703 18.284 -1.909  -0.389 -0.596 O1  Y4O 26 
Y4O C9  C23 C 0 1 Y N N N N N -14.155 -35.377 19.756 -3.178  -2.282 -0.079 C9  Y4O 27 
Y4O C12 C24 C 0 1 Y N N N N N -13.792 -37.462 21.556 -5.563  -3.673 0.184  C12 Y4O 28 
Y4O C13 C25 C 0 1 Y N N N N N -14.797 -36.542 21.759 -4.366  -4.291 0.497  C13 Y4O 29 
Y4O C14 C26 C 0 1 Y N N N N N -14.983 -35.501 20.867 -3.175  -3.608 0.360  C14 Y4O 30 
Y4O N2  N4  N 0 1 N N N N N N -11.931 -38.322 20.308 -6.789  -1.736 -0.575 N2  Y4O 31 
Y4O O2  O2  O 0 1 N N N N N N -10.916 -37.722 18.372 -6.061  0.224  0.166  O2  Y4O 32 
Y4O N4  N5  N 0 1 N N N N N N -17.632 -30.596 14.463 4.014   0.752  -0.034 N4  Y4O 33 
Y4O N6  N6  N 0 1 Y N N N N N -15.633 -29.781 13.603 6.350   0.788  -0.041 N6  Y4O 34 
Y4O C26 C27 C 0 1 Y N N N N N -12.705 -28.326 11.908 10.024  0.320  -0.049 C26 Y4O 35 
Y4O N7  N7  N 0 1 Y N N N N N -11.372 -28.262 11.958 11.139  1.005  -0.198 N7  Y4O 36 
Y4O C27 C28 C 0 1 Y N N N N N -10.770 -28.960 12.928 11.135  2.311  -0.382 C27 Y4O 37 
Y4O C28 C29 C 0 1 Y N N N N N -11.452 -29.717 13.847 9.950   3.022  -0.420 C28 Y4O 38 
Y4O H1  H1  H 0 1 N N N N N N -19.904 -31.370 16.679 1.458   2.705  -0.154 H1  Y4O 39 
Y4O H2  H2  H 0 1 N N N N N N -19.096 -30.537 18.050 0.849   2.297  1.468  H2  Y4O 40 
Y4O H3  H3  H 0 1 N N N N N N -19.029 -29.825 16.402 2.602   2.372  1.169  H3  Y4O 41 
Y4O H4  H5  H 0 1 N N N N N N -15.418 -32.052 14.294 3.742   -1.810 -0.625 H4  Y4O 42 
Y4O H6  H6  H 0 1 N N N N N N -17.736 -32.436 18.620 -0.465  0.411  0.684  H6  Y4O 43 
Y4O H8  H7  H 0 1 N N N N N N -12.485 -36.200 18.694 -4.393  -0.634 -0.733 H8  Y4O 44 
Y4O H31 H8  H 0 1 N N N N N N -8.998  -39.070 19.840 -8.570  0.134  -1.587 H31 Y4O 45 
Y4O H13 H9  H 0 1 N N N N N N -10.303 -40.095 20.529 -9.076  -0.301 0.063  H13 Y4O 46 
Y4O H14 H10 H 0 1 N N N N N N -10.748 -41.093 18.381 -8.005  1.758  0.935  H14 Y4O 47 
Y4O H32 H11 H 0 1 N N N N N N -9.640  -39.943 17.559 -7.499  2.194  -0.715 H32 Y4O 48 
Y4O H16 H12 H 0 1 N N N N N N -7.725  -40.945 18.730 -10.379 1.824  0.224  H16 Y4O 49 
Y4O H15 H13 H 0 1 N N N N N N -8.830  -42.089 19.565 -9.873  2.259  -1.426 H15 Y4O 50 
Y4O H18 H14 H 0 1 N N N N N N -7.814  -42.574 15.555 -10.702 5.510  -0.113 H18 Y4O 51 
Y4O H17 H15 H 0 1 N N N N N N -8.571  -41.015 16.027 -10.854 4.405  -1.501 H17 Y4O 52 
Y4O H19 H16 H 0 1 N N N N N N -6.927  -41.431 16.620 -11.649 4.010  0.043  H19 Y4O 53 
Y4O H20 H17 H 0 1 N N N N N N -7.591  -44.313 17.098 -10.228 3.475  1.997  H20 Y4O 54 
Y4O H21 H18 H 0 1 N N N N N N -6.694  -43.265 18.248 -8.467  3.349  1.769  H21 Y4O 55 
Y4O H22 H19 H 0 1 N N N N N N -8.174  -44.128 18.787 -9.259  4.943  1.724  H22 Y4O 56 
Y4O H24 H20 H 0 1 N N N N N N -17.588 -28.232 10.768 6.372   -2.908 0.762  H24 Y4O 57 
Y4O H25 H21 H 0 1 N N N N N N -15.149 -27.986 10.815 8.517   -1.687 0.497  H25 Y4O 58 
Y4O H29 H22 H 0 1 N N N N N N -13.382 -30.371 14.478 7.810   2.878  -0.293 H29 Y4O 59 
Y4O H5  H23 H 0 1 N N N N N N -14.507 -33.520 16.042 1.643   -3.093 -0.568 H5  Y4O 60 
Y4O H7  H24 H 0 1 N N N N N N -16.297 -34.278 19.099 -0.727  -3.090 0.322  H7  Y4O 61 
Y4O H9  H25 H 0 1 N N N N N N -13.656 -38.273 22.256 -6.491  -4.216 0.285  H9  Y4O 62 
Y4O H10 H26 H 0 1 N N N N N N -15.443 -36.634 22.619 -4.363  -5.315 0.842  H10 Y4O 63 
Y4O H11 H27 H 0 1 N N N N N N -15.773 -34.783 21.033 -2.242  -4.095 0.601  H11 Y4O 64 
Y4O H12 H28 H 0 1 N N N N N N -11.916 -39.026 21.018 -7.497  -2.244 -1.001 H12 Y4O 65 
Y4O H23 H29 H 0 1 N N N N N N -18.628 -30.508 14.455 3.991   1.714  -0.155 H23 Y4O 66 
Y4O H26 H30 H 0 1 N N N N N N -13.205 -27.779 11.122 10.068  -0.749 0.100  H26 Y4O 67 
Y4O H27 H31 H 0 1 N N N N N N -9.692  -28.926 12.991 12.073  2.834  -0.500 H27 Y4O 68 
Y4O H28 H32 H 0 1 N N N N N N -10.921 -30.262 14.613 9.959   4.091  -0.572 H28 Y4O 69 
# 
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 
Y4O C1  C2  SING N N 1  
Y4O C2  C3  DOUB Y N 2  
Y4O C2  C7  SING Y N 3  
Y4O C3  C4  SING Y N 4  
Y4O C3  N4  SING N N 5  
Y4O C4  C5  DOUB Y N 6  
Y4O C5  C6  SING Y N 7  
Y4O C6  C7  DOUB Y N 8  
Y4O C6  N1  SING N N 9  
Y4O N1  C8  SING N N 10 
Y4O C8  O1  DOUB N N 11 
Y4O C8  C9  SING N N 12 
Y4O C9  C10 DOUB Y N 13 
Y4O C9  C14 SING Y N 14 
Y4O C10 C11 SING Y N 15 
Y4O C11 C12 DOUB Y N 16 
Y4O C11 N2  SING N N 17 
Y4O C12 C13 SING Y N 18 
Y4O C13 C14 DOUB Y N 19 
Y4O N2  C15 SING N N 20 
Y4O C15 O2  DOUB N N 21 
Y4O C15 C16 SING N N 22 
Y4O C16 C17 SING N N 23 
Y4O C17 C18 SING N N 24 
Y4O C18 N3  SING N N 25 
Y4O N3  C19 SING N N 26 
Y4O N3  C20 SING N N 27 
Y4O N4  C21 SING N N 28 
Y4O C21 N5  DOUB Y N 29 
Y4O C21 N6  SING Y N 30 
Y4O N5  C22 SING Y N 31 
Y4O C22 C23 DOUB Y N 32 
Y4O C23 C24 SING Y N 33 
Y4O C24 N6  DOUB Y N 34 
Y4O C24 C25 SING N N 35 
Y4O C25 C26 DOUB Y N 36 
Y4O C25 C29 SING Y N 37 
Y4O C26 N7  SING Y N 38 
Y4O N7  C27 DOUB Y N 39 
Y4O C27 C28 SING Y N 40 
Y4O C28 C29 DOUB Y N 41 
Y4O C1  H1  SING N N 42 
Y4O C1  H2  SING N N 43 
Y4O C1  H3  SING N N 44 
Y4O C4  H4  SING N N 45 
Y4O C7  H6  SING N N 46 
Y4O C10 H8  SING N N 47 
Y4O C16 H31 SING N N 48 
Y4O C16 H13 SING N N 49 
Y4O C17 H14 SING N N 50 
Y4O C17 H32 SING N N 51 
Y4O C18 H16 SING N N 52 
Y4O C18 H15 SING N N 53 
Y4O C19 H18 SING N N 54 
Y4O C19 H17 SING N N 55 
Y4O C19 H19 SING N N 56 
Y4O C20 H20 SING N N 57 
Y4O C20 H21 SING N N 58 
Y4O C20 H22 SING N N 59 
Y4O C22 H24 SING N N 60 
Y4O C23 H25 SING N N 61 
Y4O C29 H29 SING N N 62 
Y4O C5  H5  SING N N 63 
Y4O N1  H7  SING N N 64 
Y4O C12 H9  SING N N 65 
Y4O C13 H10 SING N N 66 
Y4O C14 H11 SING N N 67 
Y4O N2  H12 SING N N 68 
Y4O N4  H23 SING N N 69 
Y4O C26 H26 SING N N 70 
Y4O C27 H27 SING N N 71 
Y4O C28 H28 SING N N 72 
# 
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 
Y4O InChI            InChI                1.06  "InChI=1S/C29H31N7O2/c1-20-17-24(11-12-25(20)34-29-31-15-13-26(35-29)22-8-5-14-30-19-22)33-28(38)21-7-4-9-23(18-21)32-27(37)10-6-16-36(2)3/h4-5,7-9,11-15,17-19H,6,10,16H2,1-3H3,(H,32,37)(H,33,38)(H,31,34,35)" 
Y4O InChIKey         InChI                1.06  JCQSXSKNIVAALC-UHFFFAOYSA-N                                                                                                                                                                                      
Y4O SMILES_CANONICAL CACTVS               3.385 "CN(C)CCCC(=O)Nc1cccc(c1)C(=O)Nc2ccc(Nc3nccc(n3)c4cccnc4)c(C)c2"                                                                                                                                                 
Y4O SMILES           CACTVS               3.385 "CN(C)CCCC(=O)Nc1cccc(c1)C(=O)Nc2ccc(Nc3nccc(n3)c4cccnc4)c(C)c2"                                                                                                                                                 
Y4O SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1cc(ccc1Nc2nccc(n2)c3cccnc3)NC(=O)c4cccc(c4)NC(=O)CCCN(C)C"                                                                                                                                                   
Y4O SMILES           "OpenEye OEToolkits" 2.0.7 "Cc1cc(ccc1Nc2nccc(n2)c3cccnc3)NC(=O)c4cccc(c4)NC(=O)CCCN(C)C"                                                                                                                                                   
# 
_pdbx_chem_comp_identifier.comp_id           Y4O 
_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        "3-[4-(dimethylamino)butanoylamino]-~{N}-[3-methyl-4-[(4-pyridin-3-ylpyrimidin-2-yl)amino]phenyl]benzamide" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
Y4O "Create component" 2023-11-20 PDBJ 
Y4O "Initial release"  2023-12-27 RCSB 
# 
