data_A1L5P
# 
_chem_comp.id                                    A1L5P 
_chem_comp.name                                  "3-[1-(5,6,7,8-tetrahydro-4~{H}-cyclohepta[b]thiophen-2-ylcarbonyl)piperidin-4-yl]-1~{H}-benzimidazol-2-one" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C22 H25 N3 O2 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2024-11-08 
_chem_comp.pdbx_modified_date                    2025-10-03 
_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                        395.518 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1L5P 
_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        9KDD 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBJ 
_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 
A1L5P C10 C1  C 0 1 N N N N N N 131.279 160.439 175.493 0.862  -2.510 -0.610 C10 A1L5P 1  
A1L5P C12 C2  C 0 1 Y N N N N N 126.954 158.446 176.600 4.755  0.371  -0.266 C12 A1L5P 2  
A1L5P C13 C3  C 0 1 N N N N N N 132.702 158.397 174.594 -1.476 -1.922 -0.185 C13 A1L5P 3  
A1L5P C14 C4  C 0 1 N N N N N N 127.627 159.888 178.363 3.572  0.303  1.613  C14 A1L5P 4  
A1L5P C15 C5  C 0 1 Y N N N N N 132.430 159.995 170.966 -4.352 0.225  0.744  C15 A1L5P 5  
A1L5P C16 C6  C 0 1 Y N N N N N 132.822 158.925 173.163 -2.557 -0.934 -0.111 C16 A1L5P 6  
A1L5P C17 C7  C 0 1 N N N N N N 131.921 160.744 169.729 -5.427 0.556  1.782  C17 A1L5P 7  
A1L5P C18 C8  C 0 1 Y N N N N N 133.747 159.389 170.855 -4.227 0.877  -0.417 C18 A1L5P 8  
A1L5P C19 C9  C 0 1 N N N N N N 131.393 159.754 168.700 -6.787 0.236  1.159  C19 A1L5P 9  
A1L5P C20 C10 C 0 1 N N N N N N 134.421 159.622 169.496 -5.116 2.040  -0.849 C20 A1L5P 10 
A1L5P C22 C11 C 0 1 N N N N N N 132.284 158.524 168.607 -7.260 1.352  0.259  C22 A1L5P 11 
A1L5P C23 C12 C 0 1 N N N N N N 133.734 158.907 168.333 -6.530 1.489  -1.056 C23 A1L5P 12 
A1L5P C07 C13 C 0 1 N N N N N N 129.502 159.120 176.605 2.384  -0.538 -0.423 C07 A1L5P 13 
A1L5P C08 C14 C 0 1 N N N N N N 129.847 160.435 176.023 2.036  -1.906 0.167  C08 A1L5P 14 
A1L5P C09 C15 C 0 1 N N N N N N 130.492 158.751 177.661 1.182  0.399  -0.286 C09 A1L5P 15 
A1L5P C11 C16 C 0 1 N N N N N N 131.874 158.567 177.049 -0.002 -0.178 -1.068 C11 A1L5P 16 
A1L5P C21 C17 C 0 1 Y N N N N N 125.767 158.736 177.438 5.548  0.869  0.770  C21 A1L5P 17 
A1L5P C24 C18 C 0 1 Y N N N N N 131.835 159.694 172.424 -3.425 -0.787 0.929  C24 A1L5P 18 
A1L5P C25 C19 C 0 1 Y N N N N N 126.841 157.528 175.361 5.262  0.311  -1.555 C25 A1L5P 19 
A1L5P C26 C20 C 0 1 Y N N N N N 124.395 158.118 177.081 6.840  1.296  0.507  C26 A1L5P 20 
A1L5P C27 C21 C 0 1 Y N N N N N 125.492 156.909 174.993 6.551  0.737  -1.808 C27 A1L5P 21 
A1L5P C28 C22 C 0 1 Y N N N N N 124.265 157.207 175.858 7.338  1.227  -0.780 C28 A1L5P 22 
A1L5P N04 N1  N 0 1 N N N N N N 131.990 159.107 175.645 -0.251 -1.550 -0.606 N04 A1L5P 23 
A1L5P N05 N2  N 0 1 N N N N N N 128.099 159.155 177.170 3.528  0.028  0.296  N05 A1L5P 24 
A1L5P N06 N3  N 0 1 N N N N N N 126.185 159.624 178.523 4.778  0.812  1.930  N06 A1L5P 25 
A1L5P O02 O1  O 0 1 N N N N N N 133.208 157.361 174.858 -1.686 -3.077 0.134  O02 A1L5P 26 
A1L5P O03 O2  O 0 1 N N N N N N 128.283 160.571 179.073 2.661  0.121  2.398  O03 A1L5P 27 
A1L5P S01 S1  S 0 1 Y N N N N N 134.040 158.704 172.223 -2.941 0.252  -1.350 S01 A1L5P 28 
A1L5P H1  H1  H 0 1 N N N N N N 131.850 161.202 176.042 1.167  -2.710 -1.637 H1  A1L5P 29 
A1L5P H2  H2  H 0 1 N N N N N N 131.253 160.699 174.424 0.546  -3.438 -0.133 H2  A1L5P 30 
A1L5P H3  H3  H 0 1 N N N N N N 132.747 161.322 169.288 -5.279 -0.050 2.676  H3  A1L5P 31 
A1L5P H4  H4  H 0 1 N N N N N N 131.112 161.428 170.025 -5.378 1.614  2.041  H4  A1L5P 32 
A1L5P H5  H5  H 0 1 N N N N N N 131.357 160.245 167.716 -6.705 -0.681 0.577  H5  A1L5P 33 
A1L5P H6  H6  H 0 1 N N N N N N 130.380 159.441 168.991 -7.517 0.088  1.955  H6  A1L5P 34 
A1L5P H7  H7  H 0 1 N N N N N N 135.459 159.263 169.558 -5.128 2.805  -0.073 H7  A1L5P 35 
A1L5P H8  H8  H 0 1 N N N N N N 134.418 160.702 169.289 -4.743 2.464  -1.781 H8  A1L5P 36 
A1L5P H9  H9  H 0 1 N N N N N N 131.923 157.882 167.790 -8.318 1.193  0.046  H9  A1L5P 37 
A1L5P H10 H10 H 0 1 N N N N N N 132.233 157.972 169.557 -7.161 2.293  0.800  H10 A1L5P 38 
A1L5P H11 H11 H 0 1 N N N N N N 134.298 157.989 168.110 -7.086 2.167  -1.705 H11 A1L5P 39 
A1L5P H12 H12 H 0 1 N N N N N N 133.756 159.572 167.457 -6.466 0.512  -1.534 H12 A1L5P 40 
A1L5P H13 H13 H 0 1 N N N N N N 129.537 158.360 175.810 2.638  -0.651 -1.477 H13 A1L5P 41 
A1L5P H14 H14 H 0 1 N N N N N N 129.748 161.209 176.798 1.758  -1.791 1.214  H14 A1L5P 42 
A1L5P H15 H15 H 0 1 N N N N N N 129.156 160.655 175.195 2.901  -2.566 0.090  H15 A1L5P 43 
A1L5P H16 H16 H 0 1 N N N N N N 130.533 159.551 178.415 0.912  0.493  0.766  H16 A1L5P 44 
A1L5P H17 H17 H 0 1 N N N N N N 130.179 157.811 178.139 1.438  1.381  -0.685 H17 A1L5P 45 
A1L5P H18 H18 H 0 1 N N N N N N 132.105 157.492 177.028 -0.888 0.433  -0.893 H18 A1L5P 46 
A1L5P H19 H19 H 0 1 N N N N N N 132.607 159.087 177.683 0.232  -0.186 -2.132 H19 A1L5P 47 
A1L5P H20 H20 H 0 1 N N N N N N 130.870 160.008 172.792 -3.393 -1.403 1.815  H20 A1L5P 48 
A1L5P H21 H21 H 0 1 N N N N N N 127.713 157.324 174.757 4.650  -0.069 -2.359 H21 A1L5P 49 
A1L5P H22 H22 H 0 1 N N N N N N 123.531 158.329 177.693 7.457  1.682  1.306  H22 A1L5P 50 
A1L5P H23 H23 H 0 1 N N N N N N 125.406 156.266 174.129 6.946  0.689  -2.812 H23 A1L5P 51 
A1L5P H24 H24 H 0 1 N N N N N N 123.308 156.775 175.606 8.346  1.558  -0.985 H24 A1L5P 52 
A1L5P H25 H25 H 0 1 N N N N N N 125.597 159.988 179.245 5.062  1.092  2.814  H25 A1L5P 53 
# 
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 
A1L5P C23 C22 SING N N 1  
A1L5P C23 C20 SING N N 2  
A1L5P C22 C19 SING N N 3  
A1L5P C19 C17 SING N N 4  
A1L5P C20 C18 SING N N 5  
A1L5P C17 C15 SING N N 6  
A1L5P C18 C15 DOUB Y N 7  
A1L5P C18 S01 SING Y N 8  
A1L5P C15 C24 SING Y N 9  
A1L5P S01 C16 SING Y N 10 
A1L5P C24 C16 DOUB Y N 11 
A1L5P C16 C13 SING N N 12 
A1L5P C13 O02 DOUB N N 13 
A1L5P C13 N04 SING N N 14 
A1L5P C27 C25 SING Y N 15 
A1L5P C27 C28 DOUB Y N 16 
A1L5P C25 C12 DOUB Y N 17 
A1L5P C10 N04 SING N N 18 
A1L5P C10 C08 SING N N 19 
A1L5P N04 C11 SING N N 20 
A1L5P C28 C26 SING Y N 21 
A1L5P C08 C07 SING N N 22 
A1L5P C12 N05 SING N N 23 
A1L5P C12 C21 SING Y N 24 
A1L5P C07 N05 SING N N 25 
A1L5P C07 C09 SING N N 26 
A1L5P C11 C09 SING N N 27 
A1L5P C26 C21 DOUB Y N 28 
A1L5P N05 C14 SING N N 29 
A1L5P C21 N06 SING N N 30 
A1L5P C14 N06 SING N N 31 
A1L5P C14 O03 DOUB N N 32 
A1L5P C10 H1  SING N N 33 
A1L5P C10 H2  SING N N 34 
A1L5P C17 H3  SING N N 35 
A1L5P C17 H4  SING N N 36 
A1L5P C19 H5  SING N N 37 
A1L5P C19 H6  SING N N 38 
A1L5P C20 H7  SING N N 39 
A1L5P C20 H8  SING N N 40 
A1L5P C22 H9  SING N N 41 
A1L5P C22 H10 SING N N 42 
A1L5P C23 H11 SING N N 43 
A1L5P C23 H12 SING N N 44 
A1L5P C07 H13 SING N N 45 
A1L5P C08 H14 SING N N 46 
A1L5P C08 H15 SING N N 47 
A1L5P C09 H16 SING N N 48 
A1L5P C09 H17 SING N N 49 
A1L5P C11 H18 SING N N 50 
A1L5P C11 H19 SING N N 51 
A1L5P C24 H20 SING N N 52 
A1L5P C25 H21 SING N N 53 
A1L5P C26 H22 SING N N 54 
A1L5P C27 H23 SING N N 55 
A1L5P C28 H24 SING N N 56 
A1L5P N06 H25 SING N N 57 
# 
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 
A1L5P InChI            InChI                1.06  "InChI=1S/C22H25N3O2S/c26-21(20-14-15-6-2-1-3-9-19(15)28-20)24-12-10-16(11-13-24)25-18-8-5-4-7-17(18)23-22(25)27/h4-5,7-8,14,16H,1-3,6,9-13H2,(H,23,27)" 
A1L5P InChIKey         InChI                1.06  AXWRAIIIBRLXBP-UHFFFAOYSA-N                                                                                                                              
A1L5P SMILES_CANONICAL CACTVS               3.385 "O=C1Nc2ccccc2N1C3CCN(CC3)C(=O)c4sc5CCCCCc5c4"                                                                                                           
A1L5P SMILES           CACTVS               3.385 "O=C1Nc2ccccc2N1C3CCN(CC3)C(=O)c4sc5CCCCCc5c4"                                                                                                           
A1L5P SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1ccc2c(c1)NC(=O)N2C3CCN(CC3)C(=O)c4cc5c(s4)CCCCC5"                                                                                                     
A1L5P SMILES           "OpenEye OEToolkits" 2.0.7 "c1ccc2c(c1)NC(=O)N2C3CCN(CC3)C(=O)c4cc5c(s4)CCCCC5"                                                                                                     
# 
_pdbx_chem_comp_identifier.comp_id           A1L5P 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           "OpenEye OEToolkits" 
_pdbx_chem_comp_identifier.program_version   2.0.7 
_pdbx_chem_comp_identifier.identifier        "3-[1-(5,6,7,8-tetrahydro-4~{H}-cyclohepta[b]thiophen-2-ylcarbonyl)piperidin-4-yl]-1~{H}-benzimidazol-2-one" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
A1L5P "Create component" 2024-11-08 PDBJ 
A1L5P "Initial release"  2025-10-08 RCSB 
# 
