data_A1JEQ
# 
_chem_comp.id                                    A1JEQ 
_chem_comp.name                                  "methyl 2-[(3~{S})-pyrrolidin-3-yl]-1~{H}-benzimidazole-5-carboxylate" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C13 H15 N3 O2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2025-06-03 
_chem_comp.pdbx_modified_date                    2025-12-26 
_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                        245.277 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1JEQ 
_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        9RE8 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
_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 
A1JEQ C10 C1  C 0 1 N N N N N N -7.541  3.332 -20.551 5.540  0.472  0.836  C10 A1JEQ 1  
A1JEQ C13 C2  C 0 1 Y N N N N N -14.339 1.920 -19.331 -2.236 -1.395 0.200  C13 A1JEQ 2  
A1JEQ C12 C3  C 0 1 Y N N N N N -13.108 1.429 -19.055 -0.937 -1.814 0.209  C12 A1JEQ 3  
A1JEQ C11 C4  C 0 1 N N N N N N -8.223  4.965 -19.070 4.241  -0.629 -0.851 C11 A1JEQ 4  
A1JEQ C01 C5  C 0 1 N N N N N N -17.138 5.669 -20.443 -6.302 0.001  0.145  C01 A1JEQ 5  
A1JEQ C02 C6  C 0 1 N N N N N N -15.902 3.727 -19.888 -3.953 0.396  -0.013 C02 A1JEQ 6  
A1JEQ C03 C7  C 0 1 Y N N N N N -14.527 3.274 -19.522 -2.545 -0.043 -0.002 C03 A1JEQ 7  
A1JEQ C04 C8  C 0 1 Y N N N N N -13.476 4.150 -19.439 -1.526 0.887  -0.190 C04 A1JEQ 8  
A1JEQ C05 C9  C 0 1 Y N N N N N -12.263 3.640 -19.173 -0.198 0.463  -0.177 C05 A1JEQ 9  
A1JEQ C06 C10 C 0 1 Y N N N N N -12.099 2.307 -18.986 0.093  -0.899 0.022  C06 A1JEQ 10 
A1JEQ C07 C11 C 0 1 Y N N N N N -10.108 3.336 -18.763 1.963  0.247  -0.229 C07 A1JEQ 11 
A1JEQ C08 C12 C 0 1 N N S N N N -8.665  3.601 -18.523 3.427  0.586  -0.342 C08 A1JEQ 12 
A1JEQ C09 C13 C 0 1 N N N N N N -7.786  2.588 -19.253 4.053  0.818  1.059  C09 A1JEQ 13 
A1JEQ N01 N1  N 0 1 Y N N N N N -10.737 2.038 -18.731 1.467  -1.002 -0.017 N01 A1JEQ 14 
A1JEQ N02 N2  N 0 1 Y N N N N N -11.050 4.300 -19.045 0.990  1.104  -0.327 N02 A1JEQ 15 
A1JEQ N03 N3  N 0 1 N N N N N N -7.174  4.651 -20.042 5.613  -0.402 -0.349 N03 A1JEQ 16 
A1JEQ O01 O1  O 0 1 N N N N N N -15.932 5.082 -19.992 -4.940 -0.502 0.169  O01 A1JEQ 17 
A1JEQ O02 O2  O 0 1 N N N N N N -16.855 2.998 -20.164 -4.223 1.568  -0.188 O02 A1JEQ 18 
A1JEQ H10 H1  H 0 1 N N N N N N -6.723  2.879 -21.130 6.111  1.384  0.660  H10 A1JEQ 19 
A1JEQ H09 H2  H 0 1 N N N N N N -8.449  3.375 -21.171 5.936  -0.050 1.707  H09 A1JEQ 20 
A1JEQ H15 H3  H 0 1 N N N N N N -15.181 1.247 -19.402 -3.031 -2.111 0.346  H15 A1JEQ 21 
A1JEQ H14 H4  H 0 1 N N N N N N -12.946 0.373 -18.897 -0.709 -2.859 0.361  H14 A1JEQ 22 
A1JEQ H12 H5  H 0 1 N N N N N N -9.064  5.478 -19.559 3.836  -1.555 -0.442 H12 A1JEQ 23 
A1JEQ H13 H6  H 0 1 N N N N N N -7.827  5.598 -18.262 4.234  -0.661 -1.940 H13 A1JEQ 24 
A1JEQ H02 H7  H 0 1 N N N N N N -17.023 6.762 -20.480 -6.430 0.741  0.935  H02 A1JEQ 25 
A1JEQ H01 H8  H 0 1 N N N N N N -17.376 5.292 -21.449 -6.502 0.463  -0.821 H01 A1JEQ 26 
A1JEQ H03 H9  H 0 1 N N N N N N -17.953 5.409 -19.752 -6.997 -0.824 0.304  H03 A1JEQ 27 
A1JEQ H04 H10 H 0 1 N N N N N N -13.618 5.211 -19.582 -1.763 1.929  -0.346 H04 A1JEQ 28 
A1JEQ H06 H11 H 0 1 N N N N N N -8.452  3.557 -17.445 3.576  1.454  -0.985 H06 A1JEQ 29 
A1JEQ H08 H12 H 0 1 N N N N N N -6.849  2.396 -18.710 3.608  0.150  1.796  H08 A1JEQ 30 
A1JEQ H07 H13 H 0 1 N N N N N N -8.313  1.638 -19.421 3.941  1.859  1.363  H07 A1JEQ 31 
A1JEQ H05 H14 H 0 1 N N N N N N -10.307 1.151 -18.566 1.985  -1.816 0.089  H05 A1JEQ 32 
A1JEQ H2  H16 H 0 1 N N N N N N -6.277  4.624 -19.600 6.196  0.005  -1.064 H2  A1JEQ 33 
# 
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 
A1JEQ C01 O01 SING N N 1  
A1JEQ O01 C02 SING N N 2  
A1JEQ C02 O02 DOUB N N 3  
A1JEQ C02 C03 SING N N 4  
A1JEQ C03 C04 DOUB Y N 5  
A1JEQ C03 C13 SING Y N 6  
A1JEQ C04 C05 SING Y N 7  
A1JEQ C05 C06 DOUB Y N 8  
A1JEQ C05 N02 SING Y N 9  
A1JEQ C06 N01 SING Y N 10 
A1JEQ C06 C12 SING Y N 11 
A1JEQ N01 C07 SING Y N 12 
A1JEQ C07 N02 DOUB Y N 13 
A1JEQ C07 C08 SING N N 14 
A1JEQ C08 C09 SING N N 15 
A1JEQ C08 C11 SING N N 16 
A1JEQ C09 C10 SING N N 17 
A1JEQ C10 N03 SING N N 18 
A1JEQ N03 C11 SING N N 19 
A1JEQ C12 C13 DOUB Y N 20 
A1JEQ C10 H10 SING N N 21 
A1JEQ C10 H09 SING N N 22 
A1JEQ C13 H15 SING N N 23 
A1JEQ C12 H14 SING N N 24 
A1JEQ C11 H12 SING N N 25 
A1JEQ C11 H13 SING N N 26 
A1JEQ C01 H02 SING N N 27 
A1JEQ C01 H01 SING N N 28 
A1JEQ C01 H03 SING N N 29 
A1JEQ C04 H04 SING N N 30 
A1JEQ C08 H06 SING N N 31 
A1JEQ C09 H08 SING N N 32 
A1JEQ C09 H07 SING N N 33 
A1JEQ N01 H05 SING N N 34 
A1JEQ N03 H2  SING N N 35 
# 
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 
A1JEQ InChI            InChI                1.06  "InChI=1S/C13H15N3O2/c1-18-13(17)8-2-3-10-11(6-8)16-12(15-10)9-4-5-14-7-9/h2-3,6,9,14H,4-5,7H2,1H3,(H,15,16)/t9-/m0/s1" 
A1JEQ InChIKey         InChI                1.06  FBNLOINYSAGAMH-VIFPVBQESA-N                                                                                             
A1JEQ SMILES_CANONICAL CACTVS               3.385 "COC(=O)c1ccc2[nH]c(nc2c1)[C@H]3CCNC3"                                                                                  
A1JEQ SMILES           CACTVS               3.385 "COC(=O)c1ccc2[nH]c(nc2c1)[CH]3CCNC3"                                                                                   
A1JEQ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "COC(=O)c1ccc2c(c1)nc([nH]2)[C@H]3CCNC3"                                                                                
A1JEQ SMILES           "OpenEye OEToolkits" 2.0.7 "COC(=O)c1ccc2c(c1)nc([nH]2)C3CCNC3"                                                                                    
# 
_pdbx_chem_comp_identifier.comp_id           A1JEQ 
_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        "methyl 2-[(3~{S})-pyrrolidin-3-yl]-1~{H}-benzimidazole-5-carboxylate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
A1JEQ "Create component" 2025-06-03 PDBE 
A1JEQ "Initial release"  2025-12-31 RCSB 
# 
