data_V9T
#

_chem_comp.id                                   V9T
_chem_comp.name                                 "4-[[(3S)-3-cyclopropyl-2-azaspiro[3.3]heptan-2-yl]methyl]-N-[[(3R)-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                              "C28 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                    2021-05-03
_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                       506.640
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    V9T
_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       7OEJ
_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
V9T  C10  C1   C  0  1  N  N  N  -11.577  18.938  -11.579    4.643  -0.664  -0.080  C10  V9T   1  
V9T  C15  C2   C  0  1  Y  N  N  -14.497  22.554  -13.506   -1.499  -1.435   0.585  C15  V9T   2  
V9T  C17  C3   C  0  1  Y  N  N  -15.665  24.043  -15.089   -3.062   0.306   1.131  C17  V9T   3  
V9T  C21  C4   C  0  1  N  N  S  -20.132  23.806  -16.312   -7.421   0.958   0.293  C21  V9T   4  
V9T  C22  C5   C  0  1  N  N  N  -20.956  22.679  -16.776   -7.371   2.472   0.076  C22  V9T   5  
V9T  C24  C6   C  0  1  N  N  N  -20.828  21.908  -18.112   -6.781   3.328   1.198  C24  V9T   6  
V9T  C26  C7   C  0  1  N  N  N  -21.202  25.870  -15.099   -9.441  -0.214  -0.996  C26  V9T   7  
V9T  C28  C8   C  0  1  N  N  N  -21.280  24.068  -13.854   -8.104   0.827  -2.282  C28  V9T   8  
V9T  C01  C9   C  0  1  N  N  N   -7.764  13.810  -14.107   10.005   2.909   0.039  C01  V9T   9  
V9T  C03  C10  C  0  1  Y  N  N   -9.201  14.467  -11.999    9.196   0.604  -0.323  C03  V9T  10  
V9T  C04  C11  C  0  1  Y  N  N   -9.529  15.805  -12.449    7.893   1.038  -0.102  C04  V9T  11  
V9T  C05  C12  C  0  1  Y  N  N  -10.219  16.721  -11.616    6.866   0.102  -0.174  C05  V9T  12  
V9T  C07  C13  C  0  1  N  N  N   -9.786  18.713  -13.248    5.162   1.564  -0.878  C07  V9T  13  
V9T  C08  C14  C  0  1  N  N  N   -9.306  20.178  -12.888    3.758   2.059  -0.520  C08  V9T  14  
V9T  C09  C15  C  0  1  N  N  N  -10.383  21.068  -12.273    2.770   0.894  -0.626  C09  V9T  15  
V9T  C11  C16  C  0  1  N  N  R  -11.089  20.362  -11.091    3.224  -0.236   0.301  C11  V9T  16  
V9T  C12  C17  C  0  1  N  N  N  -12.293  21.191  -10.567    2.275  -1.428   0.157  C12  V9T  17  
V9T  C14  C18  C  0  1  N  N  N  -13.416  22.375  -12.530   -0.114  -1.876   0.334  C14  V9T  18  
V9T  C16  C19  C  0  1  Y  N  N  -14.669  23.758  -14.150   -1.765  -0.100   0.898  C16  V9T  19  
V9T  C18  C20  C  0  1  Y  N  N  -16.595  23.043  -15.440   -4.103  -0.604   1.057  C18  V9T  20  
V9T  C19  C21  C  0  1  N  N  N  -17.702  23.306  -16.375   -5.516  -0.148   1.314  C19  V9T  21  
V9T  C23  C22  C  0  1  N  N  N  -22.051  22.756  -17.832   -8.289   3.340   0.939  C23  V9T  22  
V9T  C25  C23  C  0  1  N  N  N  -20.432  24.533  -15.050   -7.972   0.189  -0.902  C25  V9T  23  
V9T  C27  C24  C  0  1  N  N  N  -22.229  25.277  -14.102   -9.267  -0.152  -2.525  C27  V9T  24  
V9T  C29  C25  C  0  1  N  N  N  -18.984  24.443  -14.666   -6.877  -0.821  -0.581  C29  V9T  25  
V9T  C30  C26  C  0  1  Y  N  N  -16.474  21.819  -14.807   -3.854  -1.926   0.743  C30  V9T  26  
V9T  C31  C27  C  0  1  Y  N  N  -15.461  21.548  -13.873   -2.556  -2.352   0.505  C31  V9T  27  
V9T  C36  C28  C  0  1  Y  N  N  -10.209  15.055  -10.009    8.412  -1.538  -0.652  C36  V9T  28  
V9T  N02  N1   N  0  1  N  N  N   -8.514  13.534  -12.823   10.255   1.497  -0.259  N02  V9T  29  
V9T  N06  N2   N  0  1  N  N  N  -10.535  18.040  -12.111    5.550   0.484   0.038  N06  V9T  30  
V9T  N13  N3   N  0  1  N  N  N  -13.350  21.358  -11.525    0.899  -0.990   0.406  N13  V9T  31  
V9T  N20  N4   N  0  1  N  N  N  -18.923  23.215  -15.586   -6.128   0.285   0.051  N20  V9T  32  
V9T  N35  N5   N  0  1  Y  N  N  -10.561  16.317  -10.353    7.165  -1.166  -0.449  N35  V9T  33  
V9T  N37  N6   N  0  1  Y  N  N   -9.566  14.120  -10.737    9.412  -0.682  -0.594  N37  V9T  34  
V9T  O32  O1   O  0  1  N  N  N  -15.348  20.309  -13.263   -2.311  -3.650   0.196  O32  V9T  35  
V9T  O33  O2   O  0  1  N  N  N  -12.499  23.213  -12.543    0.114  -3.039   0.062  O33  V9T  36  
V9T  O34  O3   O  0  1  N  N  N  -10.195  20.207  -10.022    3.211   0.223   1.654  O34  V9T  37  
V9T  H1   H1   H  0  1  N  N  N  -12.324  19.093  -12.372    4.974  -1.459   0.588  H1   V9T  38  
V9T  H2   H2   H  0  1  N  N  N  -12.050  18.434  -10.723    4.649  -1.027  -1.108  H2   V9T  39  
V9T  H3   H3   H  0  1  N  N  N  -15.722  25.022  -15.542   -3.266   1.338   1.373  H3   V9T  40  
V9T  H4   H4   H  0  1  N  N  N  -19.832  24.481  -17.128   -7.885   0.682   1.240  H4   V9T  41  
V9T  H5   H5   H  0  1  N  N  N  -21.237  22.003  -15.955   -7.192   2.794  -0.950  H5   V9T  42  
V9T  H6   H6   H  0  1  N  N  N  -20.909  20.811  -18.125   -6.428   2.812   2.092  H6   V9T  43  
V9T  H7   H7   H  0  1  N  N  N  -20.095  22.230  -18.866   -6.214   4.213   0.911  H7   V9T  44  
V9T  H8   H8   H  0  1  N  N  N  -20.639  26.732  -14.712   -9.645  -1.216  -0.618  H8   V9T  45  
V9T  H9   H9   H  0  1  N  N  N  -21.619  26.118  -16.086  -10.127   0.537  -0.603  H9   V9T  46  
V9T  H10  H10  H  0  1  N  N  N  -21.753  23.084  -13.988   -8.411   1.873  -2.253  H10  V9T  47  
V9T  H11  H11  H  0  1  N  N  N  -20.755  24.094  -12.888   -7.242   0.656  -2.928  H11  V9T  48  
V9T  H12  H12  H  0  1  N  N  N   -7.346  12.870  -14.497    9.352   3.332  -0.724  H12  V9T  49  
V9T  H13  H13  H  0  1  N  N  N   -8.453  14.241  -14.848    9.528   2.996   1.015  H13  V9T  50  
V9T  H14  H14  H  0  1  N  N  N   -6.947  14.520  -13.909   10.951   3.451   0.048  H14  V9T  51  
V9T  H15  H15  H  0  1  N  N  N   -9.241  16.112  -13.444    7.684   2.075   0.119  H15  V9T  52  
V9T  H16  H16  H  0  1  N  N  N  -10.451  18.767  -14.123    5.165   1.191  -1.902  H16  V9T  53  
V9T  H17  H17  H  0  1  N  N  N   -8.903  18.105  -13.495    5.870   2.388  -0.790  H17  V9T  54  
V9T  H18  H18  H  0  1  N  N  N   -8.475  20.100  -12.171    3.757   2.445   0.499  H18  V9T  55  
V9T  H19  H19  H  0  1  N  N  N   -8.950  20.659  -13.811    3.464   2.849  -1.211  H19  V9T  56  
V9T  H20  H20  H  0  1  N  N  N   -9.917  21.996  -11.909    1.776   1.231  -0.331  H20  V9T  57  
V9T  H21  H21  H  0  1  N  N  N  -11.130  21.311  -13.043    2.742   0.532  -1.654  H21  V9T  58  
V9T  H22  H22  H  0  1  N  N  N  -11.927  22.188  -10.279    2.350  -1.832  -0.853  H22  V9T  59  
V9T  H23  H23  H  0  1  N  N  N  -12.705  20.682   -9.683    2.547  -2.199   0.878  H23  V9T  60  
V9T  H24  H24  H  0  1  N  N  N  -13.976  24.550  -13.910   -0.956   0.613   0.958  H24  V9T  61  
V9T  H25  H25  H  0  1  N  N  N  -17.710  22.556  -17.179   -6.093  -0.973   1.734  H25  V9T  62  
V9T  H26  H26  H  0  1  N  N  N  -17.603  24.311  -16.812   -5.507   0.684   2.018  H26  V9T  63  
V9T  H27  H27  H  0  1  N  N  N  -22.207  23.691  -18.390   -8.714   4.233   0.481  H27  V9T  64  
V9T  H28  H28  H  0  1  N  N  N  -23.022  22.272  -17.649   -8.928   2.832   1.662  H28  V9T  65  
V9T  H29  H29  H  0  1  N  N  N  -22.405  25.901  -13.213   -8.954  -1.099  -2.966  H29  V9T  66  
V9T  H30  H30  H  0  1  N  N  N  -23.193  25.006  -14.557  -10.114   0.297  -3.042  H30  V9T  67  
V9T  H31  H31  H  0  1  N  N  N  -18.798  24.235  -13.602   -7.189  -1.593   0.122  H31  V9T  68  
V9T  H32  H32  H  0  1  N  N  N  -18.365  25.294  -14.987   -6.388  -1.228  -1.466  H32  V9T  69  
V9T  H33  H33  H  0  1  N  N  N  -17.186  21.041  -15.040   -4.672  -2.630   0.687  H33  V9T  70  
V9T  H34  H34  H  0  1  N  N  N  -10.483  14.755   -9.008    8.622  -2.574  -0.873  H34  V9T  71  
V9T  H35  H35  H  0  1  N  N  N   -9.207  12.858  -13.073   11.161   1.186  -0.410  H35  V9T  72  
V9T  H36  H36  H  0  1  N  N  N  -14.107  20.706  -11.486    0.718  -0.062   0.623  H36  V9T  73  
V9T  H38  H38  H  0  1  N  N  N  -14.609  20.315  -12.667   -2.336  -3.840  -0.751  H38  V9T  74  
V9T  H39  H39  H  0  1  N  N  N  -10.635  19.773   -9.301    2.342   0.511   1.964  H39  V9T  75  
#   #
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
V9T  C24  C23  SING  N  N   1  
V9T  C24  C22  SING  N  N   2  
V9T  C23  C22  SING  N  N   3  
V9T  C22  C21  SING  N  N   4  
V9T  C19  N20  SING  N  N   5  
V9T  C19  C18  SING  N  N   6  
V9T  C21  N20  SING  N  N   7  
V9T  C21  C25  SING  N  N   8  
V9T  N20  C29  SING  N  N   9  
V9T  C18  C17  DOUB  Y  N  10  
V9T  C18  C30  SING  Y  N  11  
V9T  C26  C25  SING  N  N  12  
V9T  C26  C27  SING  N  N  13  
V9T  C17  C16  SING  Y  N  14  
V9T  C25  C29  SING  N  N  15  
V9T  C25  C28  SING  N  N  16  
V9T  C30  C31  DOUB  Y  N  17  
V9T  C16  C15  DOUB  Y  N  18  
V9T  C01  N02  SING  N  N  19  
V9T  C27  C28  SING  N  N  20  
V9T  C31  C15  SING  Y  N  21  
V9T  C31  O32  SING  N  N  22  
V9T  C15  C14  SING  N  N  23  
V9T  C07  C08  SING  N  N  24  
V9T  C07  N06  SING  N  N  25  
V9T  C08  C09  SING  N  N  26  
V9T  N02  C03  SING  N  N  27  
V9T  O33  C14  DOUB  N  N  28  
V9T  C14  N13  SING  N  N  29  
V9T  C04  C03  DOUB  Y  N  30  
V9T  C04  C05  SING  Y  N  31  
V9T  C09  C11  SING  N  N  32  
V9T  N06  C05  SING  N  N  33  
V9T  N06  C10  SING  N  N  34  
V9T  C03  N37  SING  Y  N  35  
V9T  C05  N35  DOUB  Y  N  36  
V9T  C10  C11  SING  N  N  37  
V9T  N13  C12  SING  N  N  38  
V9T  C11  C12  SING  N  N  39  
V9T  C11  O34  SING  N  N  40  
V9T  N37  C36  DOUB  Y  N  41  
V9T  N35  C36  SING  Y  N  42  
V9T  C10  H1   SING  N  N  43  
V9T  C10  H2   SING  N  N  44  
V9T  C17  H3   SING  N  N  45  
V9T  C21  H4   SING  N  N  46  
V9T  C22  H5   SING  N  N  47  
V9T  C24  H6   SING  N  N  48  
V9T  C24  H7   SING  N  N  49  
V9T  C26  H8   SING  N  N  50  
V9T  C26  H9   SING  N  N  51  
V9T  C28  H10  SING  N  N  52  
V9T  C28  H11  SING  N  N  53  
V9T  C01  H12  SING  N  N  54  
V9T  C01  H13  SING  N  N  55  
V9T  C01  H14  SING  N  N  56  
V9T  C04  H15  SING  N  N  57  
V9T  C07  H16  SING  N  N  58  
V9T  C07  H17  SING  N  N  59  
V9T  C08  H18  SING  N  N  60  
V9T  C08  H19  SING  N  N  61  
V9T  C09  H20  SING  N  N  62  
V9T  C09  H21  SING  N  N  63  
V9T  C12  H22  SING  N  N  64  
V9T  C12  H23  SING  N  N  65  
V9T  C16  H24  SING  N  N  66  
V9T  C19  H25  SING  N  N  67  
V9T  C19  H26  SING  N  N  68  
V9T  C23  H27  SING  N  N  69  
V9T  C23  H28  SING  N  N  70  
V9T  C27  H29  SING  N  N  71  
V9T  C27  H30  SING  N  N  72  
V9T  C29  H31  SING  N  N  73  
V9T  C29  H32  SING  N  N  74  
V9T  C30  H33  SING  N  N  75  
V9T  C36  H34  SING  N  N  76  
V9T  N02  H35  SING  N  N  77  
V9T  N13  H36  SING  N  N  78  
V9T  O32  H38  SING  N  N  79  
V9T  O34  H39  SING  N  N  80  
#   #
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
V9T  InChI             InChI                 1.03   "InChI=1S/C28H38N6O3/c1-29-23-13-24(32-18-31-23)33-11-3-10-28(37,17-33)15-30-26(36)21-7-4-19(12-22(21)35)14-34-16-27(8-2-9-27)25(34)20-5-6-20/h4,7,12-13,18,20,25,35,37H,2-3,5-6,8-11,14-17H2,1H3,(H,30,36)(H,29,31,32)/t25-,28+/m0/s1"  
V9T  InChIKey          InChI                 1.03   JWBZACHWPMPYIU-LBNVMWSVSA-N  
V9T  SMILES_CANONICAL  CACTVS                3.385  "CNc1cc(ncn1)N2CCC[C@@](O)(CNC(=O)c3ccc(CN4CC5(CCC5)[C@@H]4C6CC6)cc3O)C2"  
V9T  SMILES            CACTVS                3.385  "CNc1cc(ncn1)N2CCC[C](O)(CNC(=O)c3ccc(CN4CC5(CCC5)[CH]4C6CC6)cc3O)C2"  
V9T  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "CNc1cc(ncn1)N2CCC[C@](C2)(CNC(=O)c3ccc(cc3O)CN4CC5([C@@H]4C6CC6)CCC5)O"  
V9T  SMILES            "OpenEye OEToolkits"  2.0.7  "CNc1cc(ncn1)N2CCCC(C2)(CNC(=O)c3ccc(cc3O)CN4CC5(C4C6CC6)CCC5)O"  
#
_pdbx_chem_comp_identifier.comp_id          V9T
_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-[[(3~{S})-3-cyclopropyl-2-azaspiro[3.3]heptan-2-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
V9T  "Create component"  2021-05-03  PDBE  
V9T  "Modify name"       2021-10-02  PDBE  
V9T  "Initial release"   2021-10-20  RCSB  
##
