data_P62
#

_chem_comp.id                                   P62
_chem_comp.name                                 "5-[(4-chlorophenyl)methyl]-6-[[2-(dimethylamino)ethylamino]methyl]-4-oxidanyl-1~{H}-pyrimidine-2-thione"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C16 H21 Cl N4 O S"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2020-12-02
_chem_comp.pdbx_modified_date                   2021-11-05
_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                       352.882
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    P62
_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       7B4S
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 PDBE
#   #
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
P62  N    N1   N   0  1  N  N  N  24.183  13.544  46.753  -0.665   3.409  -0.449  N    P62   1  
P62  C    C1   C   0  1  N  N  N  25.604  11.947  44.981   0.604   1.070   0.114  C    P62   2  
P62  O    O1   O   0  1  N  N  N  25.604  13.001  48.415  -1.979   2.373  -2.055  O    P62   3  
P62  C1   C2   C   0  1  N  N  N  26.013  11.973  46.303  -0.363   1.098  -0.834  C1   P62   4  
P62  C10  C3   C   0  1  Y  N  N  27.027  10.152  49.092  -3.203  -0.479  -1.269  C10  P62   5  
P62  C11  C4   C   0  1  N  N  N  26.315  11.348  43.874   1.317  -0.218   0.437  C11  P62   6  
P62  C12  C5   C   0  1  N  N  N  26.115  11.588  41.556   3.458  -1.346   0.350  C12  P62   7  
P62  C13  C6   C   0  1  N  N  N  27.483  11.120  41.091   4.922  -1.192  -0.067  C13  P62   8  
P62  C14  C7   C   0  1  N  N  N  26.832   8.907  40.277   5.165  -3.542  -0.597  C14  P62   9  
P62  C15  C8   C   0  1  N  N  N  26.797  10.771  38.759   7.098  -2.245   0.069  C15  P62  10  
P62  C2   C9   C   0  1  N  N  N  25.220  12.860  47.147  -1.010   2.318  -1.113  C2   P62  11  
P62  C3   C10  C   0  1  N  N  N  23.794  13.446  45.462   0.288   3.368   0.481  C3   P62  12  
P62  C4   C11  C   0  1  N  N  N  27.185  11.147  46.778  -0.741  -0.156  -1.580  C4   P62  13  
P62  C5   C12  C   0  1  Y  N  N  26.844  10.013  47.721  -1.914  -0.812  -0.897  C5   P62  14  
P62  C6   C13  C   0  1  Y  N  N  26.268   8.839  47.245  -1.700  -1.745   0.100  C6   P62  15  
P62  C7   C14  C   0  1  Y  N  N  25.829   7.855  48.117  -2.775  -2.346   0.726  C7   P62  16  
P62  C8   C15  C   0  1  Y  N  N  25.981   8.048  49.476  -4.066  -2.014   0.355  C8   P62  17  
P62  C9   C16  C   0  1  Y  N  N  26.598   9.175  49.973  -4.280  -1.080  -0.643  C9   P62  18  
P62  N1   N2   N   0  1  N  N  N  24.492  12.664  44.583   0.926   2.219   0.771  N1   P62  19  
P62  N2   N3   N   0  1  N  N  N  25.741  10.947  42.816   2.730  -0.106   0.049  N2   P62  20  
P62  N3   N4   N   0  1  N  N  N  27.440  10.196  39.943   5.650  -2.432   0.233  N3   P62  21  
P62  S    S1   S   0  1  N  N  N  22.404  14.229  44.889   0.709   4.799   1.321  S    P62  22  
P62  CL   CL1  CL  0  0  N  N  N  25.332   6.870  50.586  -5.417  -2.769   1.141  CL   P62  23  
P62  H1   H1   H   0  1  N  N  N  25.026  13.614  48.855  -2.362   3.253  -2.174  H1   P62  24  
P62  H7   H2   H   0  1  N  N  N  27.512  11.037  49.476  -3.370   0.253  -2.045  H7   P62  25  
P62  H8   H3   H   0  1  N  N  N  26.834  10.471  44.287   1.249  -0.412   1.507  H8   P62  26  
P62  H19  H4   H   0  1  N  N  N  27.056  12.094  43.552   0.853  -1.038  -0.112  H19  P62  27  
P62  H9   H5   H   0  1  N  N  N  26.138  12.678  41.700   3.009  -2.174  -0.199  H9   P62  28  
P62  H10  H6   H   0  1  N  N  N  25.369  11.335  40.789   3.404  -1.549   1.419  H10  P62  29  
P62  H12  H7   H   0  1  N  N  N  27.977  10.608  41.930   4.975  -0.990  -1.137  H12  P62  30  
P62  H11  H8   H   0  1  N  N  N  28.072  12.003  40.803   5.371  -0.364   0.482  H11  P62  31  
P62  H13  H9   H   0  1  N  N  N  27.325   8.488  41.167   5.671  -4.462  -0.306  H13  P62  32  
P62  H14  H10  H   0  1  N  N  N  25.761   9.049  40.484   4.090  -3.658  -0.457  H14  P62  33  
P62  H15  H11  H   0  1  N  N  N  26.953   8.214  39.431   5.373  -3.329  -1.646  H15  P62  34  
P62  H16  H12  H   0  1  N  N  N  27.264  11.738  38.521   7.312  -1.954  -0.959  H16  P62  35  
P62  H18  H13  H   0  1  N  N  N  26.918  10.086  37.907   7.442  -1.464   0.747  H18  P62  36  
P62  H17  H14  H   0  1  N  N  N  25.726  10.921  38.960   7.613  -3.178   0.298  H17  P62  37  
P62  H3   H15  H   0  1  N  N  N  27.676  10.716  45.893  -1.012   0.098  -2.604  H3   P62  38  
P62  H2   H16  H   0  1  N  N  N  27.886  11.819  47.295   0.105  -0.843  -1.587  H2   P62  39  
P62  H4   H17  H   0  1  N  N  N  26.161   8.692  46.180  -0.692  -2.004   0.389  H4   P62  40  
P62  H5   H18  H   0  1  N  N  N  25.375   6.951  47.739  -2.608  -3.076   1.505  H5   P62  41  
P62  H6   H19  H   0  1  N  N  N  26.745   9.294  51.036  -5.287  -0.817  -0.930  H6   P62  42  
P62  H    H20  H   0  1  N  N  N  24.191  12.610  43.631   1.617   2.209   1.452  H    P62  43  
P62  H20  H21  H   0  1  N  N  N  24.758  11.082  42.940   3.166   0.687   0.495  H20  P62  44  
#   #
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
P62  C15  N3   SING  N  N   1  
P62  N3   C14  SING  N  N   2  
P62  N3   C13  SING  N  N   3  
P62  C13  C12  SING  N  N   4  
P62  C12  N2   SING  N  N   5  
P62  N2   C11  SING  N  N   6  
P62  C11  C    SING  N  N   7  
P62  N1   C    SING  N  N   8  
P62  N1   C3   SING  N  N   9  
P62  S    C3   DOUB  N  N  10  
P62  C    C1   DOUB  N  N  11  
P62  C3   N    SING  N  N  12  
P62  C1   C4   SING  N  N  13  
P62  C1   C2   SING  N  N  14  
P62  N    C2   DOUB  N  N  15  
P62  C4   C5   SING  N  N  16  
P62  C2   O    SING  N  N  17  
P62  C6   C5   DOUB  Y  N  18  
P62  C6   C7   SING  Y  N  19  
P62  C5   C10  SING  Y  N  20  
P62  C7   C8   DOUB  Y  N  21  
P62  C10  C9   DOUB  Y  N  22  
P62  C8   C9   SING  Y  N  23  
P62  C8   CL   SING  N  N  24  
P62  O    H1   SING  N  N  25  
P62  C10  H7   SING  N  N  26  
P62  C11  H8   SING  N  N  27  
P62  C11  H19  SING  N  N  28  
P62  C12  H9   SING  N  N  29  
P62  C12  H10  SING  N  N  30  
P62  C13  H12  SING  N  N  31  
P62  C13  H11  SING  N  N  32  
P62  C14  H13  SING  N  N  33  
P62  C14  H14  SING  N  N  34  
P62  C14  H15  SING  N  N  35  
P62  C15  H16  SING  N  N  36  
P62  C15  H18  SING  N  N  37  
P62  C15  H17  SING  N  N  38  
P62  C4   H3   SING  N  N  39  
P62  C4   H2   SING  N  N  40  
P62  C6   H4   SING  N  N  41  
P62  C7   H5   SING  N  N  42  
P62  C9   H6   SING  N  N  43  
P62  N1   H    SING  N  N  44  
P62  N2   H20  SING  N  N  45  
#   #
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
P62  InChI             InChI                 1.03   "InChI=1S/C16H21ClN4OS/c1-21(2)8-7-18-10-14-13(15(22)20-16(23)19-14)9-11-3-5-12(17)6-4-11/h3-6,18H,7-10H2,1-2H3,(H2,19,20,22,23)"  
P62  InChIKey          InChI                 1.03   BODROOXVZKSZLI-UHFFFAOYSA-N  
P62  SMILES_CANONICAL  CACTVS                3.385  "CN(C)CCNCC1=C(Cc2ccc(Cl)cc2)C(=NC(=S)N1)O"  
P62  SMILES            CACTVS                3.385  "CN(C)CCNCC1=C(Cc2ccc(Cl)cc2)C(=NC(=S)N1)O"  
P62  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "CN(C)CCNCC1=C(C(=NC(=S)N1)O)Cc2ccc(cc2)Cl"  
P62  SMILES            "OpenEye OEToolkits"  2.0.7  "CN(C)CCNCC1=C(C(=NC(=S)N1)O)Cc2ccc(cc2)Cl"  
#
_pdbx_chem_comp_identifier.comp_id          P62
_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       "5-[(4-chlorophenyl)methyl]-6-[[2-(dimethylamino)ethylamino]methyl]-4-oxidanyl-1~{H}-pyrimidine-2-thione"
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
P62  "Create component"  2020-12-02  PDBE  
P62  "Initial release"   2021-11-10  RCSB  
##
