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 ? ##