data_VB2
#

_chem_comp.id                                   VB2
_chem_comp.name                                 "4-[(4,4-dimethylpiperidin-1-yl)methyl]-~{N}-[[(3~{S})-1-[6-(methylamino)pyrimidin-4-yl]-3-oxidanyl-piperidin-3-yl]methyl]-2-oxidanyl-benzamide"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C26 H38 N6 O3"
_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                       482.618
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    VB2
_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       7OEE
_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
VB2  C10  C1   C  0  1  Y  N  N  -45.104  31.249  22.099  -2.205  -1.217  -0.731  C10  VB2   1  
VB2  C15  C2   C  0  1  N  N  N  -44.967  33.298  23.514  -0.149  -1.447   0.654  C15  VB2   2  
VB2  C17  C3   C  0  1  N  N  N  -44.951  35.746  24.070   2.086  -1.143  -0.269  C17  VB2   3  
VB2  C20  C4   C  0  1  N  N  N  -43.827  35.263  27.721   2.687   1.629  -1.083  C20  VB2   4  
VB2  C21  C5   C  0  1  N  N  N  -42.492  36.058  27.651   4.210   1.588  -0.949  C21  VB2   5  
VB2  C22  C6   C  0  1  N  N  N  -42.885  36.540  25.177   4.250  -0.779  -1.469  C22  VB2   6  
VB2  C24  C7   C  0  1  Y  N  N  -41.279  37.928  26.474   5.990   0.221  -0.239  C24  VB2   7  
VB2  C26  C8   C  0  1  Y  N  N  -39.785  39.159  27.756   8.066  -0.707  -0.612  C26  VB2   8  
VB2  C28  C9   C  0  1  Y  N  N  -40.180  39.778  25.565   7.935   1.051   0.871  C28  VB2   9  
VB2  C01  C10  C  0  1  N  N  N  -43.633  24.039  22.682  -8.591   1.802  -1.549  C01  VB2  10  
VB2  C02  C11  C  0  1  N  N  N  -42.618  25.016  23.294  -7.975   2.145  -0.191  C02  VB2  11  
VB2  C03  C12  C  0  1  N  N  N  -41.932  24.369  24.503  -8.444   3.534   0.247  C03  VB2  12  
VB2  C04  C13  C  0  1  N  N  N  -43.398  26.235  23.710  -6.448   2.132  -0.303  C04  VB2  13  
VB2  C05  C14  C  0  1  N  N  N  -43.627  27.136  22.524  -5.981   0.725  -0.684  C05  VB2  14  
VB2  C07  C15  C  0  1  N  N  N  -42.714  28.482  21.091  -5.874  -1.569   0.079  C07  VB2  15  
VB2  C08  C16  C  0  1  Y  N  N  -43.274  29.754  21.740  -4.376  -1.537   0.234  C08  VB2  16  
VB2  C09  C17  C  0  1  Y  N  N  -44.589  30.111  21.502  -3.577  -1.249  -0.861  C09  VB2  17  
VB2  C11  C18  C  0  1  Y  N  N  -42.479  30.563  22.551  -3.807  -1.795   1.465  C11  VB2  18  
VB2  C12  C19  C  0  1  Y  N  N  -42.993  31.710  23.141  -2.429  -1.761   1.615  C12  VB2  19  
VB2  C14  C20  C  0  1  Y  N  N  -44.319  32.055  22.903  -1.617  -1.475   0.509  C14  VB2  20  
VB2  C18  C21  C  0  1  N  N  S  -44.308  36.098  25.414   2.725  -0.808  -1.618  C18  VB2  21  
VB2  C19  C22  C  0  1  N  N  N  -44.347  34.880  26.331   2.237   0.565  -2.088  C19  VB2  22  
VB2  C30  C23  C  0  1  N  N  N  -40.892  41.379  23.709   7.761   2.938   2.456  C30  VB2  23  
VB2  C31  C24  C  0  1  Y  N  N  -41.061  38.750  25.412   6.563   1.123   0.652  C31  VB2  24  
VB2  C34  C25  C  0  1  N  N  N  -41.964  26.495  21.308  -7.887  -0.272   0.432  C34  VB2  25  
VB2  C35  C26  C  0  1  N  N  N  -41.532  25.353  22.264  -8.411   1.105   0.845  C35  VB2  26  
VB2  N06  N1   N  0  1  N  N  N  -42.496  27.515  21.962  -6.422  -0.231   0.339  N06  VB2  27  
VB2  N16  N2   N  0  1  N  N  N  -44.297  34.589  23.467   0.628  -1.171  -0.412  N16  VB2  28  
VB2  N23  N3   N  0  1  N  N  N  -42.206  36.806  26.410   4.628   0.255  -0.496  N23  VB2  29  
VB2  N25  N4   N  0  1  Y  N  N  -40.648  38.136  27.625   6.770  -0.672  -0.846  N25  VB2  30  
VB2  N27  N5   N  0  1  Y  N  N  -39.555  39.960  26.707   8.645   0.129   0.225  N27  VB2  31  
VB2  N29  N6   N  0  1  N  N  N  -39.863  40.713  24.494   8.553   1.927   1.750  N29  VB2  32  
VB2  O13  O1   O  0  1  N  N  N  -42.183  32.504  23.971  -1.868  -2.013   2.825  O13  VB2  33  
VB2  O32  O2   O  0  1  N  N  N  -44.984  37.183  25.995   2.359  -1.801  -2.579  O32  VB2  34  
VB2  O33  O3   O  0  1  N  N  N  -46.036  33.211  24.041   0.360  -1.672   1.735  O33  VB2  35  
VB2  H1   H1   H  0  1  N  N  N  -46.138  31.512  21.934  -1.586  -0.996  -1.588  H1   VB2  36  
VB2  H2   H2   H  0  1  N  N  N  -44.859  36.606  23.391   2.437  -2.119   0.068  H2   VB2  37  
VB2  H3   H3   H  0  1  N  N  N  -46.015  35.516  24.229   2.365  -0.385   0.463  H3   VB2  38  
VB2  H4   H4   H  0  1  N  N  N  -44.583  35.884  28.223   2.231   1.429  -0.113  H4   VB2  39  
VB2  H5   H5   H  0  1  N  N  N  -43.662  34.344  28.303   2.378   2.614  -1.433  H5   VB2  40  
VB2  H6   H6   H  0  1  N  N  N  -41.673  35.339  27.798   4.666   1.802  -1.916  H6   VB2  41  
VB2  H7   H7   H  0  1  N  N  N  -42.497  36.783  28.478   4.532   2.335  -0.224  H7   VB2  42  
VB2  H8   H8   H  0  1  N  N  N  -42.349  35.745  24.638   4.599  -1.751  -1.120  H8   VB2  43  
VB2  H9   H9   H  0  1  N  N  N  -42.892  37.456  24.568   4.705  -0.553  -2.433  H9   VB2  44  
VB2  H10  H10  H  0  1  N  N  N  -39.283  39.333  28.696   8.670  -1.444  -1.120  H10  VB2  45  
VB2  H11  H11  H  0  1  N  N  N  -44.408  23.802  23.425  -8.258   0.811  -1.859  H11  VB2  46  
VB2  H12  H12  H  0  1  N  N  N  -44.100  24.501  21.800  -9.678   1.811  -1.468  H12  VB2  47  
VB2  H13  H13  H  0  1  N  N  N  -43.117  23.115  22.382  -8.275   2.539  -2.287  H13  VB2  48  
VB2  H14  H14  H  0  1  N  N  N  -42.687  24.115  25.261  -9.531   3.541   0.329  H14  VB2  49  
VB2  H15  H15  H  0  1  N  N  N  -41.412  23.454  24.183  -8.006   3.777   1.215  H15  VB2  50  
VB2  H16  H16  H  0  1  N  N  N  -41.204  25.074  24.932  -8.131   4.272  -0.491  H16  VB2  51  
VB2  H17  H17  H  0  1  N  N  N  -42.833  26.783  24.479  -6.134   2.840  -1.070  H17  VB2  52  
VB2  H18  H18  H  0  1  N  N  N  -44.369  25.922  24.121  -6.011   2.415   0.654  H18  VB2  53  
VB2  H19  H19  H  0  1  N  N  N  -44.174  28.030  22.858  -6.408   0.449  -1.648  H19  VB2  54  
VB2  H20  H20  H  0  1  N  N  N  -44.229  26.595  21.779  -4.893   0.710  -0.750  H20  VB2  55  
VB2  H21  H21  H  0  1  N  N  N  -43.435  28.124  20.342  -6.129  -1.875  -0.936  H21  VB2  56  
VB2  H22  H22  H  0  1  N  N  N  -41.763  28.730  20.596  -6.298  -2.280   0.790  H22  VB2  57  
VB2  H23  H23  H  0  1  N  N  N  -45.209  29.507  20.856  -4.031  -1.049  -1.820  H23  VB2  58  
VB2  H24  H24  H  0  1  N  N  N  -41.447  30.293  22.723  -4.436  -2.018   2.314  H24  VB2  59  
VB2  H25  H25  H  0  1  N  N  N  -45.382  34.518  26.415   1.149   0.562  -2.154  H25  VB2  60  
VB2  H26  H26  H  0  1  N  N  N  -43.714  34.085  25.910   2.661   0.787  -3.067  H26  VB2  61  
VB2  H27  H27  H  0  1  N  N  N  -40.418  42.034  22.963   7.276   3.591   1.730  H27  VB2  62  
VB2  H28  H28  H  0  1  N  N  N  -41.507  40.625  23.196   7.003   2.445   3.065  H28  VB2  63  
VB2  H29  H29  H  0  1  N  N  N  -41.528  41.981  24.374   8.415   3.529   3.097  H29  VB2  64  
VB2  H30  H30  H  0  1  N  N  N  -41.572  38.592  24.474   5.958   1.859   1.160  H30  VB2  65  
VB2  H31  H31  H  0  1  N  N  N  -42.707  26.102  20.598  -8.184  -1.012   1.175  H31  VB2  66  
VB2  H32  H32  H  0  1  N  N  N  -41.081  26.849  20.756  -8.305  -0.543  -0.538  H32  VB2  67  
VB2  H33  H33  H  0  1  N  N  N  -41.318  24.454  21.668  -8.005   1.372   1.821  H33  VB2  68  
VB2  H34  H34  H  0  1  N  N  N  -40.622  25.664  22.798  -9.500   1.079   0.899  H34  VB2  69  
VB2  H36  H36  H  0  1  N  N  N  -43.403  34.682  23.029   0.223  -0.991  -1.275  H36  VB2  70  
VB2  H37  H37  H  0  1  N  N  N  -39.299  40.207  23.841   9.510   1.871   1.897  H37  VB2  71  
VB2  H38  H38  H  0  1  N  N  N  -42.685  33.244  24.290  -1.663  -2.946   2.976  H38  VB2  72  
VB2  H39  H39  H  0  1  N  N  N  -44.582  37.398  26.828   1.406  -1.874  -2.725  H39  VB2  73  
#   #
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
VB2  C07  C08  SING  N  N   1  
VB2  C07  N06  SING  N  N   2  
VB2  C34  N06  SING  N  N   3  
VB2  C34  C35  SING  N  N   4  
VB2  C09  C08  DOUB  Y  N   5  
VB2  C09  C10  SING  Y  N   6  
VB2  C08  C11  SING  Y  N   7  
VB2  N06  C05  SING  N  N   8  
VB2  C10  C14  DOUB  Y  N   9  
VB2  C35  C02  SING  N  N  10  
VB2  C05  C04  SING  N  N  11  
VB2  C11  C12  DOUB  Y  N  12  
VB2  C01  C02  SING  N  N  13  
VB2  C14  C12  SING  Y  N  14  
VB2  C14  C15  SING  N  N  15  
VB2  C12  O13  SING  N  N  16  
VB2  C02  C04  SING  N  N  17  
VB2  C02  C03  SING  N  N  18  
VB2  N16  C15  SING  N  N  19  
VB2  N16  C17  SING  N  N  20  
VB2  C15  O33  DOUB  N  N  21  
VB2  C30  N29  SING  N  N  22  
VB2  C17  C18  SING  N  N  23  
VB2  N29  C28  SING  N  N  24  
VB2  C22  C18  SING  N  N  25  
VB2  C22  N23  SING  N  N  26  
VB2  C31  C28  DOUB  Y  N  27  
VB2  C31  C24  SING  Y  N  28  
VB2  C18  O32  SING  N  N  29  
VB2  C18  C19  SING  N  N  30  
VB2  C28  N27  SING  Y  N  31  
VB2  C19  C20  SING  N  N  32  
VB2  N23  C24  SING  N  N  33  
VB2  N23  C21  SING  N  N  34  
VB2  C24  N25  DOUB  Y  N  35  
VB2  N27  C26  DOUB  Y  N  36  
VB2  N25  C26  SING  Y  N  37  
VB2  C21  C20  SING  N  N  38  
VB2  C10  H1   SING  N  N  39  
VB2  C17  H2   SING  N  N  40  
VB2  C17  H3   SING  N  N  41  
VB2  C20  H4   SING  N  N  42  
VB2  C20  H5   SING  N  N  43  
VB2  C21  H6   SING  N  N  44  
VB2  C21  H7   SING  N  N  45  
VB2  C22  H8   SING  N  N  46  
VB2  C22  H9   SING  N  N  47  
VB2  C26  H10  SING  N  N  48  
VB2  C01  H11  SING  N  N  49  
VB2  C01  H12  SING  N  N  50  
VB2  C01  H13  SING  N  N  51  
VB2  C03  H14  SING  N  N  52  
VB2  C03  H15  SING  N  N  53  
VB2  C03  H16  SING  N  N  54  
VB2  C04  H17  SING  N  N  55  
VB2  C04  H18  SING  N  N  56  
VB2  C05  H19  SING  N  N  57  
VB2  C05  H20  SING  N  N  58  
VB2  C07  H21  SING  N  N  59  
VB2  C07  H22  SING  N  N  60  
VB2  C09  H23  SING  N  N  61  
VB2  C11  H24  SING  N  N  62  
VB2  C19  H25  SING  N  N  63  
VB2  C19  H26  SING  N  N  64  
VB2  C30  H27  SING  N  N  65  
VB2  C30  H28  SING  N  N  66  
VB2  C30  H29  SING  N  N  67  
VB2  C31  H30  SING  N  N  68  
VB2  C34  H31  SING  N  N  69  
VB2  C34  H32  SING  N  N  70  
VB2  C35  H33  SING  N  N  71  
VB2  C35  H34  SING  N  N  72  
VB2  N16  H36  SING  N  N  73  
VB2  N29  H37  SING  N  N  74  
VB2  O13  H38  SING  N  N  75  
VB2  O32  H39  SING  N  N  76  
#   #
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
VB2  InChI             InChI                 1.03   "InChI=1S/C26H38N6O3/c1-25(2)8-11-31(12-9-25)15-19-5-6-20(21(33)13-19)24(34)28-16-26(35)7-4-10-32(17-26)23-14-22(27-3)29-18-30-23/h5-6,13-14,18,33,35H,4,7-12,15-17H2,1-3H3,(H,28,34)(H,27,29,30)/t26-/m0/s1"  
VB2  InChIKey          InChI                 1.03   BEGALFNTKBNFJE-SANMLTNESA-N  
VB2  SMILES_CANONICAL  CACTVS                3.385  "CNc1cc(ncn1)N2CCC[C@](O)(CNC(=O)c3ccc(CN4CCC(C)(C)CC4)cc3O)C2"  
VB2  SMILES            CACTVS                3.385  "CNc1cc(ncn1)N2CCC[C](O)(CNC(=O)c3ccc(CN4CCC(C)(C)CC4)cc3O)C2"  
VB2  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "CC1(CCN(CC1)Cc2ccc(c(c2)O)C(=O)NC[C@]3(CCCN(C3)c4cc(ncn4)NC)O)C"  
VB2  SMILES            "OpenEye OEToolkits"  2.0.7  "CC1(CCN(CC1)Cc2ccc(c(c2)O)C(=O)NCC3(CCCN(C3)c4cc(ncn4)NC)O)C"  
#
_pdbx_chem_comp_identifier.comp_id          VB2
_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]-~{N}-[[(3~{S})-1-[6-(methylamino)pyrimidin-4-yl]-3-oxidanyl-piperidin-3-yl]methyl]-2-oxidanyl-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
VB2  "Create component"  2021-05-04  PDBE  
VB2  "Initial release"   2021-10-20  RCSB  
##
