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  
##
