data_A1D5N
# 
_chem_comp.id                                    A1D5N 
_chem_comp.name                                  "(3~{S})-5-methyl-3-[[1-pentan-3-yl-2-(thiophen-2-ylmethyl)benzimidazol-5-yl]carbonylamino]hexanoic acid" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C25 H33 N3 O3 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         CMF019 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2024-01-24 
_chem_comp.pdbx_modified_date                    2024-03-15 
_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                        455.613 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1D5N 
_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        8XZI 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBC 
# 
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 
A1D5N C08  C1  C 0 1 N N N N N N 85.352 121.070 111.074 3.419  2.001  0.693  C08  A1D5N 1  
A1D5N C09  C2  C 0 1 N N N N N N 84.223 122.068 110.837 4.521  1.291  1.482  C09  A1D5N 2  
A1D5N C10  C3  C 0 1 N N N N N N 85.325 120.611 112.530 4.052  2.989  -0.289 C10  A1D5N 3  
A1D5N C11  C4  C 0 1 Y N N N N N 87.118 122.771 111.362 1.274  0.811  0.048  C11  A1D5N 4  
A1D5N C12  C5  C 0 1 Y N N N N N 87.552 121.245 109.892 3.114  0.117  -0.955 C12  A1D5N 5  
A1D5N C13  C6  C 0 1 N N S N N N 89.497 128.771 113.589 -5.115 -0.303 0.171  C13  A1D5N 6  
A1D5N C14  C7  C 0 1 N N N N N N 89.000 130.030 112.882 -5.446 -1.515 1.044  C14  A1D5N 7  
A1D5N C15  C8  C 0 1 N N N N N N 89.225 129.927 111.375 -6.876 -1.976 0.754  C15  A1D5N 8  
A1D5N C16  C9  C 0 1 Y N N N N N 88.364 123.022 110.819 0.973  -0.235 -0.845 C16  A1D5N 9  
A1D5N C17  C10 C 0 1 N N N N N N 87.417 120.014 109.001 4.560  -0.009 -1.360 C17  A1D5N 10 
A1D5N C18  C11 C 0 1 Y N N N N N 86.526 123.713 112.462 0.263  1.406  0.792  C18  A1D5N 11 
A1D5N C19  C12 C 0 1 N N N N N N 89.253 128.911 115.089 -6.021 0.867  0.558  C19  A1D5N 12 
A1D5N C20  C13 C 0 1 Y N N N N N 88.646 125.168 112.350 -1.345 -0.059 -0.223 C20  A1D5N 13 
A1D5N C21  C14 C 0 1 Y N N N N N 89.202 124.256 111.295 -0.345 -0.667 -0.977 C21  A1D5N 14 
A1D5N C22  C15 C 0 1 N N N N N N 82.963 121.312 110.431 5.235  2.301  2.383  C22  A1D5N 15 
A1D5N C23  C16 C 0 1 N N N N N N 86.552 119.755 112.835 2.955  3.837  -0.937 C23  A1D5N 16 
A1D5N C24  C17 C 0 1 Y N N N N N 87.315 124.898 112.931 -1.027 0.980  0.661  C24  A1D5N 17 
A1D5N C25  C18 C 0 1 N N N N N N 89.443 126.372 112.832 -2.745 -0.511 -0.356 C25  A1D5N 18 
A1D5N C26  C19 C 0 1 N N N N N N 90.620 129.375 111.089 -6.966 -2.481 -0.688 C26  A1D5N 19 
A1D5N C27  C20 C 0 1 N N N N N N 89.089 131.312 110.749 -7.252 -3.106 1.715  C27  A1D5N 20 
A1D5N C28  C21 C 0 1 Y N N N N N 86.999 120.461 107.607 5.154  -1.240 -0.726 C28  A1D5N 21 
A1D5N C29  C22 C 0 1 N N N N N N 90.197 129.957 115.674 -5.780 2.021  -0.382 C29  A1D5N 22 
A1D5N C30  C23 C 0 1 Y N N N N N 87.861 121.012 106.582 5.244  -2.437 -1.307 C30  A1D5N 23 
A1D5N C31  C24 C 0 1 Y N N N N N 86.970 121.330 105.300 5.830  -3.421 -0.528 C31  A1D5N 24 
A1D5N C32  C25 C 0 1 Y N N N N N 85.601 120.964 105.594 6.216  -3.022 0.685  C32  A1D5N 25 
A1D5N N05  N1  N 0 1 Y N N N N N 86.634 121.687 110.789 2.634  1.011  -0.048 N05  A1D5N 26 
A1D5N N06  N2  N 0 1 Y N N N N N 88.615 122.084 109.926 2.144  -0.612 -1.423 N06  A1D5N 27 
A1D5N N07  N3  N 0 1 N N N N N N 88.759 127.617 113.115 -3.714 0.076  0.374  N07  A1D5N 28 
A1D5N O02  O1  O 0 1 N N N N N N 90.610 126.281 112.987 -3.023 -1.413 -1.122 O02  A1D5N 29 
A1D5N O03  O2  O 0 1 N N N N N N 89.733 130.954 116.286 -6.469 3.163  -0.232 O03  A1D5N 30 
A1D5N O04  O3  O 0 1 N N N N N N 91.441 129.822 115.545 -4.967 1.918  -1.269 O04  A1D5N 31 
A1D5N S01  S1  S 0 1 Y N N N N N 85.562 120.409 107.042 5.843  -1.315 0.891  S01  A1D5N 32 
A1D5N H081 H1  H 0 0 N N N N N N 85.201 120.198 110.421 2.768  2.539  1.382  H081 A1D5N 33 
A1D5N H092 H2  H 0 0 N N N N N N 84.509 122.764 110.035 4.079  0.505  2.096  H092 A1D5N 34 
A1D5N H091 H3  H 0 0 N N N N N N 84.031 122.633 111.761 5.238  0.851  0.790  H091 A1D5N 35 
A1D5N H101 H4  H 0 0 N N N N N N 85.323 121.492 113.189 4.745  3.639  0.246  H101 A1D5N 36 
A1D5N H102 H5  H 0 0 N N N N N N 84.415 120.019 112.708 4.591  2.440  -1.061 H102 A1D5N 37 
A1D5N H131 H6  H 0 0 N N N N N N 90.574 128.645 113.402 -5.275 -0.555 -0.877 H131 A1D5N 38 
A1D5N H141 H7  H 0 0 N N N N N N 89.547 130.902 113.270 -4.751 -2.324 0.821  H141 A1D5N 39 
A1D5N H142 H8  H 0 0 N N N N N N 87.925 130.154 113.079 -5.359 -1.240 2.095  H142 A1D5N 40 
A1D5N H151 H9  H 0 0 N N N N N N 88.471 129.255 110.939 -7.562 -1.140 0.890  H151 A1D5N 41 
A1D5N H172 H10 H 0 0 N N N N N N 86.655 119.338 109.417 4.628  -0.091 -2.445 H172 A1D5N 42 
A1D5N H171 H11 H 0 0 N N N N N N 88.382 119.489 108.947 5.109  0.872  -1.028 H171 A1D5N 43 
A1D5N H181 H12 H 0 0 N N N N N N 85.552 123.510 112.882 0.498  2.208  1.476  H181 A1D5N 44 
A1D5N H192 H13 H 0 0 N N N N N N 88.212 129.222 115.262 -7.064 0.557  0.492  H192 A1D5N 45 
A1D5N H191 H14 H 0 0 N N N N N N 89.432 127.943 115.579 -5.798 1.178  1.579  H191 A1D5N 46 
A1D5N H211 H15 H 0 0 N N N N N N 90.174 124.450 110.867 -0.590 -1.469 -1.658 H211 A1D5N 47 
A1D5N H221 H16 H 0 0 N N N N N N 82.145 122.027 110.259 5.763  3.027  1.766  H221 A1D5N 48 
A1D5N H222 H17 H 0 0 N N N N N N 83.156 120.747 109.507 4.502  2.816  3.004  H222 A1D5N 49 
A1D5N H223 H18 H 0 0 N N N N N N 82.678 120.616 111.234 5.949  1.778  3.020  H223 A1D5N 50 
A1D5N H231 H19 H 0 0 N N N N N N 86.521 119.431 113.886 2.218  3.182  -1.402 H231 A1D5N 51 
A1D5N H232 H20 H 0 0 N N N N N N 86.555 118.872 112.179 2.470  4.447  -0.176 H232 A1D5N 52 
A1D5N H233 H21 H 0 0 N N N N N N 87.463 120.345 112.660 3.397  4.484  -1.695 H233 A1D5N 53 
A1D5N H241 H22 H 0 0 N N N N N N 86.912 125.552 113.690 -1.808 1.446  1.243  H241 A1D5N 54 
A1D5N H263 H23 H 0 0 N N N N N N 90.719 128.377 111.540 -7.997 -2.756 -0.912 H263 A1D5N 55 
A1D5N H261 H24 H 0 0 N N N N N N 90.770 129.303 110.002 -6.643 -1.695 -1.369 H261 A1D5N 56 
A1D5N H262 H25 H 0 0 N N N N N N 91.376 130.048 111.519 -6.324 -3.354 -0.808 H262 A1D5N 57 
A1D5N H271 H26 H 0 0 N N N N N N 88.085 131.711 110.954 -7.187 -2.746 2.742  H271 A1D5N 58 
A1D5N H273 H27 H 0 0 N N N N N N 89.845 131.985 111.179 -8.271 -3.435 1.508  H273 A1D5N 59 
A1D5N H272 H28 H 0 0 N N N N N N 89.239 131.239 109.662 -6.566 -3.942 1.579  H272 A1D5N 60 
A1D5N H301 H29 H 0 0 N N N N N N 88.924 121.179 106.671 4.886  -2.625 -2.308 H301 A1D5N 61 
A1D5N H311 H30 H 0 0 N N N N N N 87.327 121.748 104.370 5.960  -4.435 -0.875 H311 A1D5N 62 
A1D5N H321 H31 H 0 0 N N N N N N 84.758 121.060 104.926 6.689  -3.649 1.425  H321 A1D5N 63 
A1D5N H071 H32 H 0 0 N N N N N N 87.770 127.681 112.982 -3.485 0.750  1.033  H071 A1D5N 64 
A1D5N H1   H33 H 0 1 N N N N N N 90.448 131.503 116.585 -6.280 3.875  -0.859 H1   A1D5N 65 
# 
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 
A1D5N C31 C32  DOUB Y N 1  
A1D5N C31 C30  SING Y N 2  
A1D5N C32 S01  SING Y N 3  
A1D5N C30 C28  DOUB Y N 4  
A1D5N S01 C28  SING Y N 5  
A1D5N C28 C17  SING N N 6  
A1D5N C17 C12  SING N N 7  
A1D5N C12 N06  DOUB Y N 8  
A1D5N C12 N05  SING Y N 9  
A1D5N N06 C16  SING Y N 10 
A1D5N C22 C09  SING N N 11 
A1D5N C27 C15  SING N N 12 
A1D5N N05 C08  SING N N 13 
A1D5N N05 C11  SING Y N 14 
A1D5N C16 C21  DOUB Y N 15 
A1D5N C16 C11  SING Y N 16 
A1D5N C09 C08  SING N N 17 
A1D5N C08 C10  SING N N 18 
A1D5N C26 C15  SING N N 19 
A1D5N C21 C20  SING Y N 20 
A1D5N C11 C18  DOUB Y N 21 
A1D5N C15 C14  SING N N 22 
A1D5N C20 C25  SING N N 23 
A1D5N C20 C24  DOUB Y N 24 
A1D5N C18 C24  SING Y N 25 
A1D5N C10 C23  SING N N 26 
A1D5N C25 O02  DOUB N N 27 
A1D5N C25 N07  SING N N 28 
A1D5N C14 C13  SING N N 29 
A1D5N N07 C13  SING N N 30 
A1D5N C13 C19  SING N N 31 
A1D5N C19 C29  SING N N 32 
A1D5N O04 C29  DOUB N N 33 
A1D5N C29 O03  SING N N 34 
A1D5N C08 H081 SING N N 35 
A1D5N C09 H092 SING N N 36 
A1D5N C09 H091 SING N N 37 
A1D5N C10 H101 SING N N 38 
A1D5N C10 H102 SING N N 39 
A1D5N C13 H131 SING N N 40 
A1D5N C14 H141 SING N N 41 
A1D5N C14 H142 SING N N 42 
A1D5N C15 H151 SING N N 43 
A1D5N C17 H172 SING N N 44 
A1D5N C17 H171 SING N N 45 
A1D5N C18 H181 SING N N 46 
A1D5N C19 H192 SING N N 47 
A1D5N C19 H191 SING N N 48 
A1D5N C21 H211 SING N N 49 
A1D5N C22 H221 SING N N 50 
A1D5N C22 H222 SING N N 51 
A1D5N C22 H223 SING N N 52 
A1D5N C23 H231 SING N N 53 
A1D5N C23 H232 SING N N 54 
A1D5N C23 H233 SING N N 55 
A1D5N C24 H241 SING N N 56 
A1D5N C26 H263 SING N N 57 
A1D5N C26 H261 SING N N 58 
A1D5N C26 H262 SING N N 59 
A1D5N C27 H271 SING N N 60 
A1D5N C27 H273 SING N N 61 
A1D5N C27 H272 SING N N 62 
A1D5N C30 H301 SING N N 63 
A1D5N C31 H311 SING N N 64 
A1D5N C32 H321 SING N N 65 
A1D5N N07 H071 SING N N 66 
A1D5N O03 H1   SING N N 67 
# 
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 
A1D5N InChI            InChI                1.06  "InChI=1S/C25H33N3O3S/c1-5-19(6-2)28-22-10-9-17(25(31)26-18(12-16(3)4)14-24(29)30)13-21(22)27-23(28)15-20-8-7-11-32-20/h7-11,13,16,18-19H,5-6,12,14-15H2,1-4H3,(H,26,31)(H,29,30)/t18-/m0/s1" 
A1D5N InChIKey         InChI                1.06  VCQKKZXFASLXAH-SFHVURJKSA-N                                                                                                                                                                   
A1D5N SMILES_CANONICAL CACTVS               3.385 "CCC(CC)n1c(Cc2sccc2)nc3cc(ccc13)C(=O)N[C@@H](CC(C)C)CC(O)=O"                                                                                                                                 
A1D5N SMILES           CACTVS               3.385 "CCC(CC)n1c(Cc2sccc2)nc3cc(ccc13)C(=O)N[CH](CC(C)C)CC(O)=O"                                                                                                                                   
A1D5N SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CCC(CC)n1c2ccc(cc2nc1Cc3cccs3)C(=O)N[C@@H](CC(C)C)CC(=O)O"                                                                                                                                   
A1D5N SMILES           "OpenEye OEToolkits" 2.0.7 "CCC(CC)n1c2ccc(cc2nc1Cc3cccs3)C(=O)NC(CC(C)C)CC(=O)O"                                                                                                                                        
# 
_pdbx_chem_comp_identifier.comp_id           A1D5N 
_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~{S})-5-methyl-3-[[1-pentan-3-yl-2-(thiophen-2-ylmethyl)benzimidazol-5-yl]carbonylamino]hexanoic acid" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
A1D5N "Create component" 2024-01-24 PDBC 
A1D5N "Initial release"  2024-03-20 RCSB 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      A1D5N 
_pdbx_chem_comp_synonyms.name         CMF019 
_pdbx_chem_comp_synonyms.provenance   PUBCHEM 
_pdbx_chem_comp_synonyms.type         ? 
# 
