data_VB5
#

_chem_comp.id                                   VB5
_chem_comp.name                                 "4-[(4,4-dimethylpiperidin-1-yl)methyl]-~{N}-[[(3~{R})-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                    VB5
_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       7OED
_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
VB5  C10  C1   C  0  1  Y  N  N  14.328  -23.899  -13.879   -2.074   1.660  -0.392  C10  VB5   1  
VB5  C15  C2   C  0  1  N  N  N  13.121  -22.451  -12.216   -0.145   1.082   1.073  C15  VB5   2  
VB5  C17  C3   C  0  1  N  N  N  11.923  -21.145  -10.433    2.166   1.295   0.331  C17  VB5   3  
VB5  C20  C4   C  0  1  N  N  N   9.070  -20.171  -12.904    2.741  -0.564  -1.887  C20  VB5   4  
VB5  C21  C5   C  0  1  N  N  N   9.562  -18.760  -13.301    4.244  -0.739  -1.662  C21  VB5   5  
VB5  C22  C6   C  0  1  N  N  N  11.326  -18.934  -11.401    4.422   1.490  -0.728  C22  VB5   6  
VB5  C24  C7   C  0  1  Y  N  N  10.034  -16.759  -11.750    5.993  -0.178  -0.191  C24  VB5   7  
VB5  C26  C8   C  0  1  Y  N  N  10.141  -15.120  -10.103    8.127   0.613   0.168  C26  VB5   8  
VB5  C28  C9   C  0  1  Y  N  N   9.077  -14.624  -12.122    7.780  -1.654   0.386  C28  VB5   9  
VB5  C01  C10  C  0  1  N  N  N  20.703  -26.264  -15.814   -8.993  -1.786   0.581  C01  VB5  10  
VB5  C02  C11  C  0  1  N  N  N  20.915  -24.998  -14.968   -8.045  -2.027  -0.595  C02  VB5  11  
VB5  C03  C12  C  0  1  N  N  N  22.242  -25.118  -14.183   -8.432  -3.326  -1.306  C03  VB5  12  
VB5  C04  C13  C  0  1  N  N  N  20.906  -23.804  -15.899   -8.143  -0.858  -1.579  C04  VB5  13  
VB5  C05  C14  C  0  1  N  N  N  19.506  -23.604  -16.483   -7.698   0.429  -0.879  C05  VB5  14  
VB5  C07  C15  C  0  1  N  N  N  17.350  -23.350  -16.258   -5.807   1.540   0.147  C07  VB5  15  
VB5  C08  C16  C  0  1  Y  N  N  16.210  -23.105  -15.199   -4.326   1.420   0.393  C08  VB5  16  
VB5  C09  C17  C  0  1  Y  N  N  15.315  -24.131  -14.851   -3.431   1.765  -0.607  C09  VB5  17  
VB5  C11  C18  C  0  1  Y  N  N  16.115  -21.861  -14.589   -3.867   0.966   1.614  C11  VB5  18  
VB5  C12  C19  C  0  1  Y  N  N  15.118  -21.628  -13.627   -2.505   0.859   1.849  C12  VB5  19  
VB5  C14  C20  C  0  1  Y  N  N  14.233  -22.652  -13.279   -1.597   1.203   0.838  C14  VB5  20  
VB5  C18  C21  C  0  1  N  N  R  10.749  -20.319  -11.033    2.924   1.731  -0.925  C18  VB5  21  
VB5  C19  C22  C  0  1  N  N  N  10.221  -20.980  -12.304    2.434   0.917  -2.126  C19  VB5  22  
VB5  C30  C23  C  0  1  N  N  N   7.613  -14.201  -14.141    7.375  -4.080   0.612  C30  VB5  23  
VB5  C31  C24  C  0  1  Y  N  N   9.354  -15.891  -12.577    6.437  -1.470   0.072  C31  VB5  24  
VB5  C34  C25  C  0  1  N  N  N  18.448  -24.600  -14.808   -6.205  -0.812   0.576  C34  VB5  25  
VB5  C35  C26  C  0  1  N  N  N  19.756  -24.872  -13.967   -6.607  -2.135  -0.081  C35  VB5  26  
VB5  N06  N1   N  0  1  N  N  N  18.522  -23.539  -15.599   -6.316   0.278  -0.407  N06  VB5  27  
VB5  N16  N2   N  0  1  N  N  N  13.022  -21.218  -11.423    0.725   1.414   0.098  N16  VB5  28  
VB5  N23  N3   N  0  1  N  N  N  10.359  -18.144  -12.210    4.663   0.059  -0.503  N23  VB5  29  
VB5  N25  N4   N  0  1  Y  N  N  10.421  -16.378  -10.539    6.863   0.829  -0.133  N25  VB5  30  
VB5  N27  N5   N  0  1  Y  N  N   9.470  -14.244  -10.910    8.586  -0.595   0.423  N27  VB5  31  
VB5  N29  N6   N  0  1  N  N  N   8.348  -13.683  -12.985    8.272  -2.922   0.655  N29  VB5  32  
VB5  O13  O1   O  0  1  N  N  N  15.040  -20.378  -13.030   -2.053   0.414   3.049  O13  VB5  33  
VB5  O32  O2   O  0  1  N  N  N   9.746  -20.188  -10.081    2.691   3.121  -1.163  O32  VB5  34  
VB5  O33  O3   O  0  1  N  N  N  12.346  -23.330  -12.031    0.267   0.684   2.145  O33  VB5  35  
VB5  H1   H1   H  0  1  N  N  N  13.646  -24.688  -13.600   -1.380   1.926  -1.176  H1   VB5  36  
VB5  H2   H2   H  0  1  N  N  N  11.574  -22.161  -10.195    2.412   0.259   0.562  H2   VB5  37  
VB5  H3   H3   H  0  1  N  N  N  12.285  -20.657   -9.516    2.453   1.932   1.168  H3   VB5  38  
VB5  H4   H4   H  0  1  N  N  N   8.264  -20.079  -12.161    2.433  -1.144  -2.758  H4   VB5  39  
VB5  H5   H5   H  0  1  N  N  N   8.689  -20.688  -13.797    2.198  -0.911  -1.008  H5   VB5  40  
VB5  H6   H6   H  0  1  N  N  N  10.188  -18.838  -14.202    4.464  -1.790  -1.478  H6   VB5  41  
VB5  H7   H7   H  0  1  N  N  N   8.691  -18.123  -13.513    4.785  -0.404  -2.548  H7   VB5  42  
VB5  H8   H8   H  0  1  N  N  N  12.250  -19.073  -11.982    4.962   1.814  -1.617  H8   VB5  43  
VB5  H9   H9   H  0  1  N  N  N  11.554  -18.383  -10.476    4.771   2.057   0.136  H9   VB5  44  
VB5  H10  H10  H  0  1  N  N  N  10.450  -14.812   -9.115    8.807   1.451   0.206  H10  VB5  45  
VB5  H11  H11  H  0  1  N  N  N  20.706  -27.148  -15.159   -8.921  -2.618   1.282  H11  VB5  46  
VB5  H12  H12  H  0  1  N  N  N  19.737  -26.198  -16.337   -8.716  -0.861   1.087  H12  VB5  47  
VB5  H13  H13  H  0  1  N  N  N  21.514  -26.352  -16.552  -10.016  -1.708   0.214  H13  VB5  48  
VB5  H14  H14  H  0  1  N  N  N  22.200  -25.997  -13.523   -9.455  -3.248  -1.673  H14  VB5  49  
VB5  H15  H15  H  0  1  N  N  N  23.077  -25.230  -14.890   -7.757  -3.497  -2.144  H15  VB5  50  
VB5  H16  H16  H  0  1  N  N  N  22.393  -24.212  -13.578   -8.360  -4.158  -0.606  H16  VB5  51  
VB5  H17  H17  H  0  1  N  N  N  21.621  -23.975  -16.717   -7.497  -1.048  -2.436  H17  VB5  52  
VB5  H18  H18  H  0  1  N  N  N  21.199  -22.904  -15.339   -9.174  -0.751  -1.916  H18  VB5  53  
VB5  H19  H19  H  0  1  N  N  N  19.509  -22.665  -17.056   -7.752   1.261  -1.581  H19  VB5  54  
VB5  H20  H20  H  0  1  N  N  N  19.298  -24.446  -17.160   -8.352   0.626  -0.031  H20  VB5  55  
VB5  H21  H21  H  0  1  N  N  N  17.434  -22.476  -16.920   -6.316   1.755   1.087  H21  VB5  56  
VB5  H22  H22  H  0  1  N  N  N  17.114  -24.242  -16.857   -5.994   2.348  -0.560  H22  VB5  57  
VB5  H23  H23  H  0  1  N  N  N  15.386  -25.096  -15.330   -3.799   2.119  -1.558  H23  VB5  58  
VB5  H24  H24  H  0  1  N  N  N  16.806  -21.074  -14.854   -4.571   0.699   2.389  H24  VB5  59  
VB5  H25  H25  H  0  1  N  N  N   9.862  -21.991  -12.061    2.945   1.255  -3.027  H25  VB5  60  
VB5  H26  H26  H  0  1  N  N  N  11.036  -21.047  -13.040    1.359   1.053  -2.243  H26  VB5  61  
VB5  H27  H27  H  0  1  N  N  N   7.130  -13.368  -14.672    6.575  -3.948   1.339  H27  VB5  62  
VB5  H28  H28  H  0  1  N  N  N   8.311  -14.713  -14.820    6.947  -4.171  -0.387  H28  VB5  63  
VB5  H29  H29  H  0  1  N  N  N   6.846  -14.912  -13.799    7.937  -4.984   0.850  H29  VB5  64  
VB5  H30  H30  H  0  1  N  N  N   9.045  -16.201  -13.564    5.757  -2.308   0.034  H30  VB5  65  
VB5  H31  H31  H  0  1  N  N  N  17.613  -24.451  -14.108   -6.867  -0.609   1.418  H31  VB5  66  
VB5  H32  H32  H  0  1  N  N  N  18.250  -25.483  -15.433   -5.177  -0.880   0.930  H32  VB5  67  
VB5  H33  H33  H  0  1  N  N  N  19.649  -25.804  -13.393   -6.541  -2.939   0.651  H33  VB5  68  
VB5  H34  H34  H  0  1  N  N  N  19.942  -24.036  -13.277   -5.937  -2.345  -0.915  H34  VB5  69  
VB5  H36  H36  H  0  1  N  N  N  13.667  -20.463  -11.546    0.396   1.732  -0.757  H36  VB5  70  
VB5  H37  H37  H  0  1  N  N  N   9.017  -13.027  -13.334    9.209  -3.043   0.873  H37  VB5  71  
VB5  H38  H38  H  0  1  N  N  N  14.324  -20.369  -12.406   -1.935  -0.545   3.093  H38  VB5  72  
VB5  H39  H39  H  0  1  N  N  N  10.100  -19.775   -9.302    1.761   3.347  -1.297  H39  VB5  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
VB5  C05  C04  SING  N  N   1  
VB5  C05  N06  SING  N  N   2  
VB5  C07  N06  SING  N  N   3  
VB5  C07  C08  SING  N  N   4  
VB5  C04  C02  SING  N  N   5  
VB5  C01  C02  SING  N  N   6  
VB5  N06  C34  SING  N  N   7  
VB5  C08  C09  DOUB  Y  N   8  
VB5  C08  C11  SING  Y  N   9  
VB5  C02  C03  SING  N  N  10  
VB5  C02  C35  SING  N  N  11  
VB5  C09  C10  SING  Y  N  12  
VB5  C34  C35  SING  N  N  13  
VB5  C11  C12  DOUB  Y  N  14  
VB5  C30  N29  SING  N  N  15  
VB5  C10  C14  DOUB  Y  N  16  
VB5  C12  C14  SING  Y  N  17  
VB5  C12  O13  SING  N  N  18  
VB5  C21  C20  SING  N  N  19  
VB5  C21  N23  SING  N  N  20  
VB5  C14  C15  SING  N  N  21  
VB5  N29  C28  SING  N  N  22  
VB5  C20  C19  SING  N  N  23  
VB5  C31  C28  DOUB  Y  N  24  
VB5  C31  C24  SING  Y  N  25  
VB5  C19  C18  SING  N  N  26  
VB5  C15  O33  DOUB  N  N  27  
VB5  C15  N16  SING  N  N  28  
VB5  N23  C24  SING  N  N  29  
VB5  N23  C22  SING  N  N  30  
VB5  C28  N27  SING  Y  N  31  
VB5  C24  N25  DOUB  Y  N  32  
VB5  N16  C17  SING  N  N  33  
VB5  C22  C18  SING  N  N  34  
VB5  C18  C17  SING  N  N  35  
VB5  C18  O32  SING  N  N  36  
VB5  N27  C26  DOUB  Y  N  37  
VB5  N25  C26  SING  Y  N  38  
VB5  C10  H1   SING  N  N  39  
VB5  C17  H2   SING  N  N  40  
VB5  C17  H3   SING  N  N  41  
VB5  C20  H4   SING  N  N  42  
VB5  C20  H5   SING  N  N  43  
VB5  C21  H6   SING  N  N  44  
VB5  C21  H7   SING  N  N  45  
VB5  C22  H8   SING  N  N  46  
VB5  C22  H9   SING  N  N  47  
VB5  C26  H10  SING  N  N  48  
VB5  C01  H11  SING  N  N  49  
VB5  C01  H12  SING  N  N  50  
VB5  C01  H13  SING  N  N  51  
VB5  C03  H14  SING  N  N  52  
VB5  C03  H15  SING  N  N  53  
VB5  C03  H16  SING  N  N  54  
VB5  C04  H17  SING  N  N  55  
VB5  C04  H18  SING  N  N  56  
VB5  C05  H19  SING  N  N  57  
VB5  C05  H20  SING  N  N  58  
VB5  C07  H21  SING  N  N  59  
VB5  C07  H22  SING  N  N  60  
VB5  C09  H23  SING  N  N  61  
VB5  C11  H24  SING  N  N  62  
VB5  C19  H25  SING  N  N  63  
VB5  C19  H26  SING  N  N  64  
VB5  C30  H27  SING  N  N  65  
VB5  C30  H28  SING  N  N  66  
VB5  C30  H29  SING  N  N  67  
VB5  C31  H30  SING  N  N  68  
VB5  C34  H31  SING  N  N  69  
VB5  C34  H32  SING  N  N  70  
VB5  C35  H33  SING  N  N  71  
VB5  C35  H34  SING  N  N  72  
VB5  N16  H36  SING  N  N  73  
VB5  N29  H37  SING  N  N  74  
VB5  O13  H38  SING  N  N  75  
VB5  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
VB5  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-/m1/s1"  
VB5  InChIKey          InChI                 1.03   BEGALFNTKBNFJE-AREMUKBSSA-N  
VB5  SMILES_CANONICAL  CACTVS                3.385  "CNc1cc(ncn1)N2CCC[C@@](O)(CNC(=O)c3ccc(CN4CCC(C)(C)CC4)cc3O)C2"  
VB5  SMILES            CACTVS                3.385  "CNc1cc(ncn1)N2CCC[C](O)(CNC(=O)c3ccc(CN4CCC(C)(C)CC4)cc3O)C2"  
VB5  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"  
VB5  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          VB5
_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~{R})-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
VB5  "Create component"  2021-05-04  PDBE  
VB5  "Initial release"   2021-10-20  RCSB  
##
