data_5NK
#

_chem_comp.id                                   5NK
_chem_comp.name                                 "2-[[2-[[1-(2-azanylethyl)piperidin-4-yl]amino]-4-methyl-benzimidazol-1-yl]methyl]-6-methyl-pyridin-3-ol"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C22 H30 N6 O"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        JNJ-2408068
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2015-10-27
_chem_comp.pdbx_modified_date                   2020-06-17
_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                       394.513
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    5NK
_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       5EA3
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 RCSB
#   #
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
5NK  C10  C1   C  0  1  N  N  N  23.738  16.920  23.869  -1.276   4.513   1.543  C10  5NK   1  
5NK  C15  C2   C  0  1  Y  N  N  16.094  21.366  22.018  -2.974  -3.901   1.092  C15  5NK   2  
5NK  C17  C3   C  0  1  Y  N  N  18.462  22.280  22.034  -3.776  -2.066  -0.203  C17  5NK   3  
5NK  C20  C4   C  0  1  N  N  N  24.482  22.656  22.928   2.664   1.216  -1.027  C20  5NK   4  
5NK  C21  C5   C  0  1  N  N  N  24.406  22.795  24.437   4.051   1.519  -0.456  C21  5NK   5  
5NK  C24  C6   C  0  1  N  N  N  23.065  24.596  22.656   2.781  -1.037   0.041  C24  5NK   6  
5NK  C26  C7   C  0  1  N  N  N  25.790  25.665  25.968   7.029  -0.739  -0.053  C26  5NK   7  
5NK  C28  C8   C  0  1  N  N  N  15.506  19.244  20.527  -0.546  -4.488   1.054  C28  5NK   8  
5NK  C01  C9   C  0  1  Y  N  N  22.743  17.239  22.721  -2.185   3.553   0.819  C01  5NK   9  
5NK  C02  C10  C  0  1  Y  N  N  22.190  16.133  21.845  -3.529   3.829   0.702  C02  5NK  10  
5NK  C03  C11  C  0  1  Y  N  N  21.237  16.461  20.748  -4.372   2.951   0.037  C03  5NK  11  
5NK  C04  C12  C  0  1  Y  N  N  20.837  17.894  20.520  -3.875   1.789  -0.517  C04  5NK  12  
5NK  C05  C13  C  0  1  Y  N  N  22.319  18.723  22.471  -1.665   2.384   0.258  C05  5NK  13  
5NK  C06  C14  C  0  1  Y  N  N  21.426  19.031  21.439  -2.524   1.496  -0.410  C06  5NK  14  
5NK  N07  N1   N  0  1  Y  N  N  21.224  20.396  21.451  -1.732   0.445  -0.842  N07  5NK  15  
5NK  C08  C15  C  0  1  Y  N  N  21.998  20.947  22.486  -0.455   0.707  -0.436  C08  5NK  16  
5NK  N09  N2   N  0  1  Y  N  N  22.670  19.902  23.111  -0.416   1.850   0.202  N09  5NK  17  
5NK  C11  C16  C  0  1  N  N  N  20.367  21.120  20.530  -2.181  -0.730  -1.594  C11  5NK  18  
5NK  C12  C17  C  0  1  Y  N  N  18.893  21.184  21.042  -2.476  -1.856  -0.637  C12  5NK  19  
5NK  N13  N3   N  0  1  Y  N  N  17.921  20.217  20.565  -1.496  -2.638  -0.229  N13  5NK  20  
5NK  C14  C18  C  0  1  Y  N  N  16.526  20.274  21.031  -1.705  -3.632   0.612  C14  5NK  21  
5NK  C16  C19  C  0  1  Y  N  N  17.070  22.347  22.498  -4.034  -3.110   0.680  C16  5NK  22  
5NK  N18  N4   N  0  1  N  N  N  22.088  22.367  22.847   0.634  -0.105  -0.674  N18  5NK  23  
5NK  C19  C20  C  0  1  N  N  N  23.243  23.176  22.324   1.939   0.234  -0.102  C19  5NK  24  
5NK  N22  N5   N  0  1  N  N  N  24.265  24.183  24.864   4.817   0.272  -0.339  N22  5NK  25  
5NK  C23  C21  C  0  1  N  N  N  23.182  24.897  24.137   4.165  -0.668   0.582  C23  5NK  26  
5NK  C25  C22  C  0  1  N  N  N  25.467  24.855  24.692   6.200   0.540   0.076  C25  5NK  27  
5NK  N27  N6   N  0  1  N  N  N  25.714  24.817  27.134   8.413  -0.470   0.361  N27  5NK  28  
5NK  O29  O1   O  0  1  N  N  N  19.391  23.216  22.484  -4.785  -1.263  -0.634  O29  5NK  29  
5NK  H1   H1   H  0  1  N  N  N  24.768  16.963  23.485  -1.236   4.247   2.600  H1   5NK  30  
5NK  H2   H2   H  0  1  N  N  N  23.616  17.658  24.675  -0.275   4.458   1.116  H2   5NK  31  
5NK  H3   H3   H  0  1  N  N  N  23.535  15.912  24.261  -1.661   5.527   1.438  H3   5NK  32  
5NK  H4   H4   H  0  1  N  N  N  15.070  21.411  22.359  -3.137  -4.720   1.776  H4   5NK  33  
5NK  H5   H5   H  0  1  N  N  N  24.602  21.595  22.663   2.090   2.140  -1.099  H5   5NK  34  
5NK  H6   H6   H  0  1  N  N  N  25.342  23.228  22.550   2.768   0.774  -2.018  H6   5NK  35  
5NK  H7   H7   H  0  1  N  N  N  23.539  22.224  24.801   4.575   2.207  -1.119  H7   5NK  36  
5NK  H8   H8   H  0  1  N  N  N  25.326  22.383  24.876   3.946   1.974   0.529  H8   5NK  37  
5NK  H9   H9   H  0  1  N  N  N  23.833  25.176  22.122   2.291  -1.722   0.732  H9   5NK  38  
5NK  H10  H10  H  0  1  N  N  N  22.067  24.909  22.316   2.887  -1.515  -0.933  H10  5NK  39  
5NK  H11  H11  H  0  1  N  N  N  26.806  26.080  25.887   6.603  -1.514   0.584  H11  5NK  40  
5NK  H12  H12  H  0  1  N  N  N  25.065  26.486  26.069   7.020  -1.075  -1.090  H12  5NK  41  
5NK  H13  H13  H  0  1  N  N  N  15.999  18.549  19.831  -0.101  -4.060   1.953  H13  5NK  42  
5NK  H14  H14  H  0  1  N  N  N  15.101  18.681  21.381  -0.900  -5.496   1.270  H14  5NK  43  
5NK  H15  H15  H  0  1  N  N  N  14.687  19.763  20.008   0.201  -4.526   0.262  H15  5NK  44  
5NK  H16  H16  H  0  1  N  N  N  22.486  15.109  22.016  -3.929   4.735   1.132  H16  5NK  45  
5NK  H17  H17  H  0  1  N  N  N  20.837  15.677  20.122  -5.424   3.178  -0.047  H17  5NK  46  
5NK  H18  H18  H  0  1  N  N  N  20.147  18.143  19.727  -4.537   1.110  -1.033  H18  5NK  47  
5NK  H19  H19  H  0  1  N  N  N  20.384  20.613  19.554  -3.085  -0.481  -2.151  H19  5NK  48  
5NK  H20  H20  H  0  1  N  N  N  20.750  22.145  20.417  -1.400  -1.038  -2.288  H20  5NK  49  
5NK  H21  H21  H  0  1  N  N  N  16.767  23.118  23.191  -5.036  -3.299   1.036  H21  5NK  50  
5NK  H22  H22  H  0  1  N  N  N  22.124  22.415  23.845   0.536  -0.901  -1.220  H22  5NK  51  
5NK  H23  H23  H  0  1  N  N  N  23.294  23.060  21.231   1.801   0.692   0.878  H23  5NK  52  
5NK  H25  H25  H  0  1  N  N  N  23.358  25.977  24.248   4.059  -0.203   1.562  H25  5NK  53  
5NK  H26  H26  H  0  1  N  N  N  22.226  24.630  24.611   4.772  -1.569   0.671  H26  5NK  54  
5NK  H27  H27  H  0  1  N  N  N  26.271  24.127  24.506   6.210   0.876   1.113  H27  5NK  55  
5NK  H28  H28  H  0  1  N  N  N  25.386  25.539  23.834   6.627   1.316  -0.561  H28  5NK  56  
5NK  H29  H29  H  0  1  N  N  N  25.925  25.353  27.951   8.443  -0.096   1.298  H29  5NK  57  
5NK  H30  H30  H  0  1  N  N  N  24.791  24.440  27.212   8.981  -1.300   0.285  H30  5NK  58  
5NK  H32  H32  H  0  1  N  N  N  18.969  23.818  23.086  -4.986  -0.529  -0.037  H32  5NK  59  
#   #
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
5NK  C04  C03  DOUB  Y  N   1  
5NK  C04  C06  SING  Y  N   2  
5NK  C28  C14  SING  N  N   3  
5NK  C11  C12  SING  N  N   4  
5NK  C11  N07  SING  N  N   5  
5NK  N13  C14  DOUB  Y  N   6  
5NK  N13  C12  SING  Y  N   7  
5NK  C03  C02  SING  Y  N   8  
5NK  C14  C15  SING  Y  N   9  
5NK  C12  C17  DOUB  Y  N  10  
5NK  C06  N07  SING  Y  N  11  
5NK  C06  C05  DOUB  Y  N  12  
5NK  N07  C08  SING  Y  N  13  
5NK  C02  C01  DOUB  Y  N  14  
5NK  C15  C16  DOUB  Y  N  15  
5NK  C17  O29  SING  N  N  16  
5NK  C17  C16  SING  Y  N  17  
5NK  C19  C24  SING  N  N  18  
5NK  C19  N18  SING  N  N  19  
5NK  C19  C20  SING  N  N  20  
5NK  C05  C01  SING  Y  N  21  
5NK  C05  N09  SING  Y  N  22  
5NK  C08  N18  SING  N  N  23  
5NK  C08  N09  DOUB  Y  N  24  
5NK  C24  C23  SING  N  N  25  
5NK  C01  C10  SING  N  N  26  
5NK  C20  C21  SING  N  N  27  
5NK  C23  N22  SING  N  N  28  
5NK  C21  N22  SING  N  N  29  
5NK  C25  N22  SING  N  N  30  
5NK  C25  C26  SING  N  N  31  
5NK  C26  N27  SING  N  N  32  
5NK  C10  H1   SING  N  N  33  
5NK  C10  H2   SING  N  N  34  
5NK  C10  H3   SING  N  N  35  
5NK  C15  H4   SING  N  N  36  
5NK  C20  H5   SING  N  N  37  
5NK  C20  H6   SING  N  N  38  
5NK  C21  H7   SING  N  N  39  
5NK  C21  H8   SING  N  N  40  
5NK  C24  H9   SING  N  N  41  
5NK  C24  H10  SING  N  N  42  
5NK  C26  H11  SING  N  N  43  
5NK  C26  H12  SING  N  N  44  
5NK  C28  H13  SING  N  N  45  
5NK  C28  H14  SING  N  N  46  
5NK  C28  H15  SING  N  N  47  
5NK  C02  H16  SING  N  N  48  
5NK  C03  H17  SING  N  N  49  
5NK  C04  H18  SING  N  N  50  
5NK  C11  H19  SING  N  N  51  
5NK  C11  H20  SING  N  N  52  
5NK  C16  H21  SING  N  N  53  
5NK  N18  H22  SING  N  N  54  
5NK  C19  H23  SING  N  N  55  
5NK  C23  H25  SING  N  N  56  
5NK  C23  H26  SING  N  N  57  
5NK  C25  H27  SING  N  N  58  
5NK  C25  H28  SING  N  N  59  
5NK  N27  H29  SING  N  N  60  
5NK  N27  H30  SING  N  N  61  
5NK  O29  H32  SING  N  N  62  
#   #
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
5NK  InChI             InChI                 1.03   "InChI=1S/C22H30N6O/c1-15-4-3-5-19-21(15)26-22(25-17-8-11-27(12-9-17)13-10-23)28(19)14-18-20(29)7-6-16(2)24-18/h3-7,17,29H,8-14,23H2,1-2H3,(H,25,26)"  
5NK  InChIKey          InChI                 1.03   RDQSNNMSDOHAPG-UHFFFAOYSA-N  
5NK  SMILES_CANONICAL  CACTVS                3.385  "Cc1ccc(O)c(Cn2c(NC3CCN(CCN)CC3)nc4c(C)cccc24)n1"  
5NK  SMILES            CACTVS                3.385  "Cc1ccc(O)c(Cn2c(NC3CCN(CCN)CC3)nc4c(C)cccc24)n1"  
5NK  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.4  "Cc1cccc2c1nc(n2Cc3c(ccc(n3)C)O)NC4CCN(CC4)CCN"  
5NK  SMILES            "OpenEye OEToolkits"  2.0.4  "Cc1cccc2c1nc(n2Cc3c(ccc(n3)C)O)NC4CCN(CC4)CCN"  
#
_pdbx_chem_comp_identifier.comp_id          5NK
_pdbx_chem_comp_identifier.type             "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program          "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version  2.0.4
_pdbx_chem_comp_identifier.identifier       "2-[[2-[[1-(2-azanylethyl)piperidin-4-yl]amino]-4-methyl-benzimidazol-1-yl]methyl]-6-methyl-pyridin-3-ol"
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
5NK  "Create component"  2015-10-27  RCSB  
5NK  "Initial release"   2015-12-09  RCSB  
5NK  "Modify synonyms"   2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     5NK
_pdbx_chem_comp_synonyms.name        JNJ-2408068
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
