data_P13
#

_chem_comp.id                                   P13
_chem_comp.name                                 "N-[2-(3-AMINOPROPOXY)-5-(1H-INDOL-5-YL)BENZYL]-N-(2-PIPERAZIN-1-YLETHYL)AMINE"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C24 H33 N5 O"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "RBT550 INHIBITOR"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2003-12-10
_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                       407.552
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    P13
_chem_comp.pdbx_model_coordinates_details       ?
_chem_comp.pdbx_model_coordinates_missing_flag  N
_chem_comp.pdbx_ideal_coordinates_details       ?
_chem_comp.pdbx_ideal_coordinates_missing_flag  Y
_chem_comp.pdbx_model_coordinates_db_code       ?
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 EBI
#   #
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
P13  C1    C1    C  0  1  Y  N  N  -1.085   5.150  16.435  -2.606  -1.659  -0.024  C1    P13   1  
P13  C2    C2    C  0  1  Y  N  N  -1.018   4.246  15.348  -2.647  -0.313   0.334  C2    P13   2  
P13  C3    C3    C  0  1  Y  N  N   0.141   3.446  15.163  -1.476   0.341   0.714  C3    P13   3  
P13  C4    C4    C  0  1  Y  N  N   1.233   3.548  16.068  -0.282  -0.348   0.740  C4    P13   4  
P13  C5    C5    C  0  1  Y  N  N   1.170   4.472  17.154  -0.243  -1.688   0.379  C5    P13   5  
P13  C6    C6    C  0  1  Y  N  N   0.006   5.268  17.336  -1.408  -2.341   0.000  C6    P13   6  
P13  N     N     N  0  1  N  N  N   5.265   4.811  21.004   2.886  -6.738  -0.443  N     P13   7  
P13  CB    CB    C  0  1  N  N  N   4.245   4.095  20.205   1.645  -5.953  -0.446  CB    P13   8  
P13  CA    CA    C  0  1  N  N  N   2.884   4.766  20.399   1.947  -4.519  -0.006  CA    P13   9  
P13  C     C     C  0  1  N  N  N   1.886   4.203  19.383   0.654  -3.701  -0.010  C     P13  10  
P13  O     O     O  0  1  N  N  N   2.275   4.604  18.061   0.936  -2.362   0.401  O     P13  11  
P13  CA1   CA1   C  0  1  N  N  N   2.482   2.671  15.847   0.985   0.357   1.152  CA1   P13  12  
P13  NB    NB    N  0  1  N  N  N   3.151   2.392  17.138   1.749   0.730  -0.046  NB    P13  13  
P13  CG    CG    C  0  1  N  N  N   4.156   1.311  16.958   2.964   1.410   0.423  CG    P13  14  
P13  CD    CD    C  0  1  N  N  N   3.498  -0.052  17.192   3.812   1.828  -0.781  CD    P13  15  
P13  NE    NE    N  0  1  N  N  N   3.928  -0.588  18.503   5.027   2.507  -0.312  NE    P13  16  
P13  CH1   CH1   C  0  1  N  N  N   5.346  -1.040  18.409   5.901   2.663  -1.481  CH1   P13  17  
P13  CI1   CI1   C  0  1  N  N  N   5.795  -1.601  19.768   7.242   3.255  -1.045  CI1   P13  18  
P13  NJ    NJ    N  0  1  N  N  N   4.912  -2.739  20.151   7.916   2.328  -0.129  NJ    P13  19  
P13  CI2   CI2   C  0  1  N  N  N   3.495  -2.290  20.245   7.042   2.172   1.040  CI2   P13  20  
P13  CH2   CH2   C  0  1  N  N  N   3.044  -1.725  18.886   5.702   1.580   0.605  CH2   P13  21  
P13  N1    N1    N  0  1  Y  N  N  -5.501   3.838  11.977  -7.580   2.351   0.022  N1    P13  22  
P13  C21   C21   C  0  1  Y  N  N  -6.411   3.370  12.952  -8.081   1.799  -1.126  C21   P13  23  
P13  C31   C31   C  0  1  Y  N  N  -5.776   3.222  14.206  -7.206   0.915  -1.629  C31   P13  24  
P13  C41   C41   C  0  1  Y  N  N  -3.360   3.688  14.920  -4.840   0.204  -0.721  C41   P13  25  
P13  C51   C51   C  0  1  Y  N  N  -2.098   4.152  14.459  -3.935   0.424   0.309  C51   P13  26  
P13  C61   C61   C  0  1  Y  N  N  -1.935   4.527  13.097  -4.233   1.344   1.320  C61   P13  27  
P13  C71   C71   C  0  1  Y  N  N  -3.033   4.440  12.199  -5.413   2.030   1.312  C71   P13  28  
P13  C81   C81   C  0  1  Y  N  N  -4.305   3.986  12.669  -6.337   1.822   0.293  C81   P13  29  
P13  C91   C91   C  0  1  Y  N  N  -4.468   3.614  14.016  -6.049   0.899  -0.730  C91   P13  30  
P13  H1    H1    H  0  1  N  N  N  -1.963   5.753  16.568  -3.512  -2.168  -0.319  H1    P13  31  
P13  H3    H3    H  0  1  N  N  N   0.195   2.763  14.335  -1.505   1.384   0.991  H3    P13  32  
P13  H6    H6    H  0  1  N  N  N  -0.047   5.968  18.157  -1.375  -3.385  -0.277  H6    P13  33  
P13  HN1A  1HN   H  0  0  N  N  N   6.168   4.322  20.926       ?       ?       ?  HN1A  P13  34  
P13  HN2   2HN   H  0  1  N  N  N   5.365   5.773  20.650   3.183  -6.807   0.519  HN2   P13  35  
P13  HB1   1HB   H  0  1  N  N  N   4.189   3.067  20.531   1.224  -5.944  -1.452  HB1   P13  36  
P13  HB2   2HB   H  0  1  N  N  N   4.517   4.128  19.161   0.929  -6.402   0.243  HB2   P13  37  
P13  HA1   1HA   H  0  1  N  N  N   2.526   4.572  21.400   2.368  -4.529   0.999  HA1   P13  38  
P13  HA2   2HA   H  0  1  N  N  N   2.984   5.831  20.254   2.662  -4.071  -0.696  HA2   P13  39  
P13  HC1   1HC   H  0  1  N  N  N   0.899   4.583  19.604   0.233  -3.692  -1.015  HC1   P13  40  
P13  HC2   2HC   H  0  1  N  N  N   1.878   3.126  19.445  -0.061  -4.150   0.680  HC2   P13  41  
P13  HA11  1HA1  H  0  0  N  N  N   3.168   3.183  15.190   0.734   1.255   1.716  HA11  P13  42  
P13  HA12  2HA1  H  0  0  N  N  N   2.185   1.736  15.395   1.585  -0.307   1.774  HA12  P13  43  
P13  HB11  1HB1  H  0  0  N  N  N   2.448   2.099  17.832       ?       ?       ?  HB11  P13  44  
P13  HG1   1HG   H  0  1  N  N  N   4.958   1.449  17.667   2.687   2.294   0.997  HG1   P13  45  
P13  HG2   2HG   H  0  1  N  N  N   4.556   1.349  15.954   3.539   0.732   1.054  HG2   P13  46  
P13  HD1   1HD   H  0  1  N  N  N   3.796  -0.735  16.410   4.088   0.943  -1.355  HD1   P13  47  
P13  HD2   2HD   H  0  1  N  N  N   2.424   0.059  17.183   3.237   2.505  -1.412  HD2   P13  48  
P13  HH11  1HH1  H  0  0  N  N  N   5.429  -1.809  17.656   6.067   1.689  -1.942  HH11  P13  49  
P13  HH12  2HH1  H  0  0  N  N  N   5.973  -0.203  18.140   5.427   3.329  -2.202  HH12  P13  50  
P13  HI11  1HI1  H  0  0  N  N  N   5.730  -0.827  20.517   7.868   3.419  -1.922  HI11  P13  51  
P13  HI12  2HI1  H  0  0  N  N  N   6.816  -1.946  19.695   7.071   4.205  -0.539  HI12  P13  52  
P13  HJ1   1HJ   H  0  1  N  N  N   5.213  -3.109  21.064       ?       ?       ?  HJ1   P13  53  
P13  HI21  1HI2  H  0  0  N  N  N   2.868  -3.127  20.513   7.516   1.506   1.762  HI21  P13  54  
P13  HI22  2HI2  H  0  0  N  N  N   3.409  -1.522  21.000   6.876   3.146   1.501  HI22  P13  55  
P13  HH21  1HH2  H  0  0  N  N  N   2.024  -1.378  18.962   5.075   1.416   1.482  HH21  P13  56  
P13  HH22  2HH2  H  0  0  N  N  N   3.107  -2.499  18.137   5.872   0.630   0.099  HH22  P13  57  
P13  HN1   HN1   H  0  1  N  N  N  -5.676   4.024  11.030  -8.032   3.016   0.564  HN1   P13  58  
P13  H2    H2    H  0  1  N  N  N  -7.449   3.159  12.738  -9.039   2.040  -1.562  H2    P13  59  
P13  H31   H31   H  0  1  N  N  N  -6.229   2.880  15.124  -7.330   0.327  -2.527  H31   P13  60  
P13  H4    H4    H  0  1  N  N  N  -3.488   3.405  15.954  -4.610  -0.502  -1.506  H4    P13  61  
P13  H61   H61   H  0  1  N  N  N  -0.980   4.883  12.746  -3.522   1.513   2.115  H61   P13  62  
P13  H7    H7    H  0  1  N  N  N  -2.910   4.727  11.166  -5.630   2.737   2.099  H7    P13  63  
#   #
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
P13  C1   C2    DOUB  Y  N   1  
P13  C1   C6    SING  Y  N   2  
P13  C1   H1    SING  N  N   3  
P13  C2   C3    SING  Y  N   4  
P13  C2   C51   SING  Y  N   5  
P13  C3   C4    DOUB  Y  N   6  
P13  C3   H3    SING  N  N   7  
P13  C4   C5    SING  Y  N   8  
P13  C4   CA1   SING  N  N   9  
P13  C5   C6    DOUB  Y  N  10  
P13  C5   O     SING  N  N  11  
P13  C6   H6    SING  N  N  12  
P13  N    CB    SING  N  N  13  
P13  N    HN1A  SING  N  N  14  
P13  N    HN2   SING  N  N  15  
P13  CB   CA    SING  N  N  16  
P13  CB   HB1   SING  N  N  17  
P13  CB   HB2   SING  N  N  18  
P13  CA   C     SING  N  N  19  
P13  CA   HA1   SING  N  N  20  
P13  CA   HA2   SING  N  N  21  
P13  C    O     SING  N  N  22  
P13  C    HC1   SING  N  N  23  
P13  C    HC2   SING  N  N  24  
P13  CA1  NB    SING  N  N  25  
P13  CA1  HA11  SING  N  N  26  
P13  CA1  HA12  SING  N  N  27  
P13  NB   CG    SING  N  N  28  
P13  NB   HB11  SING  N  N  29  
P13  CG   CD    SING  N  N  30  
P13  CG   HG1   SING  N  N  31  
P13  CG   HG2   SING  N  N  32  
P13  CD   NE    SING  N  N  33  
P13  CD   HD1   SING  N  N  34  
P13  CD   HD2   SING  N  N  35  
P13  NE   CH1   SING  N  N  36  
P13  NE   CH2   SING  N  N  37  
P13  CH1  CI1   SING  N  N  38  
P13  CH1  HH11  SING  N  N  39  
P13  CH1  HH12  SING  N  N  40  
P13  CI1  NJ    SING  N  N  41  
P13  CI1  HI11  SING  N  N  42  
P13  CI1  HI12  SING  N  N  43  
P13  NJ   CI2   SING  N  N  44  
P13  NJ   HJ1   SING  N  N  45  
P13  CI2  CH2   SING  N  N  46  
P13  CI2  HI21  SING  N  N  47  
P13  CI2  HI22  SING  N  N  48  
P13  CH2  HH21  SING  N  N  49  
P13  CH2  HH22  SING  N  N  50  
P13  N1   C21   SING  Y  N  51  
P13  N1   C81   SING  Y  N  52  
P13  N1   HN1   SING  N  N  53  
P13  C21  C31   DOUB  Y  N  54  
P13  C21  H2    SING  N  N  55  
P13  C31  C91   SING  Y  N  56  
P13  C31  H31   SING  N  N  57  
P13  C41  C51   DOUB  Y  N  58  
P13  C41  C91   SING  Y  N  59  
P13  C41  H4    SING  N  N  60  
P13  C51  C61   SING  Y  N  61  
P13  C61  C71   DOUB  Y  N  62  
P13  C61  H61   SING  N  N  63  
P13  C71  C81   SING  Y  N  64  
P13  C71  H7    SING  N  N  65  
P13  C81  C91   DOUB  Y  N  66  
#   #
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
P13  SMILES            ACDLabs               10.04  "O(c3ccc(c2cc1ccnc1cc2)cc3CNCCN4CCNCC4)CCCN"  
P13  SMILES_CANONICAL  CACTVS                3.341  "NCCCOc1ccc(cc1CNCCN2CCNCC2)c3ccc4[nH]ccc4c3"  
P13  SMILES            CACTVS                3.341  "NCCCOc1ccc(cc1CNCCN2CCNCC2)c3ccc4[nH]ccc4c3"  
P13  SMILES_CANONICAL  "OpenEye OEToolkits"  1.5.0  "c1cc2c(cc[nH]2)cc1c3ccc(c(c3)CNCCN4CCNCC4)OCCCN"  
P13  SMILES            "OpenEye OEToolkits"  1.5.0  "c1cc2c(cc[nH]2)cc1c3ccc(c(c3)CNCCN4CCNCC4)OCCCN"  
P13  InChI             InChI                 1.03   "InChI=1S/C24H33N5O/c25-7-1-15-30-24-5-3-20(19-2-4-23-21(16-19)6-8-28-23)17-22(24)18-27-11-14-29-12-9-26-10-13-29/h2-6,8,16-17,26-28H,1,7,9-15,18,25H2"  
P13  InChIKey          InChI                 1.03   WVRJFVULANTNJW-UHFFFAOYSA-N  
#   #
loop_
_pdbx_chem_comp_identifier.comp_id
_pdbx_chem_comp_identifier.type
_pdbx_chem_comp_identifier.program
_pdbx_chem_comp_identifier.program_version
_pdbx_chem_comp_identifier.identifier
P13  "SYSTEMATIC NAME"  ACDLabs               10.04  "3-[4-(1H-indol-5-yl)-2-{[(2-piperazin-1-ylethyl)amino]methyl}phenoxy]propan-1-amine"  
P13  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.5.0  "3-[4-(1H-indol-5-yl)-2-[(2-piperazin-1-ylethylamino)methyl]phenoxy]propan-1-amine"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
P13  "Create component"      2003-12-10  EBI   
P13  "Modify aromatic_flag"  2011-06-04  RCSB  
P13  "Modify descriptor"     2011-06-04  RCSB  
P13  "Modify synonyms"       2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     P13
_pdbx_chem_comp_synonyms.name        "RBT550 INHIBITOR"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
