data_A1A3C
# 
_chem_comp.id                                    A1A3C 
_chem_comp.name                                  "N-[3-(dimethylamino)propyl]-1-[(1r,3r)-3-(methylcarbamoyl)cyclobutyl]-2-(3,4,5-trimethoxyphenyl)-1H-1,3-benzimidazole-6-carboxamide" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C28 H37 N5 O5" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2024-08-23 
_chem_comp.pdbx_modified_date                    2024-11-22 
_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                        523.624 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1A3C 
_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        9D8F 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_chem_comp.pdbx_pcm                              ? 
# 
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.pdbx_n_terminal_atom_flag 
_chem_comp_atom.pdbx_backbone_atom_flag 
_chem_comp_atom.pdbx_c_terminal_atom_flag 
_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 
A1A3C C35  C1  C 0 1 N N N N N N 21.908 -4.770  -35.769 -4.697 2.868  -3.076 C35  A1A3C 1  
A1A3C C36  C2  C 0 1 Y N N N N N 24.711 -4.894  -35.706 -3.485 1.798  -0.912 C36  A1A3C 2  
A1A3C C38  C3  C 0 1 Y N N N N N 27.697 -7.306  -31.447 1.904  -0.304 -0.010 C38  A1A3C 3  
A1A3C C27  C4  C 0 1 Y N N N N N 26.166 -4.181  -37.958 -4.941 0.858  1.264  C27  A1A3C 4  
A1A3C C30  C5  C 0 1 Y N N N N N 24.792 -4.249  -38.026 -5.597 1.408  0.167  C30  A1A3C 5  
A1A3C C29  C6  C 0 1 N N N N N N 28.360 -3.963  -39.001 -6.300 -0.869 2.175  C29  A1A3C 6  
A1A3C C02  C7  C 0 1 N N N N N N 28.755 -8.208  -29.396 4.388  -0.372 0.020  C02  A1A3C 7  
A1A3C C04  C8  C 0 1 N N N N N N 30.826 -7.797  -27.802 6.823  -0.459 0.047  C04  A1A3C 8  
A1A3C C05  C9  C 0 1 N N N N N N 30.730 -7.709  -26.216 7.995  0.505  0.243  C05  A1A3C 9  
A1A3C C06  C10 C 0 1 N N N N N N 29.269 -7.373  -25.708 9.313  -0.263 0.125  C06  A1A3C 10 
A1A3C C08  C11 C 0 1 N N N N N N 26.985 -8.393  -25.679 11.705 -0.069 0.444  C08  A1A3C 11 
A1A3C C09  C12 C 0 1 N N N N N N 28.561 -8.828  -23.854 10.504 1.640  -0.780 C09  A1A3C 12 
A1A3C C10  C13 C 0 1 Y N N N N N 28.716 -7.084  -30.497 3.117  0.369  0.134  C10  A1A3C 13 
A1A3C C11  C14 C 0 1 Y N N N N N 29.580 -5.985  -30.621 3.132  1.748  0.385  C11  A1A3C 14 
A1A3C C12  C15 C 0 1 Y N N N N N 29.459 -5.013  -31.711 1.966  2.444  0.493  C12  A1A3C 15 
A1A3C C13  C16 C 0 1 Y N N N N N 28.399 -5.254  -32.653 0.738  1.783  0.351  C13  A1A3C 16 
A1A3C C14  C17 C 0 1 Y N N N N N 27.575 -6.333  -32.532 0.717  0.399  0.092  C14  A1A3C 17 
A1A3C C16  C18 C 0 1 N N N N N N 25.596 -7.274  -33.842 -1.146 -1.298 -0.252 C16  A1A3C 18 
A1A3C C17  C19 C 0 1 N N N N N N 24.603 -7.455  -32.651 -2.410 -1.304 -1.128 C17  A1A3C 19 
A1A3C C18  C20 C 0 1 N N N N N N 24.781 -8.989  -32.700 -2.948 -2.412 -0.206 C18  A1A3C 20 
A1A3C C19  C21 C 0 1 N N N N N N 23.608 -9.755  -33.236 -2.572 -3.802 -0.651 C19  A1A3C 21 
A1A3C C21  C22 C 0 1 N N N N N N 22.980 -8.329  -35.331 -2.612 -6.222 -0.368 C21  A1A3C 22 
A1A3C C23  C23 C 0 1 N N N N N N 25.962 -8.780  -33.704 -2.026 -1.842 0.885  C23  A1A3C 23 
A1A3C C24  C24 C 0 1 Y N N N N N 26.914 -5.183  -34.360 -1.349 1.181  0.207  C24  A1A3C 24 
A1A3C C25  C25 C 0 1 Y N N N N N 26.153 -4.820  -35.631 -2.824 1.256  0.191  C25  A1A3C 25 
A1A3C C26  C26 C 0 1 Y N N N N N 26.868 -4.476  -36.784 -3.560 0.786  1.281  C26  A1A3C 26 
A1A3C C32  C27 C 0 1 N N N N N N 24.098 -2.552  -39.529 -7.550 2.660  0.691  C32  A1A3C 27 
A1A3C C33  C28 C 0 1 Y N N N N N 24.074 -4.590  -36.919 -4.866 1.873  -0.922 C33  A1A3C 28 
A1A3C N03  N1  N 0 1 N N N N N N 29.651 -8.510  -28.297 5.561  0.277  0.159  N03  A1A3C 29 
A1A3C N07  N2  N 0 1 N N N N N N 28.454 -8.602  -25.323 10.438 0.663  0.314  N07  A1A3C 30 
A1A3C N15  N3  N 0 1 Y N N N N N 26.685 -6.308  -33.555 -0.617 0.043  0.006  N15  A1A3C 31 
A1A3C N20  N4  N 0 1 N N N N N N 22.791 -9.463  -34.405 -2.977 -4.871 0.064  N20  A1A3C 32 
A1A3C N37  N5  N 0 1 Y N N N N N 28.009 -4.500  -33.832 -0.543 2.199  0.397  N37  A1A3C 33 
A1A3C O01  O1  O 0 1 N N N N N N 27.854 -9.081  -29.468 4.377  -1.568 -0.199 O01  A1A3C 34 
A1A3C O22  O2  O 0 1 N N N N N N 23.240 -10.807 -32.630 -1.906 -3.960 -1.652 O22  A1A3C 35 
A1A3C O28  O3  O 0 1 N N N N N N 26.947 -3.798  -39.109 -5.659 0.399  2.325  O28  A1A3C 36 
A1A3C O31  O4  O 0 1 N N N N N N 24.100 -3.936  -39.275 -6.955 1.477  0.152  O31  A1A3C 37 
A1A3C O34  O5  O 0 1 N N N N N N 22.611 -4.661  -36.998 -5.510 2.411  -1.993 O34  A1A3C 38 
A1A3C H351 H1  H 0 0 N N N N N N 20.827 -4.814  -35.967 -4.116 2.034  -3.472 H351 A1A3C 39 
A1A3C H352 H2  H 0 0 N N N N N N 22.223 -5.686  -35.247 -5.334 3.272  -3.863 H352 A1A3C 40 
A1A3C H353 H3  H 0 0 N N N N N N 22.130 -3.895  -35.141 -4.021 3.645  -2.720 H353 A1A3C 41 
A1A3C H361 H4  H 0 0 N N N N N N 24.132 -5.179  -34.840 -2.918 2.164  -1.756 H361 A1A3C 42 
A1A3C H381 H5  H 0 0 N N N N N N 27.036 -8.157  -31.376 1.892  -1.366 -0.205 H381 A1A3C 43 
A1A3C H291 H6  H 0 0 N N N N N N 28.840 -3.638  -39.936 -6.757 -1.159 3.121  H291 A1A3C 44 
A1A3C H292 H7  H 0 0 N N N N N N 28.737 -3.355  -38.165 -7.070 -0.798 1.406  H292 A1A3C 45 
A1A3C H293 H8  H 0 0 N N N N N N 28.592 -5.023  -38.818 -5.563 -1.617 1.883  H293 A1A3C 46 
A1A3C H041 H9  H 0 0 N N N N N N 31.738 -8.340  -28.089 6.890  -0.916 -0.941 H041 A1A3C 47 
A1A3C H042 H10 H 0 0 N N N N N N 30.853 -6.784  -28.229 6.860  -1.236 0.810  H042 A1A3C 48 
A1A3C H052 H11 H 0 0 N N N N N N 31.036 -8.676  -25.791 7.958  1.282  -0.521 H052 A1A3C 49 
A1A3C H051 H12 H 0 0 N N N N N N 31.414 -6.922  -25.866 7.928  0.962  1.230  H051 A1A3C 50 
A1A3C H062 H13 H 0 0 N N N N N N 29.350 -6.720  -24.826 9.350  -1.040 0.889  H062 A1A3C 51 
A1A3C H061 H14 H 0 0 N N N N N N 28.737 -6.841  -26.510 9.380  -0.720 -0.862 H061 A1A3C 52 
A1A3C H081 H15 H 0 0 N N N N N N 26.408 -9.286  -25.397 11.881 -0.654 -0.458 H081 A1A3C 53 
A1A3C H083 H16 H 0 0 N N N N N N 26.597 -7.519  -25.136 12.521 0.640  0.583  H083 A1A3C 54 
A1A3C H082 H17 H 0 0 N N N N N N 26.891 -8.223  -26.762 11.653 -0.735 1.305  H082 A1A3C 55 
A1A3C H093 H18 H 0 0 N N N N N N 27.973 -9.715  -23.575 9.579  2.216  -0.810 H093 A1A3C 56 
A1A3C H092 H19 H 0 0 N N N N N N 29.615 -8.987  -23.583 11.346 2.313  -0.616 H092 A1A3C 57 
A1A3C H091 H20 H 0 0 N N N N N N 28.174 -7.948  -23.319 10.637 1.117  -1.727 H091 A1A3C 58 
A1A3C H111 H21 H 0 0 N N N N N N 30.361 -5.851  -29.888 4.075  2.263  0.496  H111 A1A3C 59 
A1A3C H121 H22 H 0 0 N N N N N N 30.125 -4.168  -31.801 1.988  3.506  0.687  H121 A1A3C 60 
A1A3C H161 H23 H 0 0 N N N N N N 25.070 -7.063  -34.785 -0.380 -1.999 -0.584 H161 A1A3C 61 
A1A3C H172 H24 H 0 0 N N N N N N 24.946 -6.997  -31.712 -2.981 -0.378 -1.076 H172 A1A3C 62 
A1A3C H171 H25 H 0 0 N N N N N N 23.579 -7.119  -32.870 -2.231 -1.635 -2.151 H171 A1A3C 63 
A1A3C H181 H26 H 0 0 N N N N N N 25.137 -9.388  -31.739 -4.009 -2.313 0.022  H181 A1A3C 64 
A1A3C H213 H27 H 0 0 N N N N N N 22.213 -8.366  -36.119 -3.013 -6.405 -1.365 H213 A1A3C 65 
A1A3C H211 H28 H 0 0 N N N N N N 22.890 -7.384  -34.776 -1.526 -6.316 -0.390 H211 A1A3C 66 
A1A3C H212 H29 H 0 0 N N N N N N 23.978 -8.392  -35.789 -3.026 -6.951 0.330  H212 A1A3C 67 
A1A3C H232 H30 H 0 0 N N N N N N 25.861 -9.352  -34.638 -1.538 -2.608 1.488  H232 A1A3C 68 
A1A3C H231 H31 H 0 0 N N N N N N 26.956 -8.961  -33.269 -2.493 -1.063 1.487  H231 A1A3C 69 
A1A3C H261 H32 H 0 0 N N N N N N 27.947 -4.439  -36.768 -3.051 0.366  2.136  H261 A1A3C 70 
A1A3C H323 H33 H 0 0 N N N N N N 23.571 -2.353  -40.474 -8.635 2.586  0.618  H323 A1A3C 71 
A1A3C H322 H34 H 0 0 N N N N N N 23.587 -2.029  -38.707 -7.263 2.767  1.736  H322 A1A3C 72 
A1A3C H321 H35 H 0 0 N N N N N N 25.135 -2.192  -39.605 -7.207 3.528  0.128  H321 A1A3C 73 
A1A3C H031 H36 H 0 0 N N N N N N 29.428 -9.345  -27.794 5.570  1.231  0.334  H031 A1A3C 74 
A1A3C H201 H38 H 0 0 N N N N N N 22.034 -10.087 -34.598 -3.510 -4.745 0.865  H201 A1A3C 75 
# 
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 
A1A3C C32 O31  SING N N 1  
A1A3C O31 C30  SING N N 2  
A1A3C O28 C29  SING N N 3  
A1A3C O28 C27  SING N N 4  
A1A3C C30 C27  DOUB Y N 5  
A1A3C C30 C33  SING Y N 6  
A1A3C C27 C26  SING Y N 7  
A1A3C O34 C33  SING N N 8  
A1A3C O34 C35  SING N N 9  
A1A3C C33 C36  DOUB Y N 10 
A1A3C C26 C25  DOUB Y N 11 
A1A3C C36 C25  SING Y N 12 
A1A3C C25 C24  SING N N 13 
A1A3C C21 N20  SING N N 14 
A1A3C N20 C19  SING N N 15 
A1A3C C24 N37  DOUB Y N 16 
A1A3C C24 N15  SING Y N 17 
A1A3C C16 C23  SING N N 18 
A1A3C C16 N15  SING N N 19 
A1A3C C16 C17  SING N N 20 
A1A3C N37 C13  SING Y N 21 
A1A3C C23 C18  SING N N 22 
A1A3C N15 C14  SING Y N 23 
A1A3C C19 C18  SING N N 24 
A1A3C C19 O22  DOUB N N 25 
A1A3C C18 C17  SING N N 26 
A1A3C C13 C14  DOUB Y N 27 
A1A3C C13 C12  SING Y N 28 
A1A3C C14 C38  SING Y N 29 
A1A3C C12 C11  DOUB Y N 30 
A1A3C C38 C10  DOUB Y N 31 
A1A3C C11 C10  SING Y N 32 
A1A3C C10 C02  SING N N 33 
A1A3C O01 C02  DOUB N N 34 
A1A3C C02 N03  SING N N 35 
A1A3C N03 C04  SING N N 36 
A1A3C C04 C05  SING N N 37 
A1A3C C05 C06  SING N N 38 
A1A3C C06 N07  SING N N 39 
A1A3C C08 N07  SING N N 40 
A1A3C N07 C09  SING N N 41 
A1A3C C35 H351 SING N N 42 
A1A3C C35 H352 SING N N 43 
A1A3C C35 H353 SING N N 44 
A1A3C C36 H361 SING N N 45 
A1A3C C38 H381 SING N N 46 
A1A3C C29 H291 SING N N 47 
A1A3C C29 H292 SING N N 48 
A1A3C C29 H293 SING N N 49 
A1A3C C04 H041 SING N N 50 
A1A3C C04 H042 SING N N 51 
A1A3C C05 H052 SING N N 52 
A1A3C C05 H051 SING N N 53 
A1A3C C06 H062 SING N N 54 
A1A3C C06 H061 SING N N 55 
A1A3C C08 H081 SING N N 56 
A1A3C C08 H083 SING N N 57 
A1A3C C08 H082 SING N N 58 
A1A3C C09 H093 SING N N 59 
A1A3C C09 H092 SING N N 60 
A1A3C C09 H091 SING N N 61 
A1A3C C11 H111 SING N N 62 
A1A3C C12 H121 SING N N 63 
A1A3C C16 H161 SING N N 64 
A1A3C C17 H172 SING N N 65 
A1A3C C17 H171 SING N N 66 
A1A3C C18 H181 SING N N 67 
A1A3C C21 H213 SING N N 68 
A1A3C C21 H211 SING N N 69 
A1A3C C21 H212 SING N N 70 
A1A3C C23 H232 SING N N 71 
A1A3C C23 H231 SING N N 72 
A1A3C C26 H261 SING N N 73 
A1A3C C32 H323 SING N N 74 
A1A3C C32 H322 SING N N 75 
A1A3C C32 H321 SING N N 76 
A1A3C N03 H031 SING N N 77 
A1A3C N20 H201 SING N N 78 
# 
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 
A1A3C SMILES           ACDLabs              14.52 "CN(C)CCCNC(=O)c1ccc2nc(c3cc(OC)c(OC)c(OC)c3)n(c2c1)C1CC(C1)C(=O)NC"                                                                                                                                      
A1A3C InChI            InChI                1.06  "InChI=1S/C28H37N5O5/c1-29-27(34)19-12-20(13-19)33-22-14-17(28(35)30-10-7-11-32(2)3)8-9-21(22)31-26(33)18-15-23(36-4)25(38-6)24(16-18)37-5/h8-9,14-16,19-20H,7,10-13H2,1-6H3,(H,29,34)(H,30,35)/t19-,20-" 
A1A3C InChIKey         InChI                1.06  COJOXDOWRKQNIY-MXVIHJGJSA-N                                                                                                                                                                               
A1A3C SMILES_CANONICAL CACTVS               3.385 "CNC(=O)[C@@H]1C[C@H](C1)n2c3cc(ccc3nc2c4cc(OC)c(OC)c(OC)c4)C(=O)NCCCN(C)C"                                                                                                                               
A1A3C SMILES           CACTVS               3.385 "CNC(=O)[CH]1C[CH](C1)n2c3cc(ccc3nc2c4cc(OC)c(OC)c(OC)c4)C(=O)NCCCN(C)C"                                                                                                                                  
A1A3C SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CNC(=O)C1CC(C1)n2c3cc(ccc3nc2c4cc(c(c(c4)OC)OC)OC)C(=O)NCCCN(C)C"                                                                                                                                        
A1A3C SMILES           "OpenEye OEToolkits" 2.0.7 "CNC(=O)C1CC(C1)n2c3cc(ccc3nc2c4cc(c(c(c4)OC)OC)OC)C(=O)NCCCN(C)C"                                                                                                                                        
# 
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 
A1A3C "SYSTEMATIC NAME" ACDLabs              14.52 "N-[3-(dimethylamino)propyl]-1-[(1r,3r)-3-(methylcarbamoyl)cyclobutyl]-2-(3,4,5-trimethoxyphenyl)-1H-1,3-benzimidazole-6-carboxamide" 
A1A3C "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "~{N}-[3-(dimethylamino)propyl]-3-[3-(methylcarbamoyl)cyclobutyl]-2-(3,4,5-trimethoxyphenyl)benzimidazole-5-carboxamide"              
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
A1A3C "Create component" 2024-08-23 RCSB 
A1A3C "Initial release"  2024-11-27 RCSB 
# 
