data_TM3
#

_chem_comp.id                                   TM3
_chem_comp.name                                 "2-[[6-[[[2-(3-hydroxypropyl)-5-methylphenyl]amino]methyl]-2-[[3-(4-morpholinyl)propyl]amino]-1H-benzimidazol-1-yl]methyl]-6-methyl-3-pyridinol"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C32 H42 N6 O3"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        TMC353121
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2009-11-20
_chem_comp.pdbx_modified_date                   2021-03-01
_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                       558.714
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    TM3
_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       3KPE
_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
TM3  C1    C1    C  0  1  N  N  N  27.938  -10.313   -9.907   10.200   1.773  -0.409  C1    TM3   1  
TM3  C2    C2    C  0  1  N  N  N  26.511   -9.888   -9.531    8.839   2.044  -1.056  C2    TM3   2  
TM3  N3    N3    N  0  1  N  N  N  26.218  -10.335   -8.156    7.781   1.456  -0.222  N3    TM3   3  
TM3  C4    C4    C  0  1  N  N  N  27.250   -9.756   -7.268    7.814   2.018   1.135  C4    TM3   4  
TM3  C5    C5    C  0  1  N  N  N  28.637  -10.279   -7.630    9.185   1.748   1.760  C5    TM3   5  
TM3  O6    O6    O  0  1  N  N  N  28.924   -9.850   -8.958   10.203   2.300   0.921  O6    TM3   6  
TM3  C13   C13   C  0  1  N  N  N  24.844   -9.931   -7.731    6.460   1.644  -0.838  C13   TM3   7  
TM3  C14   C14   C  0  1  N  N  N  24.290  -10.788   -6.591    5.422   0.813  -0.082  C14   TM3   8  
TM3  C15   C15   C  0  1  N  N  N  22.800  -10.628   -6.379    4.047   1.009  -0.723  C15   TM3   9  
TM3  N16   N16   N  0  1  N  N  N  22.508   -9.301   -5.818    3.052   0.213   0.001  N16   TM3  10  
TM3  C17   C17   C  0  1  Y  N  N  22.316   -9.089   -4.502    1.732   0.230  -0.398  C17   TM3  11  
TM3  N23   N23   N  0  1  Y  N  N  22.417  -10.071   -3.597    1.260   0.920  -1.406  N23   TM3  12  
TM3  C24   C24   C  0  1  Y  N  N  22.150   -9.474   -2.394   -0.078   0.706  -1.518  C24   TM3  13  
TM3  C25   C25   C  0  1  Y  N  N  21.891   -8.116   -2.607   -0.441  -0.184  -0.495  C25   TM3  14  
TM3  N26   N26   N  0  1  Y  N  N  21.989   -7.914   -3.957    0.724  -0.474   0.196  N26   TM3  15  
TM3  C32   C32   C  0  1  Y  N  N  21.572   -7.224   -1.566   -1.762  -0.587  -0.364  C32   TM3  16  
TM3  C33   C33   C  0  1  Y  N  N  21.528   -7.763   -0.269   -2.715  -0.110  -1.240  C33   TM3  17  
TM3  C34   C34   C  0  1  Y  N  N  21.832   -9.131   -0.043   -2.362   0.770  -2.252  C34   TM3  18  
TM3  C35   C35   C  0  1  Y  N  N  22.132   -9.987   -1.097   -1.055   1.180  -2.397  C35   TM3  19  
TM3  C41   C41   C  0  1  N  N  N  21.711   -6.660   -4.692    0.851  -1.367   1.350  C41   TM3  20  
TM3  C42   C42   C  0  1  Y  N  N  22.589   -5.522   -4.351    1.265  -2.739   0.881  C42   TM3  21  
TM3  C45   C45   C  0  1  Y  N  N  23.943   -5.608   -4.457    0.300  -3.712   0.668  C45   TM3  22  
TM3  C46   C46   C  0  1  Y  N  N  24.733   -4.515   -4.179    0.696  -4.973   0.235  C46   TM3  23  
TM3  C47   C47   C  0  1  Y  N  N  24.056   -3.355   -3.725    2.047  -5.206   0.034  C47   TM3  24  
TM3  C48   C48   C  0  1  Y  N  N  22.681   -3.312   -3.631    2.950  -4.185   0.267  C48   TM3  25  
TM3  N49   N49   N  0  1  Y  N  N  21.938   -4.395   -3.917    2.541  -2.999   0.672  N49   TM3  26  
TM3  O56   O56   O  0  1  N  N  N  24.455   -6.787   -4.924   -1.014  -3.437   0.880  O56   TM3  27  
TM3  C58   C58   C  0  1  N  N  N  21.956   -2.070   -3.161    4.421  -4.430   0.051  C58   TM3  28  
TM3  C60   C60   C  0  1  N  N  N  21.223   -6.912    0.939   -4.150  -0.549  -1.096  C60   TM3  29  
TM3  N61   N61   N  0  1  N  N  N  20.893   -5.496    0.655   -4.856   0.376  -0.206  N61   TM3  30  
TM3  C62   C62   C  0  1  Y  N  N  20.737   -4.580    1.665   -6.208   0.173   0.080  C62   TM3  31  
TM3  C66   C66   C  0  1  Y  N  N  20.895   -4.976    3.003   -6.884  -0.905  -0.478  C66   TM3  32  
TM3  C67   C67   C  0  1  Y  N  N  20.753   -4.068    4.054   -8.221  -1.102  -0.192  C67   TM3  33  
TM3  C68   C68   C  0  1  Y  N  N  20.430   -2.747    3.772   -8.886  -0.229   0.649  C68   TM3  34  
TM3  C69   C69   C  0  1  Y  N  N  20.299   -2.340    2.460   -8.217   0.845   1.206  C69   TM3  35  
TM3  C70   C70   C  0  1  Y  N  N  20.418   -3.248    1.414   -6.878   1.045   0.929  C70   TM3  36  
TM3  C77   C77   C  0  1  N  N  N  20.897   -4.514    5.495   -8.955  -2.271  -0.797  C77   TM3  37  
TM3  C79   C79   C  0  1  N  N  N  20.258   -2.722   -0.007   -6.148   2.212   1.541  C79   TM3  38  
TM3  C80   C80   C  0  1  N  N  N  18.809   -2.664   -0.499   -6.156   3.389   0.564  C80   TM3  39  
TM3  C81   C81   C  0  1  N  N  N  18.036   -3.996   -0.409   -5.414   4.574   1.186  C81   TM3  40  
TM3  O82   O82   O  0  1  N  N  N  18.700   -5.006   -1.186   -5.422   5.673   0.273  O82   TM3  41  
TM3  H1    H1    H  0  1  N  N  N  27.976  -11.412   -9.940   10.380   0.699  -0.375  H1    TM3  42  
TM3  H1A   H1A   H  0  1  N  N  N  28.179   -9.889  -10.893   10.983   2.257  -0.993  H1A   TM3  43  
TM3  H2    H2    H  0  1  N  N  N  26.426   -8.793   -9.588    8.682   3.119  -1.138  H2    TM3  44  
TM3  H2A   H2A   H  0  1  N  N  N  25.794  -10.347  -10.228    8.813   1.594  -2.049  H2A   TM3  45  
TM3  H4    H4    H  0  1  N  N  N  27.241   -8.661   -7.375    7.641   3.093   1.088  H4    TM3  46  
TM3  H4A   H4A   H  0  1  N  N  N  27.023  -10.033   -6.228    7.038   1.551   1.742  H4A   TM3  47  
TM3  H5    H5    H  0  1  N  N  N  29.387   -9.878   -6.932    9.234   2.213   2.745  H5    TM3  48  
TM3  H5A   H5A   H  0  1  N  N  N  28.654  -11.378   -7.575    9.335   0.673   1.858  H5A   TM3  49  
TM3  H13   H13   H  0  1  N  N  N  24.882   -8.886   -7.389    6.185   2.697  -0.793  H13   TM3  50  
TM3  H13A  H13A  H  0  0  N  N  N  24.172  -10.032   -8.596    6.495   1.321  -1.879  H13A  TM3  51  
TM3  H14   H14   H  0  1  N  N  N  24.490  -11.843   -6.829    5.697  -0.241  -0.127  H14   TM3  52  
TM3  H14A  H14A  H  0  0  N  N  N  24.801  -10.493   -5.663    5.386   1.135   0.959  H14A  TM3  53  
TM3  H15   H15   H  0  1  N  N  N  22.283  -10.736   -7.344    3.771   2.062  -0.678  H15   TM3  54  
TM3  H15A  H15A  H  0  0  N  N  N  22.448  -11.402   -5.681    4.082   0.687  -1.764  H15A  TM3  55  
TM3  HN16  HN16  H  0  0  N  N  N  23.294   -8.734   -6.063    3.322  -0.326   0.761  HN16  TM3  56  
TM3  H32   H32   H  0  1  N  N  N  21.371   -6.180   -1.754   -2.043  -1.272   0.422  H32   TM3  57  
TM3  H34   H34   H  0  1  N  N  N  21.830   -9.514    0.967   -3.117   1.136  -2.931  H34   TM3  58  
TM3  H35   H35   H  0  1  N  N  N  22.347  -11.030   -0.915   -0.787   1.865  -3.187  H35   TM3  59  
TM3  H41   H41   H  0  1  N  N  N  21.838   -6.868   -5.765    1.604  -0.974   2.033  H41   TM3  60  
TM3  H41A  H41A  H  0  0  N  N  N  20.677   -6.363   -4.463   -0.107  -1.434   1.865  H41A  TM3  61  
TM3  H46   H46   H  0  1  N  N  N  25.806   -4.540   -4.300   -0.031  -5.752   0.061  H46   TM3  62  
TM3  H47   H47   H  0  1  N  N  N  24.631   -2.484   -3.446    2.391  -6.173  -0.302  H47   TM3  63  
TM3  HO56  HO56  H  0  0  N  N  N  25.403   -6.731   -4.955   -1.494  -3.172   0.083  HO56  TM3  64  
TM3  H58   H58   H  0  1  N  N  N  20.874   -2.267   -3.128    4.683  -4.183  -0.978  H58   TM3  65  
TM3  H58A  H58A  H  0  0  N  N  N  22.310   -1.797   -2.156    4.998  -3.805   0.732  H58A  TM3  66  
TM3  H58B  H58B  H  0  0  N  N  N  22.157   -1.243   -3.858    4.647  -5.479   0.241  H58B  TM3  67  
TM3  H60   H60   H  0  1  N  N  N  20.356   -7.358    1.448   -4.629  -0.549  -2.075  H60   TM3  68  
TM3  H66   H66   H  0  1  N  N  N  21.132   -6.006    3.224   -6.365  -1.587  -1.135  H66   TM3  69  
TM3  H68   H68   H  0  1  N  N  N  20.282   -2.041    4.576   -9.932  -0.385   0.870  H68   TM3  70  
TM3  H69   H69   H  0  1  N  N  N  20.101   -1.301    2.243   -8.739   1.525   1.862  H69   TM3  71  
TM3  H77   H77   H  0  1  N  N  N  21.944   -4.399    5.812   -8.873  -3.134  -0.135  H77   TM3  72  
TM3  H77A  H77A  H  0  0  N  N  N  20.250   -3.897    6.136  -10.005  -2.012  -0.928  H77A  TM3  73  
TM3  H77B  H77B  H  0  0  N  N  N  20.601   -5.570    5.583   -8.517  -2.514  -1.765  H77B  TM3  74  
TM3  H79   H79   H  0  1  N  N  N  20.666   -1.701   -0.037   -6.642   2.505   2.467  H79   TM3  75  
TM3  H79A  H79A  H  0  0  N  N  N  20.816   -3.390   -0.679   -5.118   1.925   1.755  H79A  TM3  76  
TM3  H80   H80   H  0  1  N  N  N  18.276   -1.926    0.119   -5.661   3.096  -0.362  H80   TM3  77  
TM3  H80A  H80A  H  0  0  N  N  N  18.827   -2.359   -1.556   -7.186   3.677   0.350  H80A  TM3  78  
TM3  H81   H81   H  0  1  N  N  N  17.990   -4.318    0.642   -5.909   4.867   2.112  H81   TM3  79  
TM3  H81A  H81A  H  0  0  N  N  N  17.017   -3.851   -0.797   -4.385   4.286   1.399  H81A  TM3  80  
TM3  HO82  HO82  H  0  0  N  N  N  18.217   -5.822   -1.125   -4.968   6.461   0.602  HO82  TM3  81  
TM3  HO83  HO83  H  0  0  N  N  N  21.644   -5.152    0.092   -4.385   1.128   0.184  HO83  TM3  82  
TM3  HO84  HO84  H  0  0  N  N  N  22.114   -6.921    1.584   -4.182  -1.554  -0.676  HO84  TM3  83  
#   #
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
TM3  C1   C2    SING  N  N   1  
TM3  C1   O6    SING  N  N   2  
TM3  C1   H1    SING  N  N   3  
TM3  C1   H1A   SING  N  N   4  
TM3  C2   N3    SING  N  N   5  
TM3  C2   H2    SING  N  N   6  
TM3  C2   H2A   SING  N  N   7  
TM3  N3   C13   SING  N  N   8  
TM3  N3   C4    SING  N  N   9  
TM3  C5   C4    SING  N  N  10  
TM3  C4   H4    SING  N  N  11  
TM3  C4   H4A   SING  N  N  12  
TM3  O6   C5    SING  N  N  13  
TM3  C5   H5    SING  N  N  14  
TM3  C5   H5A   SING  N  N  15  
TM3  C13  C14   SING  N  N  16  
TM3  C13  H13   SING  N  N  17  
TM3  C13  H13A  SING  N  N  18  
TM3  C14  C15   SING  N  N  19  
TM3  C14  H14   SING  N  N  20  
TM3  C14  H14A  SING  N  N  21  
TM3  C15  N16   SING  N  N  22  
TM3  C15  H15   SING  N  N  23  
TM3  C15  H15A  SING  N  N  24  
TM3  N16  C17   SING  N  N  25  
TM3  N16  HN16  SING  N  N  26  
TM3  C17  N26   SING  Y  N  27  
TM3  C17  N23   DOUB  Y  N  28  
TM3  N23  C24   SING  Y  N  29  
TM3  C25  C24   DOUB  Y  N  30  
TM3  C24  C35   SING  Y  N  31  
TM3  N26  C25   SING  Y  N  32  
TM3  C25  C32   SING  Y  N  33  
TM3  C41  N26   SING  N  N  34  
TM3  C32  C33   DOUB  Y  N  35  
TM3  C32  H32   SING  N  N  36  
TM3  C33  C34   SING  Y  N  37  
TM3  C33  C60   SING  N  N  38  
TM3  C35  C34   DOUB  Y  N  39  
TM3  C34  H34   SING  N  N  40  
TM3  C35  H35   SING  N  N  41  
TM3  C41  C42   SING  N  N  42  
TM3  C41  H41   SING  N  N  43  
TM3  C41  H41A  SING  N  N  44  
TM3  C45  C42   DOUB  Y  N  45  
TM3  C42  N49   SING  Y  N  46  
TM3  O56  C45   SING  N  N  47  
TM3  C45  C46   SING  Y  N  48  
TM3  C46  C47   DOUB  Y  N  49  
TM3  C46  H46   SING  N  N  50  
TM3  C47  C48   SING  Y  N  51  
TM3  C47  H47   SING  N  N  52  
TM3  N49  C48   DOUB  Y  N  53  
TM3  C48  C58   SING  N  N  54  
TM3  O56  HO56  SING  N  N  55  
TM3  C58  H58   SING  N  N  56  
TM3  C58  H58A  SING  N  N  57  
TM3  C58  H58B  SING  N  N  58  
TM3  N61  C60   SING  N  N  59  
TM3  C60  H60   SING  N  N  60  
TM3  N61  C62   SING  N  N  61  
TM3  C70  C62   DOUB  Y  N  62  
TM3  C62  C66   SING  Y  N  63  
TM3  C66  C67   DOUB  Y  N  64  
TM3  C66  H66   SING  N  N  65  
TM3  C68  C67   SING  Y  N  66  
TM3  C67  C77   SING  N  N  67  
TM3  C69  C68   DOUB  Y  N  68  
TM3  C68  H68   SING  N  N  69  
TM3  C70  C69   SING  Y  N  70  
TM3  C69  H69   SING  N  N  71  
TM3  C79  C70   SING  N  N  72  
TM3  C77  H77   SING  N  N  73  
TM3  C77  H77A  SING  N  N  74  
TM3  C77  H77B  SING  N  N  75  
TM3  C80  C79   SING  N  N  76  
TM3  C79  H79   SING  N  N  77  
TM3  C79  H79A  SING  N  N  78  
TM3  C80  C81   SING  N  N  79  
TM3  C80  H80   SING  N  N  80  
TM3  C80  H80A  SING  N  N  81  
TM3  O82  C81   SING  N  N  82  
TM3  C81  H81   SING  N  N  83  
TM3  C81  H81A  SING  N  N  84  
TM3  O82  HO82  SING  N  N  85  
TM3  N61  HO83  SING  N  N  86  
TM3  C60  HO84  SING  N  N  87  
#   #
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
TM3  SMILES_CANONICAL  CACTVS                3.352  "Cc1ccc(CCCO)c(NCc2ccc3nc(NCCCN4CCOCC4)n(Cc5nc(C)ccc5O)c3c2)c1"  
TM3  SMILES            CACTVS                3.352  "Cc1ccc(CCCO)c(NCc2ccc3nc(NCCCN4CCOCC4)n(Cc5nc(C)ccc5O)c3c2)c1"  
TM3  SMILES_CANONICAL  "OpenEye OEToolkits"  1.7.0  "Cc1ccc(c(c1)NCc2ccc3c(c2)n(c(n3)NCCCN4CCOCC4)Cc5c(ccc(n5)C)O)CCCO"  
TM3  SMILES            "OpenEye OEToolkits"  1.7.0  "Cc1ccc(c(c1)NCc2ccc3c(c2)n(c(n3)NCCCN4CCOCC4)Cc5c(ccc(n5)C)O)CCCO"  
TM3  InChI             InChI                 1.03   "InChI=1S/C32H42N6O3/c1-23-6-9-26(5-3-16-39)28(19-23)34-21-25-8-10-27-30(20-25)38(22-29-31(40)11-7-24(2)35-29)32(36-27)33-12-4-13-37-14-17-41-18-15-37/h6-11,19-20,34,39-40H,3-5,12-18,21-22H2,1-2H3,(H,33,36)"  
TM3  InChIKey          InChI                 1.03   DKORMNNYNRPTBJ-UHFFFAOYSA-N  
#
_pdbx_chem_comp_identifier.comp_id          TM3
_pdbx_chem_comp_identifier.type             "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program          "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version  1.6.1
_pdbx_chem_comp_identifier.identifier       "2-[[6-[[[2-(3-hydroxypropyl)-5-methyl-phenyl]amino]methyl]-2-(3-morpholin-4-ylpropylamino)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
TM3  "Create component"      2009-11-20  RCSB  
TM3  "Modify aromatic_flag"  2011-06-04  RCSB  
TM3  "Modify descriptor"     2011-06-04  RCSB  
TM3  "Modify synonyms"       2021-03-01  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     TM3
_pdbx_chem_comp_synonyms.name        TMC353121
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
