data_A1A5K
# 
_chem_comp.id                                    A1A5K 
_chem_comp.name                                  "(3R,4R)-1-[2-(hydroxymethyl)-1-methyl-1H-1,3-benzimidazole-5-carbonyl]-4-methylpiperidine-3-carboxylic acid" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C17 H21 N3 O4" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2024-09-09 
_chem_comp.pdbx_modified_date                    2025-06-06 
_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                        331.366 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1A5K 
_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        7HCM 
_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 
A1A5K N2  N1  N 0 1 Y N N N N N 14.877 6.694  3.598  -3.506 0.869  0.985  N2  A1A5K 1  
A1A5K C3  C1  C 0 1 N N N N N N 14.973 -0.561 -0.983 2.048  1.565  -1.092 C3  A1A5K 2  
A1A5K C6  C2  C 0 1 Y N N N N N 15.712 3.289  2.257  -0.475 -1.186 0.276  C6  A1A5K 3  
A1A5K C9  C3  C 0 1 Y N N N N N 15.303 4.687  4.621  -3.171 -0.905 -0.311 C9  A1A5K 4  
A1A5K C12 C4  C 0 1 Y N N N N N 14.793 6.781  4.918  -4.638 0.576  0.415  C12 A1A5K 5  
A1A5K C14 C5  C 0 1 N N N N N N 15.026 5.384  7.018  -5.534 -1.138 -1.203 C14 A1A5K 6  
A1A5K C17 C6  C 0 1 N N N N N N 12.440 -0.478 2.110  5.470  0.040  -0.294 C17 A1A5K 7  
A1A5K C1  C7  C 0 1 N N N N N N 13.542 -2.334 0.089  3.851  2.374  0.437  C1  A1A5K 8  
A1A5K C10 C8  C 0 1 Y N N N N N 15.194 5.375  3.383  -2.552 -0.009 0.580  C10 A1A5K 9  
A1A5K C11 C9  C 0 1 Y N N N N N 15.402 4.665  2.191  -1.196 -0.156 0.871  C11 A1A5K 10 
A1A5K C13 C10 C 0 1 N N N N N N 14.457 8.053  5.616  -5.928 1.327  0.621  C13 A1A5K 11 
A1A5K C15 C11 C 0 1 N N N N N N 14.720 0.447  1.636  3.242  -0.465 0.675  C15 A1A5K 12 
A1A5K C16 C12 C 0 1 N N R N N N 13.382 0.076  1.012  3.985  0.081  -0.548 C16 A1A5K 13 
A1A5K C2  C13 C 0 1 N N R N N N 13.653 -0.833 -0.219 3.550  1.526  -0.801 C2  A1A5K 14 
A1A5K C4  C14 C 0 1 N N N N N N 15.792 0.682  -0.586 1.282  1.035  0.125  C4  A1A5K 15 
A1A5K C5  C15 C 0 1 N N N N N N 15.957 2.544  0.979  0.961  -1.349 0.578  C5  A1A5K 16 
A1A5K C7  C16 C 0 1 Y N N N N N 15.820 2.644  3.514  -1.108 -2.069 -0.609 C7  A1A5K 17 
A1A5K C8  C17 C 0 1 Y N N N N N 15.601 3.325  4.706  -2.434 -1.929 -0.896 C8  A1A5K 18 
A1A5K N1  N2  N 0 1 N N N N N N 15.493 1.298  0.723  1.798  -0.299 0.464  N1  A1A5K 19 
A1A5K N3  N3  N 0 1 Y N N N N N 15.028 5.631  5.588  -4.488 -0.509 -0.393 N3  A1A5K 20 
A1A5K O1  O1  O 0 1 N N N N N N 16.610 3.112  0.115  1.389  -2.431 0.931  O1  A1A5K 21 
A1A5K O2  O2  O 0 1 N N N N N N 15.442 8.414  6.549  -6.027 2.376  -0.345 O2  A1A5K 22 
A1A5K O3  O3  O 0 1 N N N N N N 11.235 -0.179 2.020  6.115  1.062  -0.316 O3  A1A5K 23 
A1A5K O4  O4  O 0 1 N N N N N N 12.906 -1.195 3.025  6.076  -1.131 -0.043 O4  A1A5K 24 
A1A5K H6  H1  H 0 1 N N N N N N 14.720 -0.460 -2.049 1.743  2.591  -1.295 H6  A1A5K 25 
A1A5K H7  H2  H 0 1 N N N N N N 15.620 -1.439 -0.841 1.829  0.941  -1.959 H7  A1A5K 26 
A1A5K H18 H3  H 0 1 N N N N N N 14.774 6.313  7.551  -6.029 -1.913 -0.618 H18 A1A5K 27 
A1A5K H17 H4  H 0 1 N N N N N N 14.280 4.611  7.255  -6.265 -0.386 -1.502 H17 A1A5K 28 
A1A5K H16 H5  H 0 1 N N N N N N 16.023 5.040  7.332  -5.087 -1.584 -2.092 H16 A1A5K 29 
A1A5K H4  H6  H 0 1 N N N N N N 12.605 -2.529 0.632  3.305  1.975  1.292  H4  A1A5K 30 
A1A5K H3  H7  H 0 1 N N N N N N 13.546 -2.903 -0.853 4.921  2.346  0.644  H3  A1A5K 31 
A1A5K H5  H8  H 0 1 N N N N N N 14.396 -2.645 0.708  3.542  3.403  0.256  H5  A1A5K 32 
A1A5K H12 H9  H 0 1 N N N N N N 15.326 5.164  1.236  -0.710 0.525  1.553  H12 A1A5K 33 
A1A5K H13 H10 H 0 1 N N N N N N 14.364 8.855  4.869  -6.769 0.644  0.502  H13 A1A5K 34 
A1A5K H14 H11 H 0 1 N N N N N N 13.499 7.928  6.141  -5.944 1.754  1.624  H14 A1A5K 35 
A1A5K H20 H12 H 0 1 N N N N N N 15.289 -0.471 1.845  3.473  -1.523 0.800  H20 A1A5K 36 
A1A5K H19 H13 H 0 1 N N N N N N 14.543 0.991  2.576  3.549  0.084  1.565  H19 A1A5K 37 
A1A5K H2  H14 H 0 1 N N N N N N 12.927 1.003  0.634  3.749  -0.529 -1.420 H2  A1A5K 38 
A1A5K H1  H15 H 0 1 N N N N N N 12.846 -0.613 -0.933 4.095  1.925  -1.656 H1  A1A5K 39 
A1A5K H8  H16 H 0 1 N N N N N N 16.853 0.391  -0.580 1.428  1.708  0.970  H8  A1A5K 40 
A1A5K H9  H17 H 0 1 N N N N N N 15.626 1.448  -1.358 0.221  0.967  -0.112 H9  A1A5K 41 
A1A5K H10 H18 H 0 1 N N N N N N 16.079 1.596  3.547  -0.541 -2.866 -1.067 H10 A1A5K 42 
A1A5K H11 H19 H 0 1 N N N N N N 15.659 2.821  5.660  -2.913 -2.615 -1.580 H11 A1A5K 43 
A1A5K H15 H20 H 0 1 N N N N N N 15.194 9.227  6.973  -6.834 2.903  -0.272 H15 A1A5K 44 
A1A5K H21 H21 H 0 1 N N N N N N 12.205 -1.457 3.611  7.030  -1.107 0.114  H21 A1A5K 45 
# 
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 
A1A5K C3  C4  SING N N 1  
A1A5K C3  C2  SING N N 2  
A1A5K C4  N1  SING N N 3  
A1A5K C2  C1  SING N N 4  
A1A5K C2  C16 SING N N 5  
A1A5K O1  C5  DOUB N N 6  
A1A5K N1  C5  SING N N 7  
A1A5K N1  C15 SING N N 8  
A1A5K C5  C6  SING N N 9  
A1A5K C16 C15 SING N N 10 
A1A5K C16 C17 SING N N 11 
A1A5K O3  C17 DOUB N N 12 
A1A5K C17 O4  SING N N 13 
A1A5K C11 C6  DOUB Y N 14 
A1A5K C11 C10 SING Y N 15 
A1A5K C6  C7  SING Y N 16 
A1A5K C10 N2  SING Y N 17 
A1A5K C10 C9  DOUB Y N 18 
A1A5K C7  C8  DOUB Y N 19 
A1A5K N2  C12 DOUB Y N 20 
A1A5K C9  C8  SING Y N 21 
A1A5K C9  N3  SING Y N 22 
A1A5K C12 N3  SING Y N 23 
A1A5K C12 C13 SING N N 24 
A1A5K N3  C14 SING N N 25 
A1A5K C13 O2  SING N N 26 
A1A5K C3  H6  SING N N 27 
A1A5K C3  H7  SING N N 28 
A1A5K C14 H18 SING N N 29 
A1A5K C14 H17 SING N N 30 
A1A5K C14 H16 SING N N 31 
A1A5K C1  H4  SING N N 32 
A1A5K C1  H3  SING N N 33 
A1A5K C1  H5  SING N N 34 
A1A5K C11 H12 SING N N 35 
A1A5K C13 H13 SING N N 36 
A1A5K C13 H14 SING N N 37 
A1A5K C15 H20 SING N N 38 
A1A5K C15 H19 SING N N 39 
A1A5K C16 H2  SING N N 40 
A1A5K C2  H1  SING N N 41 
A1A5K C4  H8  SING N N 42 
A1A5K C4  H9  SING N N 43 
A1A5K C7  H10 SING N N 44 
A1A5K C8  H11 SING N N 45 
A1A5K O2  H15 SING N N 46 
A1A5K O4  H21 SING N N 47 
# 
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 
A1A5K SMILES           ACDLabs              14.52   "O=C(c1ccc2n(C)c(CO)nc2c1)N1CCC(C)C(C1)C(=O)O"                                                                                                           
A1A5K InChI            InChI                1.06    "InChI=1S/C17H21N3O4/c1-10-5-6-20(8-12(10)17(23)24)16(22)11-3-4-14-13(7-11)18-15(9-21)19(14)2/h3-4,7,10,12,21H,5-6,8-9H2,1-2H3,(H,23,24)/t10-,12+/m1/s1" 
A1A5K InChIKey         InChI                1.06    MSAKLWZGMAUWCQ-PWSUYJOCSA-N                                                                                                                              
A1A5K SMILES_CANONICAL CACTVS               3.385   "C[C@@H]1CCN(C[C@@H]1C(O)=O)C(=O)c2ccc3n(C)c(CO)nc3c2"                                                                                                   
A1A5K SMILES           CACTVS               3.385   "C[CH]1CCN(C[CH]1C(O)=O)C(=O)c2ccc3n(C)c(CO)nc3c2"                                                                                                       
A1A5K SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "C[C@@H]1CCN(C[C@@H]1C(=O)O)C(=O)c2ccc3c(c2)nc(n3C)CO"                                                                                                   
A1A5K SMILES           "OpenEye OEToolkits" 3.1.0.0 "CC1CCN(CC1C(=O)O)C(=O)c2ccc3c(c2)nc(n3C)CO"                                                                                                             
# 
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 
A1A5K "SYSTEMATIC NAME" ACDLabs              14.52   "(3R,4R)-1-[2-(hydroxymethyl)-1-methyl-1H-1,3-benzimidazole-5-carbonyl]-4-methylpiperidine-3-carboxylic acid"  
A1A5K "SYSTEMATIC NAME" "OpenEye OEToolkits" 3.1.0.0 "(3~{R},4~{R})-1-[2-(hydroxymethyl)-1-methyl-benzimidazol-5-yl]carbonyl-4-methyl-piperidine-3-carboxylic 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 
A1A5K "Create component" 2024-09-09 RCSB 
A1A5K "Initial release"  2025-06-11 RCSB 
# 
