data_VB8
#

_chem_comp.id                                   VB8
_chem_comp.name                                 "4-[(4,4-dimethylpiperidin-1-yl)methyl]-2-methylsulfanyl-~{N}-[[(3~{R})-3-oxidanyl-1-[6-[(phenylmethyl)amino]pyrimidin-4-yl]piperidin-3-yl]methyl]benzamide"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C33 H44 N6 O2 S"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2021-05-04
_chem_comp.pdbx_modified_date                   2021-10-15
_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                       588.806
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    VB8
_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       7OEM
_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
VB8  C10  C1   C  0  1  Y  N  N  -45.710  30.712  23.736   -3.568   1.845  -0.394  C10  VB8   1  
VB8  C15  C2   C  0  1  Y  N  N  -44.785  31.332  24.549   -2.980   1.302   0.751  C15  VB8   2  
VB8  C20  C3   C  0  1  N  N  N  -45.083  36.044  25.702    0.958   2.429  -2.129  C20  VB8   3  
VB8  C21  C4   C  0  1  N  N  N  -44.798  37.312  25.049    1.586   1.032  -2.143  C21  VB8   4  
VB8  C22  C5   C  0  1  N  N  N  -43.310  37.396  24.603    3.095   1.155  -1.920  C22  VB8   5  
VB8  C01  C6   C  0  1  N  N  N  -42.697  23.323  23.798   -8.720  -4.164  -2.252  C01  VB8   6  
VB8  C02  C7   C  0  1  N  N  N  -43.175  24.582  23.032   -8.611  -2.950  -1.327  C02  VB8   7  
VB8  C03  C8   C  0  1  N  N  N  -44.326  24.147  22.067   -9.568  -3.120  -0.145  C03  VB8   8  
VB8  C04  C9   C  0  1  N  N  N  -43.702  25.553  23.934   -7.175  -2.830  -0.809  C04  VB8   9  
VB8  C05  C10  C  0  1  N  N  N  -44.095  26.817  23.141   -7.057  -1.580   0.067  C05  VB8  10  
VB8  C07  C11  C  0  1  N  N  N  -43.434  28.381  21.670   -7.179   0.838   0.046  C07  VB8  11  
VB8  C08  C12  C  0  1  Y  N  N  -43.942  29.442  22.667   -5.702   0.998   0.298  C08  VB8  12  
VB8  C09  C13  C  0  1  Y  N  N  -45.306  29.768  22.797   -4.919   1.691  -0.613  C09  VB8  13  
VB8  C11  C14  C  0  1  Y  N  N  -43.013  30.058  23.468   -5.136   0.447   1.429  C11  VB8  14  
VB8  C12  C15  C  0  1  Y  N  N  -43.453  30.984  24.406   -3.775   0.596   1.669  C12  VB8  15  
VB8  C14  C16  C  0  1  N  N  N  -41.821  33.252  24.408   -4.457  -0.901   3.933  C14  VB8  16  
VB8  C16  C17  C  0  1  N  N  N  -45.198  32.397  25.636   -1.536   1.468   0.993  C16  VB8  17  
VB8  C18  C18  C  0  1  N  N  N  -44.551  34.292  27.314    0.658   2.310   0.350  C18  VB8  18  
VB8  C19  C19  C  0  1  N  N  R  -44.242  35.732  26.826    1.279   3.111  -0.797  C19  VB8  19  
VB8  C23  C20  C  0  1  N  N  N  -42.713  35.911  26.546    2.797   3.173  -0.613  C23  VB8  20  
VB8  C25  C21  C  0  1  Y  N  N  -41.375  38.163  26.201    4.704   1.823  -0.338  C25  VB8  21  
VB8  C27  C22  C  0  1  Y  N  N  -39.971  38.971  27.815    6.620   2.988   0.195  C27  VB8  22  
VB8  C29  C23  C  0  1  Y  N  N  -39.954  40.028  25.757    6.781   0.696   0.013  C29  VB8  23  
VB8  C31  C24  C  0  1  N  N  N  -39.825  41.183  23.451    6.922  -1.761  -0.190  C31  VB8  24  
VB8  C32  C25  C  0  1  Y  N  N  -41.037  42.088  23.160    7.959  -2.847  -0.064  C32  VB8  25  
VB8  C33  C26  C  0  1  Y  N  N  -41.314  42.393  21.832    8.696  -3.231  -1.169  C33  VB8  26  
VB8  C34  C27  C  0  1  Y  N  N  -42.407  43.211  21.498    9.646  -4.228  -1.054  C34  VB8  27  
VB8  C35  C28  C  0  1  Y  N  N  -43.220  43.712  22.512    9.861  -4.841   0.166  C35  VB8  28  
VB8  C36  C29  C  0  1  Y  N  N  -42.948  43.416  23.836    9.125  -4.456   1.271  C36  VB8  29  
VB8  C37  C30  C  0  1  Y  N  N  -41.845  42.593  24.172    8.178  -3.456   1.158  C37  VB8  30  
VB8  C38  C31  C  0  1  Y  N  N  -40.929  39.140  25.302    5.425   0.633  -0.292  C38  VB8  31  
VB8  C41  C32  C  0  1  N  N  N  -42.357  26.448  21.568   -8.804  -0.465  -1.189  C41  VB8  32  
VB8  C42  C33  C  0  1  N  N  N  -42.049  25.136  22.317   -8.974  -1.681  -2.102  C42  VB8  33  
VB8  N06  N1   N  0  1  N  N  N  -43.017  27.417  22.385   -7.413  -0.393  -0.721  N06  VB8  34  
VB8  N17  N2   N  0  1  N  N  N  -44.175  33.271  26.266   -0.778   2.145   0.109  N17  VB8  35  
VB8  N24  N3   N  0  1  N  N  N  -42.391  37.192  25.780    3.350   1.813  -0.632  N24  VB8  36  
VB8  N26  N4   N  0  1  Y  N  N  -40.899  38.099  27.424    5.333   2.970  -0.090  N26  VB8  37  
VB8  N28  N5   N  0  1  Y  N  N  -39.514  39.914  26.994    7.337   1.884   0.248  N28  VB8  38  
VB8  N30  N6   N  0  1  N  N  N  -39.427  41.093  24.884    7.544  -0.460   0.071  N30  VB8  39  
VB8  O39  O1   O  0  1  N  N  N  -44.538  36.571  27.940    0.743   4.436  -0.798  O39  VB8  40  
VB8  O40  O2   O  0  1  N  N  N  -46.323  32.481  26.001   -1.029   0.993   1.991  O40  VB8  41  
VB8  S13  S1   S  0  1  N  N  N  -42.296  31.822  25.437   -3.048  -0.107   3.112  S13  VB8  42  
VB8  H1   H1   H  0  1  N  N  N  -46.757  30.961  23.829   -2.964   2.389  -1.105  H1   VB8  43  
VB8  H2   H2   H  0  1  N  N  N  -46.125  36.069  26.053    1.367   3.020  -2.949  H2   VB8  44  
VB8  H3   H3   H  0  1  N  N  N  -44.966  35.243  24.957   -0.122   2.345  -2.245  H3   VB8  45  
VB8  H4   H4   H  0  1  N  N  N  -45.008  38.132  25.751    1.149   0.429  -1.347  H4   VB8  46  
VB8  H5   H5   H  0  1  N  N  N  -45.444  37.412  24.164    1.397   0.558  -3.105  H5   VB8  47  
VB8  H6   H6   H  0  1  N  N  N  -43.113  36.617  23.852    3.543   0.161  -1.915  H6   VB8  48  
VB8  H7   H7   H  0  1  N  N  N  -43.120  38.386  24.163    3.534   1.746  -2.723  H7   VB8  49  
VB8  H8   H8   H  0  1  N  N  N  -41.885  23.599  24.487   -8.456  -5.066  -1.701  H8   VB8  50  
VB8  H9   H9   H  0  1  N  N  N  -43.536  22.902  24.371   -9.743  -4.249  -2.620  H9   VB8  51  
VB8  H10  H10  H  0  1  N  N  N  -42.331  22.574  23.080   -8.040  -4.041  -3.095  H10  VB8  52  
VB8  H11  H11  H  0  1  N  N  N  -45.160  23.733  22.653   -9.306  -4.023   0.407  H11  VB8  53  
VB8  H12  H12  H  0  1  N  N  N  -44.677  25.020  21.498   -9.489  -2.255   0.514  H12  VB8  54  
VB8  H13  H13  H  0  1  N  N  N  -43.951  23.382  21.371  -10.590  -3.204  -0.514  H13  VB8  55  
VB8  H14  H14  H  0  1  N  N  N  -44.590  25.144  24.439   -6.925  -3.712  -0.220  H14  VB8  56  
VB8  H15  H15  H  0  1  N  N  N  -42.940  25.811  24.684   -6.489  -2.750  -1.653  H15  VB8  57  
VB8  H16  H16  H  0  1  N  N  N  -44.471  27.565  23.854   -7.732  -1.668   0.918  H16  VB8  58  
VB8  H17  H17  H  0  1  N  N  N  -44.896  26.545  22.438   -6.032  -1.483   0.425  H17  VB8  59  
VB8  H18  H18  H  0  1  N  N  N  -42.615  28.788  21.058   -7.706   0.778   0.998  H18  VB8  60  
VB8  H19  H19  H  0  1  N  N  N  -44.251  28.048  21.014   -7.546   1.694  -0.520  H19  VB8  61  
VB8  H20  H20  H  0  1  N  N  N  -46.039  29.285  22.168   -5.372   2.112  -1.499  H20  VB8  62  
VB8  H21  H21  H  0  1  N  N  N  -41.962  29.828  23.371   -5.751  -0.098   2.129  H21  VB8  63  
VB8  H22  H22  H  0  1  N  N  N  -41.087  33.867  24.950   -5.211  -0.149   4.168  H22  VB8  64  
VB8  H23  H23  H  0  1  N  N  N  -41.376  32.895  23.467   -4.887  -1.653   3.272  H23  VB8  65  
VB8  H24  H24  H  0  1  N  N  N  -42.713  33.856  24.186   -4.120  -1.377   4.854  H24  VB8  66  
VB8  H25  H25  H  0  1  N  N  N  -45.627  34.208  27.528    1.132   1.330   0.407  H25  VB8  67  
VB8  H26  H26  H  0  1  N  N  N  -43.978  34.093  28.232    0.810   2.842   1.289  H26  VB8  68  
VB8  H27  H27  H  0  1  N  N  N  -42.362  35.052  25.955    3.237   3.756  -1.422  H27  VB8  69  
VB8  H28  H28  H  0  1  N  N  N  -42.181  35.935  27.509    3.028   3.645   0.342  H28  VB8  70  
VB8  H29  H29  H  0  1  N  N  N  -39.581  38.912  28.820    7.100   3.935   0.391  H29  VB8  71  
VB8  H30  H30  H  0  1  N  N  N  -40.067  40.169  23.101    6.507  -1.770  -1.197  H30  VB8  72  
VB8  H31  H31  H  0  1  N  N  N  -38.967  41.572  22.884    6.125  -1.934   0.533  H31  VB8  73  
VB8  H32  H32  H  0  1  N  N  N  -40.683  41.998  21.050    8.528  -2.752  -2.123  H32  VB8  74  
VB8  H33  H33  H  0  1  N  N  N  -42.615  43.449  20.465   10.221  -4.528  -1.918  H33  VB8  75  
VB8  H34  H34  H  0  1  N  N  N  -44.067  44.335  22.264   10.604  -5.620   0.256  H34  VB8  76  
VB8  H35  H35  H  0  1  N  N  N  -43.579  43.814  24.617    9.293  -4.935   2.225  H35  VB8  77  
VB8  H36  H36  H  0  1  N  N  N  -41.634  42.360  25.205    7.606  -3.153   2.022  H36  VB8  78  
VB8  H37  H37  H  0  1  N  N  N  -41.323  39.203  24.299    4.945  -0.314  -0.488  H37  VB8  79  
VB8  H38  H38  H  0  1  N  N  N  -41.410  26.878  21.211   -9.047   0.442  -1.743  H38  VB8  80  
VB8  H39  H39  H  0  1  N  N  N  -43.003  26.217  20.708   -9.471  -0.558  -0.332  H39  VB8  81  
VB8  H40  H40  H  0  1  N  N  N  -41.707  24.392  21.582   -8.316  -1.582  -2.966  H40  VB8  82  
VB8  H41  H41  H  0  1  N  N  N  -41.244  25.333  23.041  -10.009  -1.742  -2.437  H41  VB8  83  
VB8  H43  H43  H  0  1  N  N  N  -43.218  33.182  25.991   -1.182   2.524  -0.687  H43  VB8  84  
VB8  H44  H44  H  0  1  N  N  N  -38.431  41.003  24.897    8.488  -0.408   0.285  H44  VB8  85  
VB8  H45  H45  H  0  1  N  N  N  -43.970  36.345  28.667   -0.216   4.472  -0.913  H45  VB8  86  
#   #
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
VB8  C34  C33  DOUB  Y  N   1  
VB8  C34  C35  SING  Y  N   2  
VB8  C41  C42  SING  N  N   3  
VB8  C41  N06  SING  N  N   4  
VB8  C07  N06  SING  N  N   5  
VB8  C07  C08  SING  N  N   6  
VB8  C33  C32  SING  Y  N   7  
VB8  C03  C02  SING  N  N   8  
VB8  C42  C02  SING  N  N   9  
VB8  N06  C05  SING  N  N  10  
VB8  C35  C36  DOUB  Y  N  11  
VB8  C08  C09  DOUB  Y  N  12  
VB8  C08  C11  SING  Y  N  13  
VB8  C09  C10  SING  Y  N  14  
VB8  C02  C01  SING  N  N  15  
VB8  C02  C04  SING  N  N  16  
VB8  C05  C04  SING  N  N  17  
VB8  C32  C31  SING  N  N  18  
VB8  C32  C37  DOUB  Y  N  19  
VB8  C31  N30  SING  N  N  20  
VB8  C11  C12  DOUB  Y  N  21  
VB8  C10  C15  DOUB  Y  N  22  
VB8  C36  C37  SING  Y  N  23  
VB8  C12  C15  SING  Y  N  24  
VB8  C12  S13  SING  N  N  25  
VB8  C14  S13  SING  N  N  26  
VB8  C15  C16  SING  N  N  27  
VB8  C22  C21  SING  N  N  28  
VB8  C22  N24  SING  N  N  29  
VB8  N30  C29  SING  N  N  30  
VB8  C21  C20  SING  N  N  31  
VB8  C38  C29  DOUB  Y  N  32  
VB8  C38  C25  SING  Y  N  33  
VB8  C16  O40  DOUB  N  N  34  
VB8  C16  N17  SING  N  N  35  
VB8  C20  C19  SING  N  N  36  
VB8  C29  N28  SING  Y  N  37  
VB8  N24  C25  SING  N  N  38  
VB8  N24  C23  SING  N  N  39  
VB8  C25  N26  DOUB  Y  N  40  
VB8  N17  C18  SING  N  N  41  
VB8  C23  C19  SING  N  N  42  
VB8  C19  C18  SING  N  N  43  
VB8  C19  O39  SING  N  N  44  
VB8  N28  C27  DOUB  Y  N  45  
VB8  N26  C27  SING  Y  N  46  
VB8  C10  H1   SING  N  N  47  
VB8  C20  H2   SING  N  N  48  
VB8  C20  H3   SING  N  N  49  
VB8  C21  H4   SING  N  N  50  
VB8  C21  H5   SING  N  N  51  
VB8  C22  H6   SING  N  N  52  
VB8  C22  H7   SING  N  N  53  
VB8  C01  H8   SING  N  N  54  
VB8  C01  H9   SING  N  N  55  
VB8  C01  H10  SING  N  N  56  
VB8  C03  H11  SING  N  N  57  
VB8  C03  H12  SING  N  N  58  
VB8  C03  H13  SING  N  N  59  
VB8  C04  H14  SING  N  N  60  
VB8  C04  H15  SING  N  N  61  
VB8  C05  H16  SING  N  N  62  
VB8  C05  H17  SING  N  N  63  
VB8  C07  H18  SING  N  N  64  
VB8  C07  H19  SING  N  N  65  
VB8  C09  H20  SING  N  N  66  
VB8  C11  H21  SING  N  N  67  
VB8  C14  H22  SING  N  N  68  
VB8  C14  H23  SING  N  N  69  
VB8  C14  H24  SING  N  N  70  
VB8  C18  H25  SING  N  N  71  
VB8  C18  H26  SING  N  N  72  
VB8  C23  H27  SING  N  N  73  
VB8  C23  H28  SING  N  N  74  
VB8  C27  H29  SING  N  N  75  
VB8  C31  H30  SING  N  N  76  
VB8  C31  H31  SING  N  N  77  
VB8  C33  H32  SING  N  N  78  
VB8  C34  H33  SING  N  N  79  
VB8  C35  H34  SING  N  N  80  
VB8  C36  H35  SING  N  N  81  
VB8  C37  H36  SING  N  N  82  
VB8  C38  H37  SING  N  N  83  
VB8  C41  H38  SING  N  N  84  
VB8  C41  H39  SING  N  N  85  
VB8  C42  H40  SING  N  N  86  
VB8  C42  H41  SING  N  N  87  
VB8  N17  H43  SING  N  N  88  
VB8  N30  H44  SING  N  N  89  
VB8  O39  H45  SING  N  N  90  
#   #
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
VB8  InChI             InChI                 1.03   "InChI=1S/C33H44N6O2S/c1-32(2)13-16-38(17-14-32)21-26-10-11-27(28(18-26)42-3)31(40)35-22-33(41)12-7-15-39(23-33)30-19-29(36-24-37-30)34-20-25-8-5-4-6-9-25/h4-6,8-11,18-19,24,41H,7,12-17,20-23H2,1-3H3,(H,35,40)(H,34,36,37)/t33-/m1/s1"  
VB8  InChIKey          InChI                 1.03   CGGPQJWTZLKAFY-MGBGTMOVSA-N  
VB8  SMILES_CANONICAL  CACTVS                3.385  "CSc1cc(CN2CCC(C)(C)CC2)ccc1C(=O)NC[C@]3(O)CCCN(C3)c4cc(NCc5ccccc5)ncn4"  
VB8  SMILES            CACTVS                3.385  "CSc1cc(CN2CCC(C)(C)CC2)ccc1C(=O)NC[C]3(O)CCCN(C3)c4cc(NCc5ccccc5)ncn4"  
VB8  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "CC1(CCN(CC1)Cc2ccc(c(c2)SC)C(=O)NC[C@@]3(CCCN(C3)c4cc(ncn4)NCc5ccccc5)O)C"  
VB8  SMILES            "OpenEye OEToolkits"  2.0.7  "CC1(CCN(CC1)Cc2ccc(c(c2)SC)C(=O)NCC3(CCCN(C3)c4cc(ncn4)NCc5ccccc5)O)C"  
#
_pdbx_chem_comp_identifier.comp_id          VB8
_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       "4-[(4,4-dimethylpiperidin-1-yl)methyl]-2-methylsulfanyl-~{N}-[[(3~{R})-3-oxidanyl-1-[6-[(phenylmethyl)amino]pyrimidin-4-yl]piperidin-3-yl]methyl]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
VB8  "Create component"  2021-05-04  PDBE  
VB8  "Initial release"   2021-10-20  RCSB  
##
