data_05Y
# 
_chem_comp.id                                    05Y 
_chem_comp.name                                  "~{N}-[1-(2-pyridin-2-ylethyl)benzimidazol-2-yl]propanamide" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C17 H18 N4 O" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2021-06-03 
_chem_comp.pdbx_modified_date                    2024-09-27 
_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                        294.351 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     05Y 
_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        7OPR 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
_chem_comp.pdbx_pcm                              Y 
# 
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_backbone_atom_flag 
_chem_comp_atom.pdbx_n_terminal_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 
05Y C05 C1  C 0 1 N N N N N N -4.300 0.542  9.389  3.548  -4.649 0.010  C05 05Y 1  
05Y C06 C2  C 0 1 N N N N N N -4.857 1.889  9.857  2.199  -3.966 -0.228 C06 05Y 2  
05Y C07 C3  C 0 1 N N N N N N -5.887 2.400  8.855  2.365  -2.472 -0.113 C07 05Y 3  
05Y C09 C4  C 0 1 Y N N N N N -4.350 4.232  7.963  1.455  -0.289 -0.180 C09 05Y 4  
05Y C11 C5  C 0 1 Y N N N N N -2.246 4.706  7.961  2.375  1.667  0.104  C11 05Y 5  
05Y C12 C6  C 0 1 Y N N N N N -0.844 4.743  7.948  3.211  2.763  0.330  C12 05Y 6  
05Y C13 C7  C 0 1 Y N N N N N -0.185 5.966  7.999  2.691  4.037  0.299  C13 05Y 7  
05Y C14 C8  C 0 1 Y N N N N N -0.906 7.155  8.067  1.343  4.242  0.045  C14 05Y 8  
05Y C15 C9  C 0 1 Y N N N N N -2.294 7.117  8.082  0.504  3.170  -0.181 C15 05Y 9  
05Y C16 C10 C 0 1 Y N N N N N -2.959 5.881  8.030  1.011  1.880  -0.154 C16 05Y 10 
05Y C18 C11 C 0 1 N N N N N N -5.326 6.544  8.094  -0.950 0.333  -0.636 C18 05Y 11 
05Y C19 C12 C 0 1 N N N N N N -5.891 6.959  6.737  -1.726 0.156  0.671  C19 05Y 12 
05Y C20 C13 C 0 1 Y N N N N N -6.856 5.886  6.245  -3.170 -0.144 0.361  C20 05Y 13 
05Y C22 C14 C 0 1 Y N N N N N -7.409 4.234  4.739  -5.124 0.461  -0.700 C22 05Y 14 
05Y C23 C15 C 0 1 Y N N N N N -8.586 3.986  5.426  -5.778 -0.657 -0.217 C23 05Y 15 
05Y C24 C16 C 0 1 Y N N N N N -8.907 4.707  6.572  -5.089 -1.546 0.593  C24 05Y 16 
05Y C25 C17 C 0 1 Y N N N N N -8.012 5.682  6.990  -3.759 -1.279 0.884  C25 05Y 17 
05Y N08 N1  N 0 1 N N N N N N -5.601 3.495  7.934  1.303  -1.661 -0.285 N08 05Y 18 
05Y N10 N2  N 0 1 Y N N N N N -3.138 3.703  7.915  2.582  0.324  0.077  N10 05Y 19 
05Y N17 N3  N 0 1 Y N N N N N -4.258 5.557  8.006  0.454  0.625  -0.335 N17 05Y 20 
05Y N21 N4  N 0 1 Y N N N N N -6.585 5.176  5.163  -3.858 0.682  -0.403 N21 05Y 21 
05Y O26 O1  O 0 1 N N N N N N -6.930 1.836  8.795  3.454  -2.001 0.134  O26 05Y 22 
05Y H1  H1  H 0 1 N N N N N N -3.558 0.179  10.116 3.911  -4.399 1.007  H1  05Y 23 
05Y H2  H2  H 0 1 N N N N N N -5.121 -0.186 9.308  3.428  -5.729 -0.073 H2  05Y 24 
05Y H3  H3  H 0 1 N N N N N N -3.821 0.665  8.406  4.265  -4.305 -0.735 H3  05Y 25 
05Y H4  H4  H 0 1 N N N N N N -4.035 2.615  9.938  1.836  -4.215 -1.225 H4  05Y 26 
05Y H5  H5  H 0 1 N N N N N N -5.335 1.765  10.840 1.482  -4.310 0.517  H5  05Y 27 
05Y H6  H6  H 0 1 N N N N N N -0.278 3.824  7.899  4.262  2.611  0.530  H6  05Y 28 
05Y H7  H7  H 0 1 N N N N N N 0.895  5.994  7.986  3.338  4.884  0.475  H7  05Y 29 
05Y H8  H8  H 0 1 N N N N N N -0.388 8.102  8.108  0.948  5.246  0.024  H8  05Y 30 
05Y H9  H9  H 0 1 N N N N N N -2.860 8.035  8.133  -0.544 3.336  -0.378 H9  05Y 31 
05Y H10 H10 H 0 1 N N N N N N -4.930 7.440  8.594  -1.013 -0.583 -1.223 H10 05Y 32 
05Y H11 H11 H 0 1 N N N N N N -6.143 6.119  8.695  -1.379 1.159  -1.204 H11 05Y 33 
05Y H12 H12 H 0 1 N N N N N N -5.069 7.073  6.015  -1.297 -0.669 1.239  H12 05Y 34 
05Y H13 H13 H 0 1 N N N N N N -6.425 7.915  6.838  -1.664 1.072  1.258  H13 05Y 35 
05Y H14 H14 H 0 1 N N N N N N -7.165 3.658  3.858  -5.655 1.160  -1.328 H14 05Y 36 
05Y H15 H15 H 0 1 N N N N N N -9.262 3.224  5.068  -6.814 -0.834 -0.465 H15 05Y 37 
05Y H16 H16 H 0 1 N N N N N N -9.820 4.515  7.117  -5.574 -2.428 0.985  H16 05Y 38 
05Y H17 H17 H 0 1 N N N N N N -8.209 6.269  7.875  -3.191 -1.950 1.512  H17 05Y 39 
05Y H18 H18 H 0 1 N N N N N N -6.293 3.748  7.257  0.431  -2.039 -0.483 H18 05Y 40 
# 
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 
05Y C22 N21 DOUB Y N 1  
05Y C22 C23 SING Y N 2  
05Y N21 C20 SING Y N 3  
05Y C23 C24 DOUB Y N 4  
05Y C20 C19 SING N N 5  
05Y C20 C25 DOUB Y N 6  
05Y C24 C25 SING Y N 7  
05Y C19 C18 SING N N 8  
05Y N10 C11 SING Y N 9  
05Y N10 C09 DOUB Y N 10 
05Y N08 C09 SING N N 11 
05Y N08 C07 SING N N 12 
05Y C12 C11 DOUB Y N 13 
05Y C12 C13 SING Y N 14 
05Y C11 C16 SING Y N 15 
05Y C09 N17 SING Y N 16 
05Y C13 C14 DOUB Y N 17 
05Y N17 C16 SING Y N 18 
05Y N17 C18 SING N N 19 
05Y C16 C15 DOUB Y N 20 
05Y C14 C15 SING Y N 21 
05Y O26 C07 DOUB N N 22 
05Y C07 C06 SING N N 23 
05Y C05 C06 SING N N 24 
05Y C05 H1  SING N N 25 
05Y C05 H2  SING N N 26 
05Y C05 H3  SING N N 27 
05Y C06 H4  SING N N 28 
05Y C06 H5  SING N N 29 
05Y C12 H6  SING N N 30 
05Y C13 H7  SING N N 31 
05Y C14 H8  SING N N 32 
05Y C15 H9  SING N N 33 
05Y C18 H10 SING N N 34 
05Y C18 H11 SING N N 35 
05Y C19 H12 SING N N 36 
05Y C19 H13 SING N N 37 
05Y C22 H14 SING N N 38 
05Y C23 H15 SING N N 39 
05Y C24 H16 SING N N 40 
05Y C25 H17 SING N N 41 
05Y N08 H18 SING N N 42 
# 
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 
05Y InChI            InChI                1.03  "InChI=1S/C17H18N4O/c1-2-16(22)20-17-19-14-8-3-4-9-15(14)21(17)12-10-13-7-5-6-11-18-13/h3-9,11H,2,10,12H2,1H3,(H,19,20,22)" 
05Y InChIKey         InChI                1.03  XNCNQSNDNANIRM-UHFFFAOYSA-N                                                                                                 
05Y SMILES_CANONICAL CACTVS               3.385 "CCC(=O)Nc1nc2ccccc2n1CCc3ccccn3"                                                                                           
05Y SMILES           CACTVS               3.385 "CCC(=O)Nc1nc2ccccc2n1CCc3ccccn3"                                                                                           
05Y SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CCC(=O)Nc1nc2ccccc2n1CCc3ccccn3"                                                                                           
05Y SMILES           "OpenEye OEToolkits" 2.0.7 "CCC(=O)Nc1nc2ccccc2n1CCc3ccccn3"                                                                                           
# 
_pdbx_chem_comp_identifier.comp_id           05Y 
_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        "~{N}-[1-(2-pyridin-2-ylethyl)benzimidazol-2-yl]propanamide" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
05Y "Create component" 2021-06-03 PDBE 
05Y "Initial release"  2022-04-06 RCSB 
05Y "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            05Y 
_pdbx_chem_comp_pcm.modified_residue_id                CYS 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Covalent chemical modification" 
_pdbx_chem_comp_pcm.position                           "Amino-acid side chain" 
_pdbx_chem_comp_pcm.polypeptide_position               "Any position" 
_pdbx_chem_comp_pcm.comp_id_linking_atom               C05 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   SG 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
