data_YD8
#

_chem_comp.id                                   YD8
_chem_comp.name                                 "1-[2,4-dimethyl-5-[5-(4-methylpiperazin-1-yl)-1H-benzimidazol-2-yl]-1H-pyrrol-3-yl]ethanone"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C20 H25 N5 O"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2021-04-06
_chem_comp.pdbx_modified_date                   2022-03-25
_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                       351.445
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    YD8
_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       7EHY
_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.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
YD8  C1   C1   C  0  1  Y  N  N  28.461  30.724  41.908  -1.865  -0.359  -0.304  C1   YD8   1  
YD8  C11  C2   C  0  1  N  N  N  32.424  30.205  43.071  -5.842  -1.822   0.361  C11  YD8   2  
YD8  C12  C3   C  0  1  N  N  N  31.080  30.928  43.221  -4.477  -1.172   0.597  C12  YD8   3  
YD8  C13  C4   C  0  1  N  N  N  34.734  30.897  42.914  -8.225  -1.393   0.293  C13  YD8   4  
YD8  C15  C5   C  0  1  Y  N  N  25.171  30.582  40.656   1.531   0.665   0.004  C15  YD8   5  
YD8  C17  C6   C  0  1  Y  N  N  23.790  30.025  40.673   2.992   0.487   0.060  C17  YD8   6  
YD8  C18  C7   C  0  1  Y  N  N  22.597  30.573  39.985   3.654  -0.695  -0.056  C18  YD8   7  
YD8  C19  C8   C  0  1  Y  N  N  21.599  29.534  40.405   5.039  -0.408   0.055  C19  YD8   8  
YD8  C2   C9   C  0  1  Y  N  N  27.191  30.770  41.334  -0.596   0.212  -0.165  C2   YD8   9  
YD8  C20  C10  C  0  1  Y  N  N  22.278  28.560  41.295   5.153   0.960   0.237  C20  YD8  10  
YD8  C22  C11  C  0  1  N  N  N  21.655  27.364  41.956   6.441   1.723   0.405  C22  YD8  11  
YD8  C23  C12  C  0  1  N  N  N  20.138  29.465  40.150   6.138  -1.374  -0.010  C23  YD8  12  
YD8  C24  C13  C  0  1  N  N  N  19.473  30.809  40.147   6.828  -1.644  -1.322  C24  YD8  13  
YD8  C26  C14  C  0  1  N  N  N  22.519  31.806  39.102   3.034  -2.053  -0.264  C26  YD8  14  
YD8  C3   C15  C  0  1  Y  N  N  26.892  31.715  40.232  -0.478   1.602   0.014  C3   YD8  15  
YD8  C4   C16  C  0  1  Y  N  N  27.914  32.537  39.811  -1.614   2.396   0.051  C4   YD8  16  
YD8  C5   C17  C  0  1  Y  N  N  29.164  32.469  40.413  -2.860   1.823  -0.087  C5   YD8  17  
YD8  C6   C18  C  0  1  Y  N  N  29.452  31.581  41.442  -2.987   0.447  -0.270  C6   YD8  18  
YD8  C8   C19  C  0  1  N  N  N  31.767  32.302  41.177  -5.306   0.905  -0.331  C8   YD8  19  
YD8  C9   C20  C  0  1  N  N  N  33.044  32.308  42.004  -6.671   0.254  -0.567  C9   YD8  20  
YD8  N10  N1   N  0  1  N  N  N  33.428  30.912  42.245  -6.891  -0.795   0.438  N10  YD8  21  
YD8  N14  N2   N  0  1  Y  N  N  25.608  31.559  39.856   0.878   1.864   0.119  N14  YD8  22  
YD8  N16  N3   N  0  1  Y  N  N  26.049  30.095  41.559   0.658  -0.302  -0.162  N16  YD8  23  
YD8  N21  N4   N  0  1  Y  N  N  23.573  28.908  41.381   3.918   1.490   0.233  N21  YD8  24  
YD8  N7   N5   N  0  1  N  N  N  30.755  31.591  41.957  -4.257  -0.122  -0.408  N7   YD8  25  
YD8  O25  O1   O  0  1  N  N  N  19.499  28.439  40.069   6.494  -1.957   0.993  O25  YD8  26  
YD8  H1   H1   H  0  1  N  N  N  28.673  30.029  42.707  -1.967  -1.426  -0.442  H1   YD8  27  
YD8  H2   H2   H  0  1  N  N  N  32.234  29.224  42.611  -5.859  -2.286  -0.625  H2   YD8  28  
YD8  H3   H3   H  0  1  N  N  N  32.848  30.063  44.076  -6.020  -2.581   1.123  H3   YD8  29  
YD8  H4   H4   H  0  1  N  N  N  31.151  31.677  44.023  -4.451  -0.732   1.594  H4   YD8  30  
YD8  H5   H5   H  0  1  N  N  N  30.294  30.199  43.468  -3.695  -1.926   0.512  H5   YD8  31  
YD8  H6   H6   H  0  1  N  N  N  35.038  29.857  43.103  -8.319  -1.834  -0.700  H6   YD8  32  
YD8  H7   H7   H  0  1  N  N  N  35.481  31.386  42.271  -8.361  -2.166   1.049  H7   YD8  33  
YD8  H8   H8   H  0  1  N  N  N  34.663  31.437  43.870  -8.984  -0.622   0.421  H8   YD8  34  
YD8  H9   H9   H  0  1  N  N  N  21.729  26.494  41.287   6.806   2.040  -0.572  H9   YD8  35  
YD8  H10  H10  H  0  1  N  N  N  22.183  27.149  42.897   6.265   2.600   1.029  H10  YD8  36  
YD8  H11  H11  H  0  1  N  N  N  20.596  27.573  42.169   7.184   1.082   0.880  H11  YD8  37  
YD8  H12  H12  H  0  1  N  N  N  18.384  30.680  40.064   6.436  -0.971  -2.084  H12  YD8  38  
YD8  H13  H13  H  0  1  N  N  N  19.709  31.337  41.083   7.900  -1.481  -1.210  H13  YD8  39  
YD8  H14  H14  H  0  1  N  N  N  19.839  31.397  39.292   6.647  -2.677  -1.622  H14  YD8  40  
YD8  H15  H15  H  0  1  N  N  N  22.270  32.683  39.717   2.829  -2.511   0.703  H15  YD8  41  
YD8  H16  H16  H  0  1  N  N  N  23.490  31.967  38.610   2.102  -1.946  -0.820  H16  YD8  42  
YD8  H17  H17  H  0  1  N  N  N  21.740  31.661  38.338   3.722  -2.684  -0.827  H17  YD8  43  
YD8  H18  H18  H  0  1  N  N  N  27.742  33.239  39.008  -1.523   3.463   0.189  H18  YD8  44  
YD8  H19  H19  H  0  1  N  N  N  29.943  33.133  40.067  -3.743   2.444  -0.057  H19  YD8  45  
YD8  H20  H20  H  0  1  N  N  N  31.939  31.786  40.221  -5.128   1.663  -1.093  H20  YD8  46  
YD8  H21  H21  H  0  1  N  N  N  31.438  33.334  40.983  -5.289   1.368   0.655  H21  YD8  47  
YD8  H22  H22  H  0  1  N  N  N  33.843  32.827  41.455  -7.453   1.009  -0.481  H22  YD8  48  
YD8  H23  H23  H  0  1  N  N  N  32.867  32.818  42.962  -6.698  -0.186  -1.564  H23  YD8  49  
YD8  H25  H25  H  0  1  N  N  N  25.104  32.055  39.149   1.288   2.733   0.248  H25  YD8  50  
YD8  H27  H27  H  0  1  N  N  N  24.270  28.409  41.896   3.712   2.432   0.338  H27  YD8  51  
#   #
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
YD8  C26  C18  SING  N  N   1  
YD8  C4   C3   DOUB  Y  N   2  
YD8  C4   C5   SING  Y  N   3  
YD8  N14  C3   SING  Y  N   4  
YD8  N14  C15  SING  Y  N   5  
YD8  C18  C19  SING  Y  N   6  
YD8  C18  C17  DOUB  Y  N   7  
YD8  O25  C23  DOUB  N  N   8  
YD8  C24  C23  SING  N  N   9  
YD8  C23  C19  SING  N  N  10  
YD8  C3   C2   SING  Y  N  11  
YD8  C19  C20  DOUB  Y  N  12  
YD8  C5   C6   DOUB  Y  N  13  
YD8  C15  C17  SING  N  N  14  
YD8  C15  N16  DOUB  Y  N  15  
YD8  C17  N21  SING  Y  N  16  
YD8  C8   N7   SING  N  N  17  
YD8  C8   C9   SING  N  N  18  
YD8  C20  N21  SING  Y  N  19  
YD8  C20  C22  SING  N  N  20  
YD8  C2   N16  SING  Y  N  21  
YD8  C2   C1   DOUB  Y  N  22  
YD8  C6   C1   SING  Y  N  23  
YD8  C6   N7   SING  N  N  24  
YD8  N7   C12  SING  N  N  25  
YD8  C9   N10  SING  N  N  26  
YD8  N10  C13  SING  N  N  27  
YD8  N10  C11  SING  N  N  28  
YD8  C11  C12  SING  N  N  29  
YD8  C1   H1   SING  N  N  30  
YD8  C11  H2   SING  N  N  31  
YD8  C11  H3   SING  N  N  32  
YD8  C12  H4   SING  N  N  33  
YD8  C12  H5   SING  N  N  34  
YD8  C13  H6   SING  N  N  35  
YD8  C13  H7   SING  N  N  36  
YD8  C13  H8   SING  N  N  37  
YD8  C22  H9   SING  N  N  38  
YD8  C22  H10  SING  N  N  39  
YD8  C22  H11  SING  N  N  40  
YD8  C24  H12  SING  N  N  41  
YD8  C24  H13  SING  N  N  42  
YD8  C24  H14  SING  N  N  43  
YD8  C26  H15  SING  N  N  44  
YD8  C26  H16  SING  N  N  45  
YD8  C26  H17  SING  N  N  46  
YD8  C4   H18  SING  N  N  47  
YD8  C5   H19  SING  N  N  48  
YD8  C8   H20  SING  N  N  49  
YD8  C8   H21  SING  N  N  50  
YD8  C9   H22  SING  N  N  51  
YD8  C9   H23  SING  N  N  52  
YD8  N14  H25  SING  N  N  53  
YD8  N21  H27  SING  N  N  54  
#   #
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
YD8  InChI             InChI                 1.03   "InChI=1S/C20H25N5O/c1-12-18(14(3)26)13(2)21-19(12)20-22-16-6-5-15(11-17(16)23-20)25-9-7-24(4)8-10-25/h5-6,11,21H,7-10H2,1-4H3,(H,22,23)"  
YD8  InChIKey          InChI                 1.03   AESBJGGTJKBCMI-UHFFFAOYSA-N  
YD8  SMILES_CANONICAL  CACTVS                3.385  "CN1CCN(CC1)c2ccc3[nH]c(nc3c2)c4[nH]c(C)c(C(C)=O)c4C"  
YD8  SMILES            CACTVS                3.385  "CN1CCN(CC1)c2ccc3[nH]c(nc3c2)c4[nH]c(C)c(C(C)=O)c4C"  
YD8  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "Cc1c(c([nH]c1c2[nH]c3ccc(cc3n2)N4CCN(CC4)C)C)C(=O)C"  
YD8  SMILES            "OpenEye OEToolkits"  2.0.7  "Cc1c(c([nH]c1c2[nH]c3ccc(cc3n2)N4CCN(CC4)C)C)C(=O)C"  
#
_pdbx_chem_comp_identifier.comp_id          YD8
_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       "1-[2,4-dimethyl-5-[5-(4-methylpiperazin-1-yl)-1~{H}-benzimidazol-2-yl]-1~{H}-pyrrol-3-yl]ethanone"
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
YD8  "Create component"  2021-04-06  PDBJ  
YD8  "Initial release"   2022-03-30  RCSB  
##
