data_X7Y # _chem_comp.id X7Y _chem_comp.name "2-{[2-methoxy-4-(4-methylpiperazin-1-yl)phenyl]amino}-5,11-dimethyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C25 H29 N7 O2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-12-03 _chem_comp.pdbx_modified_date 2021-09-17 _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 459.543 _chem_comp.one_letter_code ? _chem_comp.three_letter_code X7Y _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 7KX6 _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 X7Y N1 N1 N 0 1 Y N N -10.385 24.501 -10.215 2.045 -1.383 -0.186 N1 X7Y 1 X7Y C7 C1 C 0 1 N N N -10.598 27.167 -4.617 -3.579 -4.155 -0.826 C7 X7Y 2 X7Y C8 C2 C 0 1 Y N N -12.282 27.894 -6.752 -3.920 -1.615 0.033 C8 X7Y 3 X7Y N2 N2 N 0 1 N N N -9.839 25.610 -8.277 -0.238 -1.785 0.122 N2 X7Y 4 X7Y C9 C3 C 0 1 Y N N -13.165 28.137 -7.807 -4.131 -0.317 0.476 C9 X7Y 5 X7Y O1 O1 O 0 1 N N N -10.328 26.693 -5.933 -2.421 -3.378 -0.513 O1 X7Y 6 X7Y C1 C4 C 0 1 N N N -8.206 20.344 -11.123 3.510 2.493 -2.384 C1 X7Y 7 X7Y C5 C5 C 0 1 Y N N -10.944 26.468 -8.166 -1.547 -1.291 0.239 C5 X7Y 8 X7Y C6 C6 C 0 1 Y N N -11.198 27.055 -6.926 -2.630 -2.105 -0.084 C6 X7Y 9 X7Y N3 N3 N 0 1 N N N -14.308 28.891 -7.620 -5.435 0.177 0.599 N3 X7Y 10 X7Y C4 C7 C 0 1 Y N N -9.495 24.701 -9.234 0.801 -0.926 -0.199 C4 X7Y 11 X7Y C3 C8 C 0 1 Y N N -10.137 23.497 -11.059 3.062 -0.584 -0.488 C3 X7Y 12 X7Y C2 C9 C 0 1 Y N N -8.977 22.691 -10.942 2.806 0.741 -0.852 C2 X7Y 13 X7Y N4 N4 N 0 1 N N N -16.593 30.593 -7.409 -7.598 1.931 0.004 N4 X7Y 14 X7Y N N5 N 0 1 N N N -8.727 21.551 -11.757 3.821 1.603 -1.263 N X7Y 15 X7Y C C10 C 0 1 N N N -8.949 21.489 -13.112 5.037 1.703 -0.747 C X7Y 16 X7Y O O2 O 0 1 N N N -8.715 20.469 -13.734 5.786 2.522 -1.243 O X7Y 17 X7Y C10 C11 C 0 1 N N N -15.171 29.141 -8.775 -6.162 0.068 -0.674 C10 X7Y 18 X7Y C11 C12 C 0 1 N N N -16.580 29.452 -8.319 -7.603 0.543 -0.477 C11 X7Y 19 X7Y C12 C13 C 0 1 N N N -17.962 30.909 -6.996 -8.966 2.449 0.134 C12 X7Y 20 X7Y C13 C14 C 0 1 N N N -15.757 30.299 -6.247 -6.871 2.040 1.277 C13 X7Y 21 X7Y C14 C15 C 0 1 N N N -14.330 30.002 -6.668 -5.429 1.565 1.081 C14 X7Y 22 X7Y C15 C16 C 0 1 Y N N -12.912 27.545 -9.038 -3.050 0.493 0.797 C15 X7Y 23 X7Y C16 C17 C 0 1 Y N N -11.832 26.703 -9.211 -1.762 0.007 0.676 C16 X7Y 24 X7Y C17 C18 C 0 1 Y N N -8.111 23.034 -9.913 1.490 1.181 -0.837 C17 X7Y 25 X7Y C18 C19 C 0 1 N N N -12.425 23.795 -11.779 4.812 -2.171 -1.235 C18 X7Y 26 X7Y C19 C20 C 0 1 Y N N -10.526 23.498 -13.347 5.240 -0.449 0.497 C19 X7Y 27 X7Y C20 C21 C 0 1 Y N N -9.491 22.686 -13.829 5.558 0.909 0.373 C20 X7Y 28 X7Y C21 C22 C 0 1 Y N N -8.926 22.970 -15.071 6.399 1.507 1.316 C21 X7Y 29 X7Y C22 C23 C 0 1 Y N N -9.393 24.037 -15.816 6.932 0.753 2.340 C22 X7Y 30 X7Y C23 C24 C 0 1 Y N N -10.419 24.826 -15.340 6.638 -0.596 2.442 C23 X7Y 31 X7Y C24 C25 C 0 1 Y N N -10.992 24.564 -14.108 5.795 -1.197 1.528 C24 X7Y 32 X7Y N5 N6 N 0 1 Y N N -8.350 24.029 -9.048 0.527 0.332 -0.509 N5 X7Y 33 X7Y N6 N7 N 0 1 N N N -11.085 23.278 -12.057 4.365 -1.054 -0.399 N6 X7Y 34 X7Y H1 H1 H 0 1 N N N -9.822 26.801 -3.928 -4.207 -4.245 0.060 H1 X7Y 35 X7Y H2 H2 H 0 1 N N N -10.598 28.267 -4.617 -4.140 -3.667 -1.622 H2 X7Y 36 X7Y H3 H3 H 0 1 N N N -11.582 26.800 -4.290 -3.272 -5.148 -1.155 H3 X7Y 37 X7Y H4 H4 H 0 1 N N N -12.448 28.365 -5.794 -4.762 -2.245 -0.217 H4 X7Y 38 X7Y H5 H5 H 0 1 N N N -9.189 25.677 -7.520 -0.061 -2.728 0.266 H5 X7Y 39 X7Y H6 H6 H 0 1 N N N -8.073 20.523 -10.046 3.094 3.426 -2.003 H6 X7Y 40 X7Y H7 H7 H 0 1 N N N -8.915 19.516 -11.272 4.421 2.703 -2.945 H7 X7Y 41 X7Y H8 H8 H 0 1 N N N -7.237 20.083 -11.573 2.783 2.012 -3.039 H8 X7Y 42 X7Y H10 H10 H 0 1 N N N -15.186 28.248 -9.417 -5.674 0.688 -1.426 H10 X7Y 43 X7Y H11 H11 H 0 1 N N N -14.777 29.996 -9.345 -6.163 -0.971 -1.004 H11 X7Y 44 X7Y H12 H12 H 0 1 N N N -17.200 29.685 -9.197 -8.100 -0.094 0.255 H12 X7Y 45 X7Y H13 H13 H 0 1 N N N -16.993 28.574 -7.801 -8.137 0.490 -1.427 H13 X7Y 46 X7Y H14 H14 H 0 1 N N N -17.950 31.770 -6.312 -8.931 3.499 0.427 H14 X7Y 47 X7Y H15 H15 H 0 1 N N N -18.565 31.154 -7.883 -9.481 2.356 -0.822 H15 X7Y 48 X7Y H16 H16 H 0 1 N N N -18.400 30.040 -6.483 -9.501 1.878 0.892 H16 X7Y 49 X7Y H17 H17 H 0 1 N N N -15.760 31.168 -5.572 -6.870 3.079 1.607 H17 X7Y 50 X7Y H18 H18 H 0 1 N N N -16.167 29.424 -5.721 -7.359 1.421 2.029 H18 X7Y 51 X7Y H19 H19 H 0 1 N N N -13.737 29.733 -5.781 -4.896 1.618 2.030 H19 X7Y 52 X7Y H20 H20 H 0 1 N N N -13.897 30.895 -7.141 -4.933 2.203 0.349 H20 X7Y 53 X7Y H21 H21 H 0 1 N N N -13.569 27.746 -9.871 -3.215 1.503 1.141 H21 X7Y 54 X7Y H22 H22 H 0 1 N N N -11.675 26.223 -10.165 -0.922 0.638 0.927 H22 X7Y 55 X7Y H23 H23 H 0 1 N N N -7.197 22.469 -9.804 1.253 2.204 -1.089 H23 X7Y 56 X7Y H24 H24 H 0 1 N N N -12.709 23.543 -10.747 4.633 -3.110 -0.712 H24 X7Y 57 X7Y H25 H25 H 0 1 N N N -12.430 24.888 -11.904 4.258 -2.166 -2.174 H25 X7Y 58 X7Y H26 H26 H 0 1 N N N -13.145 23.343 -12.478 5.877 -2.066 -1.441 H26 X7Y 59 X7Y H27 H27 H 0 1 N N N -8.123 22.356 -15.452 6.632 2.559 1.243 H27 X7Y 60 X7Y H28 H28 H 0 1 N N N -8.951 24.254 -16.777 7.583 1.217 3.067 H28 X7Y 61 X7Y H29 H29 H 0 1 N N N -10.778 25.654 -15.933 7.070 -1.182 3.240 H29 X7Y 62 X7Y H30 H30 H 0 1 N N N -11.796 25.184 -13.740 5.568 -2.249 1.614 H30 X7Y 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 X7Y C22 C23 DOUB Y N 1 X7Y C22 C21 SING Y N 2 X7Y C23 C24 SING Y N 3 X7Y C21 C20 DOUB Y N 4 X7Y C24 C19 DOUB Y N 5 X7Y C20 C19 SING Y N 6 X7Y C20 C SING N N 7 X7Y O C DOUB N N 8 X7Y C19 N6 SING N N 9 X7Y C N SING N N 10 X7Y N6 C18 SING N N 11 X7Y N6 C3 SING N N 12 X7Y N C1 SING N N 13 X7Y N C2 SING N N 14 X7Y C3 C2 DOUB Y N 15 X7Y C3 N1 SING Y N 16 X7Y C2 C17 SING Y N 17 X7Y N1 C4 DOUB Y N 18 X7Y C17 N5 DOUB Y N 19 X7Y C4 N5 SING Y N 20 X7Y C4 N2 SING N N 21 X7Y C16 C15 DOUB Y N 22 X7Y C16 C5 SING Y N 23 X7Y C15 C9 SING Y N 24 X7Y C10 C11 SING N N 25 X7Y C10 N3 SING N N 26 X7Y C11 N4 SING N N 27 X7Y N2 C5 SING N N 28 X7Y C5 C6 DOUB Y N 29 X7Y C9 N3 SING N N 30 X7Y C9 C8 DOUB Y N 31 X7Y N3 C14 SING N N 32 X7Y N4 C12 SING N N 33 X7Y N4 C13 SING N N 34 X7Y C6 C8 SING Y N 35 X7Y C6 O1 SING N N 36 X7Y C14 C13 SING N N 37 X7Y O1 C7 SING N N 38 X7Y C7 H1 SING N N 39 X7Y C7 H2 SING N N 40 X7Y C7 H3 SING N N 41 X7Y C8 H4 SING N N 42 X7Y N2 H5 SING N N 43 X7Y C1 H6 SING N N 44 X7Y C1 H7 SING N N 45 X7Y C1 H8 SING N N 46 X7Y C10 H10 SING N N 47 X7Y C10 H11 SING N N 48 X7Y C11 H12 SING N N 49 X7Y C11 H13 SING N N 50 X7Y C12 H14 SING N N 51 X7Y C12 H15 SING N N 52 X7Y C12 H16 SING N N 53 X7Y C13 H17 SING N N 54 X7Y C13 H18 SING N N 55 X7Y C14 H19 SING N N 56 X7Y C14 H20 SING N N 57 X7Y C15 H21 SING N N 58 X7Y C16 H22 SING N N 59 X7Y C17 H23 SING N N 60 X7Y C18 H24 SING N N 61 X7Y C18 H25 SING N N 62 X7Y C18 H26 SING N N 63 X7Y C21 H27 SING N N 64 X7Y C22 H28 SING N N 65 X7Y C23 H29 SING N N 66 X7Y C24 H30 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 X7Y SMILES ACDLabs 12.01 "n3c(Nc2c(cc(N1CCN(C)CC1)cc2)OC)ncc4c3N(C)c5c(C(N4C)=O)cccc5" X7Y InChI InChI 1.03 "InChI=1S/C25H29N7O2/c1-29-11-13-32(14-12-29)17-9-10-19(22(15-17)34-4)27-25-26-16-21-23(28-25)30(2)20-8-6-5-7-18(20)24(33)31(21)3/h5-10,15-16H,11-14H2,1-4H3,(H,26,27,28)" X7Y InChIKey InChI 1.03 DDTPGANIPBKTNU-UHFFFAOYSA-N X7Y SMILES_CANONICAL CACTVS 3.385 "COc1cc(ccc1Nc2ncc3N(C)C(=O)c4ccccc4N(C)c3n2)N5CCN(C)CC5" X7Y SMILES CACTVS 3.385 "COc1cc(ccc1Nc2ncc3N(C)C(=O)c4ccccc4N(C)c3n2)N5CCN(C)CC5" X7Y SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CN1CCN(CC1)c2ccc(c(c2)OC)Nc3ncc4c(n3)N(c5ccccc5C(=O)N4C)C" X7Y SMILES "OpenEye OEToolkits" 2.0.7 "CN1CCN(CC1)c2ccc(c(c2)OC)Nc3ncc4c(n3)N(c5ccccc5C(=O)N4C)C" # # 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 X7Y "SYSTEMATIC NAME" ACDLabs 12.01 "2-{[2-methoxy-4-(4-methylpiperazin-1-yl)phenyl]amino}-5,11-dimethyl-5,11-dihydro-6H-pyrimido[4,5-b][1,4]benzodiazepin-6-one" X7Y "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "2-[[2-methoxy-4-(4-methylpiperazin-1-yl)phenyl]amino]-5,11-dimethyl-pyrimido[4,5-b][1,4]benzodiazepin-6-one" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site X7Y "Create component" 2020-12-03 RCSB X7Y "Initial release" 2021-09-22 RCSB ##