data_VA8
#

_chem_comp.id                                   VA8
_chem_comp.name                                 "~{N}-[[(3~{R})-1-[6-(3~{H}-benzimidazol-4-ylmethylamino)pyrimidin-4-yl]-3-oxidanyl-piperidin-3-yl]methyl]-4-[(4,4-dimethylpiperidin-1-yl)methyl]benzamide"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C33 H42 N8 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                       582.739
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    VA8
_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       7OEL
_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
VA8  C10  C1   C  0  1  Y  N  N  -43.256  31.256  24.387   -4.559  -0.357  -2.112  C10  VA8   1  
VA8  C13  C2   C  0  1  Y  N  N  -44.552  31.716  24.482   -3.885  -1.186  -1.213  C13  VA8   2  
VA8  C17  C3   C  0  1  N  N  R  -44.351  35.889  26.673    0.132  -3.411   0.446  C17  VA8   3  
VA8  C20  C4   C  0  1  N  N  N  -43.472  37.509  24.288    1.987  -1.688   1.854  C20  VA8   4  
VA8  C21  C5   C  0  1  N  N  N  -42.875  35.976  26.124    1.652  -3.565   0.357  C21  VA8   5  
VA8  C01  C6   C  0  1  N  N  N  -44.660  24.125  22.498  -10.187   3.627  -0.330  C01  VA8   6  
VA8  C02  C7   C  0  1  N  N  N  -43.262  24.746  22.880   -9.337   3.275   0.893  C02  VA8   7  
VA8  C03  C8   C  0  1  N  N  N  -42.441  23.802  23.736   -9.432   4.403   1.923  C03  VA8   8  
VA8  C04  C9   C  0  1  N  N  N  -43.521  25.936  23.706   -7.878   3.093   0.467  C04  VA8   9  
VA8  C05  C10  C  0  1  N  N  N  -43.778  27.204  22.928   -7.781   1.925  -0.517  C05  VA8  10  
VA8  C07  C11  C  0  1  N  N  N  -43.251  28.848  21.266   -8.074  -0.467  -0.743  C07  VA8  11  
VA8  C08  C12  C  0  1  Y  N  N  -43.675  29.860  22.377   -6.597  -0.718  -0.907  C08  VA8  12  
VA8  C09  C13  C  0  1  Y  N  N  -42.813  30.354  23.379   -5.911  -0.129  -1.954  C09  VA8  13  
VA8  C11  C14  C  0  1  Y  N  N  -44.975  30.355  22.445   -5.937  -1.549  -0.019  C11  VA8  14  
VA8  C12  C15  C  0  1  Y  N  N  -45.415  31.238  23.445   -4.585  -1.782  -0.163  C12  VA8  15  
VA8  C14  C16  C  0  1  N  N  N  -44.984  32.727  25.523   -2.436  -1.432  -1.374  C14  VA8  16  
VA8  C16  C17  C  0  1  N  N  N  -44.531  34.487  27.269   -0.352  -2.475  -0.663  C16  VA8  17  
VA8  C18  C18  C  0  1  N  N  N  -45.245  36.062  25.438   -0.237  -2.821   1.810  C18  VA8  18  
VA8  C19  C19  C  0  1  N  N  N  -44.956  37.345  24.708    0.477  -1.479   1.987  C19  VA8  19  
VA8  C23  C20  C  0  1  Y  N  N  -41.477  38.178  25.781    3.659  -2.335   0.328  C23  VA8  20  
VA8  C25  C21  C  0  1  Y  N  N  -40.112  39.126  27.398    5.528  -3.583  -0.179  C25  VA8  21  
VA8  C27  C22  C  0  1  Y  N  N  -40.051  40.193  25.309    5.824  -1.332   0.214  C27  VA8  22  
VA8  C29  C23  C  0  1  N  N  N  -40.130  41.551  22.971    6.108   1.084   0.640  C29  VA8  23  
VA8  C30  C24  C  0  1  Y  N  N  -41.463  42.443  22.749    7.219   2.102   0.678  C30  VA8  24  
VA8  C31  C25  C  0  1  Y  N  N  -42.136  43.048  23.877    7.708   2.645  -0.502  C31  VA8  25  
VA8  C33  C26  C  0  1  Y  N  N  -42.948  43.850  25.927    8.231   3.289  -2.548  C33  VA8  26  
VA8  C35  C27  C  0  1  Y  N  N  -43.340  43.868  23.687    8.744   3.593  -0.458  C35  VA8  27  
VA8  C36  C28  C  0  1  Y  N  N  -43.815  44.042  22.354    9.271   3.979   0.777  C36  VA8  28  
VA8  C37  C29  C  0  1  Y  N  N  -43.192  43.475  21.281    8.777   3.434   1.929  C37  VA8  29  
VA8  C38  C30  C  0  1  Y  N  N  -42.013  42.678  21.493    7.751   2.501   1.886  C38  VA8  30  
VA8  C39  C31  C  0  1  Y  N  N  -40.995  39.195  24.908    4.456  -1.199   0.433  C39  VA8  31  
VA8  C42  C32  C  0  1  N  N  N  -42.719  26.466  20.936   -9.693   0.836   0.498  C42  VA8  32  
VA8  C43  C33  C  0  1  N  N  N  -42.413  25.113  21.628   -9.847   1.971   1.513  C43  VA8  33  
VA8  N06  N1   N  0  1  N  N  N  -42.821  27.570  21.895   -8.280   0.701   0.123  N06  VA8  34  
VA8  N15  N2   N  0  1  N  N  N  -44.112  33.476  26.307   -1.788  -2.232  -0.504  N15  VA8  35  
VA8  N22  N3   N  0  1  N  N  N  -42.426  37.167  25.311    2.290  -2.254   0.532  N22  VA8  36  
VA8  N24  N4   N  0  1  Y  N  N  -41.008  38.176  27.072    4.228  -3.499   0.022  N24  VA8  37  
VA8  N26  N5   N  0  1  Y  N  N  -39.605  40.129  26.623    6.317  -2.532  -0.088  N26  VA8  38  
VA8  N28  N6   N  0  1  N  N  N  -39.597  41.201  24.382    6.661  -0.231   0.307  N28  VA8  39  
VA8  N32  N7   N  0  1  Y  N  N  -41.926  43.071  25.320    7.405   2.474  -1.837  N32  VA8  40  
VA8  N34  N8   N  0  1  Y  N  N  -43.795  44.330  24.990    9.014   3.944  -1.742  N34  VA8  41  
VA8  O40  O1   O  0  1  N  N  N  -44.684  36.762  27.670   -0.486  -4.690   0.296  O40  VA8  42  
VA8  O41  O2   O  0  1  N  N  N  -46.184  32.989  25.684   -1.829  -0.912  -2.290  O41  VA8  43  
VA8  H1   H1   H  0  1  N  N  N  -42.538  31.599  25.117   -4.023   0.107  -2.927  H1   VA8  44  
VA8  H2   H2   H  0  1  N  N  N  -43.303  36.864  23.413    2.497  -0.731   1.966  H2   VA8  45  
VA8  H3   H3   H  0  1  N  N  N  -43.324  38.561  24.002    2.328  -2.374   2.629  H3   VA8  46  
VA8  H4   H4   H  0  1  N  N  N  -42.721  35.088  25.493    1.995  -4.242   1.139  H4   VA8  47  
VA8  H5   H5   H  0  1  N  N  N  -42.210  35.924  26.999    1.920  -3.972  -0.618  H5   VA8  48  
VA8  H6   H6   H  0  1  N  N  N  -45.218  23.884  23.415  -10.121   2.822  -1.062  H6   VA8  49  
VA8  H7   H7   H  0  1  N  N  N  -45.232  24.850  21.900  -11.226   3.756  -0.025  H7   VA8  50  
VA8  H8   H8   H  0  1  N  N  N  -44.505  23.207  21.912   -9.820   4.552  -0.773  H8   VA8  51  
VA8  H9   H9   H  0  1  N  N  N  -43.016  23.524  24.631  -10.471   4.531   2.227  H9   VA8  52  
VA8  H10  H10  H  0  1  N  N  N  -42.202  22.897  23.158   -8.827   4.152   2.794  H10  VA8  53  
VA8  H11  H11  H  0  1  N  N  N  -41.508  24.300  24.040   -9.067   5.330   1.481  H11  VA8  54  
VA8  H12  H12  H  0  1  N  N  N  -44.403  25.733  24.331   -7.523   4.004  -0.013  H12  VA8  55  
VA8  H13  H13  H  0  1  N  N  N  -42.645  26.102  24.351   -7.267   2.882   1.345  H13  VA8  56  
VA8  H14  H14  H  0  1  N  N  N  -43.813  28.032  23.652   -8.382   2.144  -1.400  H14  VA8  57  
VA8  H15  H15  H  0  1  N  N  N  -44.760  27.099  22.444   -6.741   1.783  -0.811  H15  VA8  58  
VA8  H16  H16  H  0  1  N  N  N  -42.417  29.269  20.685   -8.521  -0.279  -1.720  H16  VA8  59  
VA8  H17  H17  H  0  1  N  N  N  -44.104  28.659  20.598   -8.543  -1.342  -0.292  H17  VA8  60  
VA8  H18  H18  H  0  1  N  N  N  -41.781  30.036  23.381   -6.433   0.512  -2.648  H18  VA8  61  
VA8  H19  H19  H  0  1  N  N  N  -45.681  30.044  21.690   -6.482  -2.016   0.788  H19  VA8  62  
VA8  H20  H20  H  0  1  N  N  N  -46.443  31.569  23.431   -4.071  -2.431   0.531  H20  VA8  63  
VA8  H21  H21  H  0  1  N  N  N  -45.590  34.332  27.521    0.186  -1.529  -0.601  H21  VA8  64  
VA8  H22  H22  H  0  1  N  N  N  -43.920  34.398  28.180   -0.167  -2.936  -1.634  H22  VA8  65  
VA8  H23  H23  H  0  1  N  N  N  -46.297  36.065  25.759   -1.316  -2.670   1.861  H23  VA8  66  
VA8  H24  H24  H  0  1  N  N  N  -45.073  35.218  24.754    0.072  -3.507   2.599  H24  VA8  67  
VA8  H25  H25  H  0  1  N  N  N  -45.225  38.185  25.365    0.251  -1.074   2.974  H25  VA8  68  
VA8  H26  H26  H  0  1  N  N  N  -45.578  37.375  23.801    0.137  -0.782   1.221  H26  VA8  69  
VA8  H27  H27  H  0  1  N  N  N  -39.743  39.090  28.412    5.959  -4.542  -0.425  H27  VA8  70  
VA8  H28  H28  H  0  1  N  N  N  -40.315  40.591  22.466    5.623   1.038   1.615  H28  VA8  71  
VA8  H29  H29  H  0  1  N  N  N  -39.315  42.084  22.459    5.377   1.373  -0.116  H29  VA8  72  
VA8  H30  H30  H  0  1  N  N  N  -43.035  44.033  26.988    8.236   3.378  -3.624  H30  VA8  73  
VA8  H31  H31  H  0  1  N  N  N  -44.697  44.643  22.188   10.068   4.707   0.822  H31  VA8  74  
VA8  H32  H32  H  0  1  N  N  N  -43.579  43.623  20.284    9.185   3.737   2.882  H32  VA8  75  
VA8  H33  H33  H  0  1  N  N  N  -41.530  42.239  20.632    7.371   2.079   2.805  H33  VA8  76  
VA8  H34  H34  H  0  1  N  N  N  -41.360  39.214  23.892    4.025  -0.240   0.679  H34  VA8  77  
VA8  H35  H35  H  0  1  N  N  N  -41.911  26.690  20.223  -10.042  -0.097   0.941  H35  VA8  78  
VA8  H36  H36  H  0  1  N  N  N  -43.672  26.379  20.394  -10.285   1.059  -0.390  H36  VA8  79  
VA8  H37  H37  H  0  1  N  N  N  -42.563  24.319  20.882   -9.267   1.741   2.406  H37  VA8  80  
VA8  H38  H38  H  0  1  N  N  N  -41.358  25.131  21.938  -10.898   2.081   1.779  H38  VA8  81  
VA8  H40  H40  H  0  1  N  N  N  -43.131  33.309  26.203   -2.272  -2.647   0.227  H40  VA8  82  
VA8  H41  H41  H  0  1  N  N  N  -38.632  40.984  24.234    7.614  -0.331   0.153  H41  VA8  83  
VA8  H42  H42  H  0  1  N  N  N  -41.182  42.612  25.805    6.728   1.881  -2.202  H42  VA8  84  
VA8  H44  H44  H  0  1  N  N  N  -44.111  36.626  28.415   -1.452  -4.668   0.343  H44  VA8  85  
#   #
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
VA8  C42  C43  SING  N  N   1  
VA8  C42  N06  SING  N  N   2  
VA8  C07  N06  SING  N  N   3  
VA8  C07  C08  SING  N  N   4  
VA8  C37  C38  DOUB  Y  N   5  
VA8  C37  C36  SING  Y  N   6  
VA8  C38  C30  SING  Y  N   7  
VA8  C43  C02  SING  N  N   8  
VA8  N06  C05  SING  N  N   9  
VA8  C36  C35  DOUB  Y  N  10  
VA8  C08  C11  DOUB  Y  N  11  
VA8  C08  C09  SING  Y  N  12  
VA8  C11  C12  SING  Y  N  13  
VA8  C01  C02  SING  N  N  14  
VA8  C30  C29  SING  N  N  15  
VA8  C30  C31  DOUB  Y  N  16  
VA8  C02  C04  SING  N  N  17  
VA8  C02  C03  SING  N  N  18  
VA8  C05  C04  SING  N  N  19  
VA8  C29  N28  SING  N  N  20  
VA8  C09  C10  DOUB  Y  N  21  
VA8  C12  C13  DOUB  Y  N  22  
VA8  C35  C31  SING  Y  N  23  
VA8  C35  N34  SING  Y  N  24  
VA8  C31  N32  SING  Y  N  25  
VA8  C20  C19  SING  N  N  26  
VA8  C20  N22  SING  N  N  27  
VA8  N28  C27  SING  N  N  28  
VA8  C10  C13  SING  Y  N  29  
VA8  C13  C14  SING  N  N  30  
VA8  C19  C18  SING  N  N  31  
VA8  C39  C27  DOUB  Y  N  32  
VA8  C39  C23  SING  Y  N  33  
VA8  N34  C33  DOUB  Y  N  34  
VA8  C27  N26  SING  Y  N  35  
VA8  N22  C23  SING  N  N  36  
VA8  N22  C21  SING  N  N  37  
VA8  N32  C33  SING  Y  N  38  
VA8  C18  C17  SING  N  N  39  
VA8  C14  O41  DOUB  N  N  40  
VA8  C14  N15  SING  N  N  41  
VA8  C23  N24  DOUB  Y  N  42  
VA8  C21  C17  SING  N  N  43  
VA8  N15  C16  SING  N  N  44  
VA8  N26  C25  DOUB  Y  N  45  
VA8  C17  C16  SING  N  N  46  
VA8  C17  O40  SING  N  N  47  
VA8  N24  C25  SING  Y  N  48  
VA8  C10  H1   SING  N  N  49  
VA8  C20  H2   SING  N  N  50  
VA8  C20  H3   SING  N  N  51  
VA8  C21  H4   SING  N  N  52  
VA8  C21  H5   SING  N  N  53  
VA8  C01  H6   SING  N  N  54  
VA8  C01  H7   SING  N  N  55  
VA8  C01  H8   SING  N  N  56  
VA8  C03  H9   SING  N  N  57  
VA8  C03  H10  SING  N  N  58  
VA8  C03  H11  SING  N  N  59  
VA8  C04  H12  SING  N  N  60  
VA8  C04  H13  SING  N  N  61  
VA8  C05  H14  SING  N  N  62  
VA8  C05  H15  SING  N  N  63  
VA8  C07  H16  SING  N  N  64  
VA8  C07  H17  SING  N  N  65  
VA8  C09  H18  SING  N  N  66  
VA8  C11  H19  SING  N  N  67  
VA8  C12  H20  SING  N  N  68  
VA8  C16  H21  SING  N  N  69  
VA8  C16  H22  SING  N  N  70  
VA8  C18  H23  SING  N  N  71  
VA8  C18  H24  SING  N  N  72  
VA8  C19  H25  SING  N  N  73  
VA8  C19  H26  SING  N  N  74  
VA8  C25  H27  SING  N  N  75  
VA8  C29  H28  SING  N  N  76  
VA8  C29  H29  SING  N  N  77  
VA8  C33  H30  SING  N  N  78  
VA8  C36  H31  SING  N  N  79  
VA8  C37  H32  SING  N  N  80  
VA8  C38  H33  SING  N  N  81  
VA8  C39  H34  SING  N  N  82  
VA8  C42  H35  SING  N  N  83  
VA8  C42  H36  SING  N  N  84  
VA8  C43  H37  SING  N  N  85  
VA8  C43  H38  SING  N  N  86  
VA8  N15  H40  SING  N  N  87  
VA8  N28  H41  SING  N  N  88  
VA8  N32  H42  SING  N  N  89  
VA8  O40  H44  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
VA8  InChI             InChI                 1.03   "InChI=1S/C33H42N8O2/c1-32(2)12-15-40(16-13-32)19-24-7-9-25(10-8-24)31(42)35-20-33(43)11-4-14-41(21-33)29-17-28(37-23-38-29)34-18-26-5-3-6-27-30(26)39-22-36-27/h3,5-10,17,22-23,43H,4,11-16,18-21H2,1-2H3,(H,35,42)(H,36,39)(H,34,37,38)/t33-/m1/s1"  
VA8  InChIKey          InChI                 1.03   IASLOXMPEUOUSU-MGBGTMOVSA-N  
VA8  SMILES_CANONICAL  CACTVS                3.385  "CC1(C)CCN(CC1)Cc2ccc(cc2)C(=O)NC[C@]3(O)CCCN(C3)c4cc(NCc5cccc6nc[nH]c56)ncn4"  
VA8  SMILES            CACTVS                3.385  "CC1(C)CCN(CC1)Cc2ccc(cc2)C(=O)NC[C]3(O)CCCN(C3)c4cc(NCc5cccc6nc[nH]c56)ncn4"  
VA8  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "CC1(CCN(CC1)Cc2ccc(cc2)C(=O)NC[C@@]3(CCCN(C3)c4cc(ncn4)NCc5cccc6c5[nH]cn6)O)C"  
VA8  SMILES            "OpenEye OEToolkits"  2.0.7  "CC1(CCN(CC1)Cc2ccc(cc2)C(=O)NCC3(CCCN(C3)c4cc(ncn4)NCc5cccc6c5[nH]cn6)O)C"  
#
_pdbx_chem_comp_identifier.comp_id          VA8
_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       "~{N}-[[(3~{R})-1-[6-(3~{H}-benzimidazol-4-ylmethylamino)pyrimidin-4-yl]-3-oxidanyl-piperidin-3-yl]methyl]-4-[(4,4-dimethylpiperidin-1-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
VA8  "Create component"  2021-05-04  PDBE  
VA8  "Initial release"   2021-10-20  RCSB  
##
