data_VAT
#

_chem_comp.id                                   VAT
_chem_comp.name                                 "4-(2-azaspiro[3.4]octan-2-ylmethyl)-~{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                              "C32 H40 N6 O2"
_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                       540.699
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    VAT
_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       7OEF
_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
VAT  C10  C1   C  0  1  N  N  N  -43.028  28.772  21.007    7.376  -0.833   0.465  C10  VAT   1  
VAT  C13  C2   C  0  1  N  N  N  -42.569  26.369  21.060    9.043   0.495  -0.705  C13  VAT   2  
VAT  C15  C3   C  0  1  N  N  N  -44.237  24.840  22.308   10.234   2.478   0.458  C15  VAT   3  
VAT  C17  C4   C  0  1  N  N  N  -42.563  24.162  24.002    9.962   3.698  -1.640  C17  VAT   4  
VAT  C20  C5   C  0  1  Y  N  N  -45.366  31.190  22.969    3.939  -0.627   2.009  C20  VAT   5  
VAT  C22  C6   C  0  1  N  N  N  -45.349  35.912  25.637   -0.714  -2.348  -1.928  C22  VAT   6  
VAT  C24  C7   C  0  1  N  N  N  -43.823  37.522  24.247   -2.849  -1.065  -1.740  C24  VAT   7  
VAT  C02  C8   C  0  1  N  N  R  -44.167  35.616  26.573   -1.069  -3.056  -0.617  C02  VAT   8  
VAT  C03  C9   C  0  1  N  N  N  -44.332  34.169  27.101   -0.470  -2.283   0.559  C03  VAT   9  
VAT  C05  C10  C  0  1  N  N  N  -44.919  32.646  25.171    1.714  -1.467   1.270  C05  VAT  10  
VAT  C06  C11  C  0  1  Y  N  N  -44.464  31.599  24.023    3.168  -1.304   1.063  C06  VAT  11  
VAT  C07  C12  C  0  1  Y  N  N  -43.135  31.129  24.061    3.777  -1.827  -0.079  C07  VAT  12  
VAT  C08  C13  C  0  1  Y  N  N  -42.690  30.224  23.050    5.135  -1.671  -0.266  C08  VAT  13  
VAT  C09  C14  C  0  1  Y  N  N  -43.579  29.786  22.006    5.893  -0.999   0.675  C09  VAT  14  
VAT  C12  C15  C  0  1  N  N  N  -43.502  27.182  22.777    7.826   1.549   0.660  C12  VAT  15  
VAT  C14  C16  C  0  1  N  N  N  -43.028  25.797  22.394    8.983   1.957  -0.255  C14  VAT  16  
VAT  C16  C17  C  0  1  N  N  N  -43.781  23.682  23.161   10.602   3.809  -0.234  C16  VAT  17  
VAT  C18  C18  C  0  1  N  N  N  -41.865  25.238  23.208    8.625   2.966  -1.354  C18  VAT  18  
VAT  C19  C19  C  0  1  Y  N  N  -44.925  30.258  21.936    5.296  -0.478   1.810  C19  VAT  19  
VAT  C23  C20  C  0  1  N  N  N  -45.212  37.283  24.974   -1.334  -0.947  -1.926  C23  VAT  20  
VAT  C25  C21  C  0  1  N  N  N  -42.832  35.770  25.720   -2.591  -3.112  -0.469  C25  VAT  21  
VAT  C27  C22  C  0  1  Y  N  N  -41.583  38.172  25.701   -4.497  -1.757  -0.209  C27  VAT  22  
VAT  C29  C23  C  0  1  Y  N  N  -40.303  39.014  27.535   -6.429  -2.921   0.261  C29  VAT  23  
VAT  C31  C24  C  0  1  Y  N  N  -39.989  40.092  25.368   -6.577  -0.627   0.108  C31  VAT  24  
VAT  C33  C25  C  0  1  N  N  N  -39.635  41.636  23.110   -6.701   1.835  -0.053  C33  VAT  25  
VAT  C34  C26  C  0  1  Y  N  N  -41.147  42.317  22.756   -7.736   2.924   0.065  C34  VAT  26  
VAT  C35  C27  C  0  1  Y  N  N  -41.574  42.385  21.377   -7.984   3.511   1.292  C35  VAT  27  
VAT  C36  C28  C  0  1  Y  N  N  -42.853  42.953  21.021   -8.934   4.510   1.400  C36  VAT  28  
VAT  C37  C29  C  0  1  Y  N  N  -43.717  43.466  22.055   -9.634   4.922   0.282  C37  VAT  29  
VAT  C38  C30  C  0  1  Y  N  N  -43.303  43.406  23.441   -9.386   4.335  -0.945  C38  VAT  30  
VAT  C39  C31  C  0  1  Y  N  N  -42.023  42.834  23.795   -8.433   3.339  -1.054  C39  VAT  31  
VAT  C40  C32  C  0  1  Y  N  N  -40.987  39.140  24.816   -5.213  -0.565  -0.161  C40  VAT  32  
VAT  N04  N1   N  0  1  N  N  N  -43.979  33.208  26.054    0.972  -2.121   0.355  N04  VAT  33  
VAT  N11  N2   N  0  1  N  N  N  -42.437  27.703  21.790    7.630   0.413  -0.271  N11  VAT  34  
VAT  N26  N3   N  0  1  N  N  N  -42.611  37.145  25.109   -3.136  -1.749  -0.472  N26  VAT  35  
VAT  N28  N4   N  0  1  Y  N  N  -41.221  38.134  27.042   -5.137  -2.905   0.005  N28  VAT  36  
VAT  N30  N5   N  0  1  Y  N  N  -39.690  39.980  26.743   -7.142  -1.815   0.316  N30  VAT  37  
VAT  N32  N6   N  0  1  N  N  N  -39.322  41.136  24.521   -7.336   0.532   0.167  N32  VAT  38  
VAT  O01  O1   O  0  1  N  N  N  -44.237  36.438  27.686   -0.541  -4.383  -0.634  O01  VAT  39  
VAT  O21  O2   O  0  1  N  N  N  -46.111  32.963  25.299    1.186  -1.011   2.266  O21  VAT  40  
VAT  H1   H1   H  0  1  N  N  N  -43.840  28.378  20.378    7.878  -0.793   1.431  H1   VAT  41  
VAT  H2   H2   H  0  1  N  N  N  -42.265  29.243  20.369    7.758  -1.677  -0.109  H2   VAT  42  
VAT  H3   H3   H  0  1  N  N  N  -41.624  25.954  20.678    9.181   0.371  -1.780  H3   VAT  43  
VAT  H4   H4   H  0  1  N  N  N  -43.326  26.350  20.263    9.722  -0.120  -0.114  H4   VAT  44  
VAT  H5   H5   H  0  1  N  N  N  -45.145  25.305  22.718   10.020   2.650   1.513  H5   VAT  45  
VAT  H6   H6   H  0  1  N  N  N  -44.423  24.524  21.271   11.050   1.763   0.353  H6   VAT  46  
VAT  H7   H7   H  0  1  N  N  N  -42.907  24.568  24.965    9.778   4.687  -2.060  H7   VAT  47  
VAT  H8   H8   H  0  1  N  N  N  -41.876  23.322  24.183   10.591   3.106  -2.305  H8   VAT  48  
VAT  H9   H9   H  0  1  N  N  N  -46.374  31.577  22.946    3.474  -0.217   2.893  H9   VAT  49  
VAT  H10  H10  H  0  1  N  N  N  -45.387  35.139  24.855    0.369  -2.266  -2.016  H10  VAT  50  
VAT  H11  H11  H  0  1  N  N  N  -46.281  35.889  26.221   -1.108  -2.919  -2.768  H11  VAT  51  
VAT  H12  H12  H  0  1  N  N  N  -43.801  36.915  23.330   -3.291  -0.069  -1.724  H12  VAT  52  
VAT  H13  H13  H  0  1  N  N  N  -43.746  38.587  23.984   -3.272  -1.638  -2.565  H13  VAT  53  
VAT  H14  H14  H  0  1  N  N  N  -43.672  34.021  27.968   -0.939  -1.301   0.626  H14  VAT  54  
VAT  H15  H15  H  0  1  N  N  N  -45.377  34.009  27.404   -0.646  -2.833   1.484  H15  VAT  55  
VAT  H16  H16  H  0  1  N  N  N  -42.463  31.449  24.844    3.186  -2.352  -0.815  H16  VAT  56  
VAT  H17  H17  H  0  1  N  N  N  -41.672  29.863  23.069    5.607  -2.075  -1.150  H17  VAT  57  
VAT  H18  H18  H  0  1  N  N  N  -44.542  27.410  22.501    8.139   1.249   1.660  H18  VAT  58  
VAT  H19  H19  H  0  1  N  N  N  -43.334  27.456  23.829    6.999   2.260   0.667  H19  VAT  59  
VAT  H20  H20  H  0  1  N  N  N  -44.596  23.366  23.829   10.179   4.652   0.312  H20  VAT  60  
VAT  H21  H21  H  0  1  N  N  N  -43.484  22.839  22.520   11.684   3.911  -0.314  H21  VAT  61  
VAT  H22  H22  H  0  1  N  N  N  -41.426  26.004  23.864    7.873   3.669  -0.997  H22  VAT  62  
VAT  H23  H23  H  0  1  N  N  N  -41.082  24.818  22.559    8.273   2.449  -2.247  H23  VAT  63  
VAT  H24  H24  H  0  1  N  N  N  -45.591  29.938  21.149    5.894   0.046   2.541  H24  VAT  64  
VAT  H25  H25  H  0  1  N  N  N  -46.013  37.386  24.228   -0.911  -0.363  -1.108  H25  VAT  65  
VAT  H26  H26  H  0  1  N  N  N  -45.332  38.054  25.749   -1.121  -0.454  -2.874  H26  VAT  66  
VAT  H27  H27  H  0  1  N  N  N  -41.979  35.549  26.379   -3.016  -3.675  -1.300  H27  VAT  67  
VAT  H28  H28  H  0  1  N  N  N  -42.864  35.035  24.902   -2.847  -3.603   0.470  H28  VAT  68  
VAT  H29  H29  H  0  1  N  N  N  -40.042  38.959  28.581   -6.918  -3.869   0.431  H29  VAT  69  
VAT  H30  H30  H  0  1  N  N  N  -38.881  42.401  22.872   -6.260   1.860  -1.049  H30  VAT  70  
VAT  H31  H31  H  0  1  N  N  N  -39.511  40.776  22.436   -5.923   1.990   0.694  H31  VAT  71  
VAT  H32  H32  H  0  1  N  N  N  -40.926  42.005  20.601   -7.437   3.189   2.165  H32  VAT  72  
VAT  H33  H33  H  0  1  N  N  N  -43.161  42.993  19.986   -9.128   4.969   2.358  H33  VAT  73  
VAT  H34  H34  H  0  1  N  N  N  -44.673  43.895  21.795  -10.377   5.702   0.367  H34  VAT  74  
VAT  H35  H35  H  0  1  N  N  N  -43.953  43.790  24.214   -9.933   4.657  -1.818  H35  VAT  75  
VAT  H36  H36  H  0  1  N  N  N  -41.718  42.791  24.830   -8.236   2.884  -2.013  H36  VAT  76  
VAT  H37  H37  H  0  1  N  N  N  -41.260  39.173  23.772   -4.723   0.383  -0.326  H37  VAT  77  
VAT  H38  H38  H  0  1  N  N  N  -43.021  32.937  25.962    1.392  -2.485  -0.440  H38  VAT  78  
VAT  H40  H40  H  0  1  N  N  N  -39.365  41.962  25.082   -8.286   0.481   0.354  H40  VAT  79  
VAT  H41  H41  H  0  1  N  N  N  -43.505  36.253  28.263    0.421  -4.423  -0.728  H41  VAT  80  
#   #
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
VAT  C10  C09  SING  N  N   1  
VAT  C10  N11  SING  N  N   2  
VAT  C13  C14  SING  N  N   3  
VAT  C13  N11  SING  N  N   4  
VAT  C15  C14  SING  N  N   5  
VAT  C15  C16  SING  N  N   6  
VAT  C17  C16  SING  N  N   7  
VAT  C17  C18  SING  N  N   8  
VAT  C20  C06  DOUB  Y  N   9  
VAT  C20  C19  SING  Y  N  10  
VAT  C22  C02  SING  N  N  11  
VAT  C22  C23  SING  N  N  12  
VAT  C24  C23  SING  N  N  13  
VAT  C24  N26  SING  N  N  14  
VAT  C02  C03  SING  N  N  15  
VAT  C02  C25  SING  N  N  16  
VAT  C02  O01  SING  N  N  17  
VAT  C03  N04  SING  N  N  18  
VAT  C05  C06  SING  N  N  19  
VAT  C05  N04  SING  N  N  20  
VAT  C05  O21  DOUB  N  N  21  
VAT  C06  C07  SING  Y  N  22  
VAT  C07  C08  DOUB  Y  N  23  
VAT  C08  C09  SING  Y  N  24  
VAT  C09  C19  DOUB  Y  N  25  
VAT  C12  C14  SING  N  N  26  
VAT  C12  N11  SING  N  N  27  
VAT  C14  C18  SING  N  N  28  
VAT  C25  N26  SING  N  N  29  
VAT  C27  C40  DOUB  Y  N  30  
VAT  C27  N26  SING  N  N  31  
VAT  C27  N28  SING  Y  N  32  
VAT  C29  N28  DOUB  Y  N  33  
VAT  C29  N30  SING  Y  N  34  
VAT  C31  C40  SING  Y  N  35  
VAT  C31  N30  DOUB  Y  N  36  
VAT  C31  N32  SING  N  N  37  
VAT  C33  N32  SING  N  N  38  
VAT  C34  C35  DOUB  Y  N  39  
VAT  C34  C39  SING  Y  N  40  
VAT  C35  C36  SING  Y  N  41  
VAT  C36  C37  DOUB  Y  N  42  
VAT  C37  C38  SING  Y  N  43  
VAT  C38  C39  DOUB  Y  N  44  
VAT  C33  C34  SING  N  N  45  
VAT  C10  H1   SING  N  N  46  
VAT  C10  H2   SING  N  N  47  
VAT  C13  H3   SING  N  N  48  
VAT  C13  H4   SING  N  N  49  
VAT  C15  H5   SING  N  N  50  
VAT  C15  H6   SING  N  N  51  
VAT  C17  H7   SING  N  N  52  
VAT  C17  H8   SING  N  N  53  
VAT  C20  H9   SING  N  N  54  
VAT  C22  H10  SING  N  N  55  
VAT  C22  H11  SING  N  N  56  
VAT  C24  H12  SING  N  N  57  
VAT  C24  H13  SING  N  N  58  
VAT  C03  H14  SING  N  N  59  
VAT  C03  H15  SING  N  N  60  
VAT  C07  H16  SING  N  N  61  
VAT  C08  H17  SING  N  N  62  
VAT  C12  H18  SING  N  N  63  
VAT  C12  H19  SING  N  N  64  
VAT  C16  H20  SING  N  N  65  
VAT  C16  H21  SING  N  N  66  
VAT  C18  H22  SING  N  N  67  
VAT  C18  H23  SING  N  N  68  
VAT  C19  H24  SING  N  N  69  
VAT  C23  H25  SING  N  N  70  
VAT  C23  H26  SING  N  N  71  
VAT  C25  H27  SING  N  N  72  
VAT  C25  H28  SING  N  N  73  
VAT  C29  H29  SING  N  N  74  
VAT  C33  H30  SING  N  N  75  
VAT  C33  H31  SING  N  N  76  
VAT  C35  H32  SING  N  N  77  
VAT  C36  H33  SING  N  N  78  
VAT  C37  H34  SING  N  N  79  
VAT  C38  H35  SING  N  N  80  
VAT  C39  H36  SING  N  N  81  
VAT  C40  H37  SING  N  N  82  
VAT  N04  H38  SING  N  N  83  
VAT  N32  H40  SING  N  N  84  
VAT  O01  H41  SING  N  N  85  
#   #
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
VAT  InChI             InChI                 1.03   "InChI=1S/C32H40N6O2/c39-30(27-11-9-26(10-12-27)19-37-21-31(22-37)13-4-5-14-31)34-20-32(40)15-6-16-38(23-32)29-17-28(35-24-36-29)33-18-25-7-2-1-3-8-25/h1-3,7-12,17,24,40H,4-6,13-16,18-23H2,(H,34,39)(H,33,35,36)/t32-/m1/s1"  
VAT  InChIKey          InChI                 1.03   SVCYBAWPGFFEQO-JGCGQSQUSA-N  
VAT  SMILES_CANONICAL  CACTVS                3.385  "O[C@]1(CCCN(C1)c2cc(NCc3ccccc3)ncn2)CNC(=O)c4ccc(CN5CC6(CCCC6)C5)cc4"  
VAT  SMILES            CACTVS                3.385  "O[C]1(CCCN(C1)c2cc(NCc3ccccc3)ncn2)CNC(=O)c4ccc(CN5CC6(CCCC6)C5)cc4"  
VAT  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "c1ccc(cc1)CNc2cc(ncn2)N3CCC[C@](C3)(CNC(=O)c4ccc(cc4)CN5CC6(C5)CCCC6)O"  
VAT  SMILES            "OpenEye OEToolkits"  2.0.7  "c1ccc(cc1)CNc2cc(ncn2)N3CCCC(C3)(CNC(=O)c4ccc(cc4)CN5CC6(C5)CCCC6)O"  
#
_pdbx_chem_comp_identifier.comp_id          VAT
_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-(2-azaspiro[3.4]octan-2-ylmethyl)-~{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
VAT  "Create component"  2021-05-04  PDBE  
VAT  "Initial release"   2021-10-20  RCSB  
##
