data_A1D46
# 
_chem_comp.id                                    A1D46 
_chem_comp.name                                  "3-(1~{H}-benzimidazol-5-ylmethylidene)-4-piperidin-4-yloxy-1~{H}-indol-2-one" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C21 H20 N4 O2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "(Z)-3-((1H-benzo[d]imidazol-5-yl)methylene)-4-(piperidin-4-yloxy)indolin-2-one" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-12-21 
_chem_comp.pdbx_modified_date                    2024-06-07 
_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                        360.409 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1D46 
_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        8XFV 
_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 
A1D46 O01 O1  O 0 1 N N N N N N -16.095 -9.724  22.541 -2.532 -2.056 -0.482 O01 A1D46 1  
A1D46 C02 C1  C 0 1 N N N N N N -16.406 -10.093 23.612 -1.326 -2.103 -0.327 C02 A1D46 2  
A1D46 C03 C2  C 0 1 N N N N N N -15.945 -11.342 24.308 -0.416 -0.947 -0.242 C03 A1D46 3  
A1D46 C04 C3  C 0 1 Y N N N N N -16.617 -11.407 25.669 0.930  -1.532 -0.053 C04 A1D46 4  
A1D46 C05 C4  C 0 1 Y N N N N N -16.573 -12.388 26.774 2.202  -0.977 0.094  C05 A1D46 5  
A1D46 O06 O2  O 0 1 N N N N N N -15.769 -13.613 26.728 2.364  0.372  0.079  O06 A1D46 6  
A1D46 C07 C5  C 0 1 N N N N N N -16.463 -14.830 27.063 3.674  0.871  0.355  C07 A1D46 7  
A1D46 C08 C6  C 0 1 N N N N N N -16.173 -15.312 28.467 3.574  2.301  0.892  C08 A1D46 8  
A1D46 C09 C7  C 0 1 N N N N N N -16.994 -16.595 28.844 4.983  2.852  1.128  C09 A1D46 9  
A1D46 N10 N1  N 0 1 N N N N N N -16.966 -17.699 27.855 5.734  2.835  -0.133 N10 A1D46 10 
A1D46 C11 C8  C 0 1 N N N N N N -16.957 -17.220 26.398 5.884  1.466  -0.644 C11 A1D46 11 
A1D46 C12 C9  C 0 1 N N N N N N -16.109 -15.959 26.131 4.503  0.874  -0.933 C12 A1D46 12 
A1D46 C13 C10 C 0 1 Y N N N N N -17.325 -12.105 27.916 3.298  -1.809 0.257  C13 A1D46 13 
A1D46 C14 C11 C 0 1 Y N N N N N -18.144 -10.902 28.013 3.128  -3.182 0.273  C14 A1D46 14 
A1D46 C15 C12 C 0 1 Y N N N N N -18.199 -9.962  26.949 1.873  -3.739 0.128  C15 A1D46 15 
A1D46 C16 C13 C 0 1 Y N N N N N -17.439 -10.214 25.784 0.759  -2.922 -0.037 C16 A1D46 16 
A1D46 N17 N2  N 0 1 N N N N N N -17.313 -9.393  24.498 -0.589 -3.220 -0.197 N17 A1D46 17 
A1D46 C18 C14 C 0 1 N N N N N N -15.130 -12.289 23.842 -0.744 0.375  -0.321 C18 A1D46 18 
A1D46 C19 C15 C 0 1 Y N N N N N -13.600 -12.168 23.492 -2.153 0.783  -0.312 C19 A1D46 19 
A1D46 C20 C16 C 0 1 Y N N N N N -13.121 -13.026 22.529 -2.588 1.820  -1.154 C20 A1D46 20 
A1D46 C21 C17 C 0 1 Y N N N N N -11.792 -13.035 22.140 -3.895 2.207  -1.153 C21 A1D46 21 
A1D46 C22 C18 C 0 1 Y N N N N N -10.880 -12.141 22.747 -4.811 1.578  -0.316 C22 A1D46 22 
A1D46 N23 N3  N 0 1 Y N N N N N -9.567  -11.934 22.575 -6.161 1.735  -0.090 N23 A1D46 23 
A1D46 C24 C19 C 0 1 Y N N N N N -9.176  -10.959 23.411 -6.524 0.825  0.855  C24 A1D46 24 
A1D46 N25 N4  N 0 1 Y N N N N N -10.236 -10.555 24.108 -5.492 0.123  1.221  N25 A1D46 25 
A1D46 C26 C20 C 0 1 Y N N N N N -11.321 -11.273 23.709 -4.394 0.537  0.534  C26 A1D46 26 
A1D46 C27 C21 C 0 1 Y N N N N N -12.688 -11.275 24.099 -3.060 0.137  0.529  C27 A1D46 27 
A1D46 H2  H2  H 0 1 N N N N N N -17.546 -14.653 26.984 4.157  0.235  1.097  H2  A1D46 28 
A1D46 H3  H3  H 0 1 N N N N N N -15.101 -15.544 28.546 3.056  2.927  0.166  H3  A1D46 29 
A1D46 H4  H4  H 0 1 N N N N N N -16.428 -14.510 29.175 3.022  2.299  1.832  H4  A1D46 30 
A1D46 H5  H5  H 0 1 N N N N N N -18.043 -16.294 28.983 4.915  3.875  1.497  H5  A1D46 31 
A1D46 H6  H6  H 0 1 N N N N N N -16.595 -16.983 29.793 5.496  2.233  1.865  H6  A1D46 32 
A1D46 H7  H7  H 0 1 N N N N N N -17.775 -18.269 27.995 6.633  3.281  -0.024 H7  A1D46 33 
A1D46 H9  H9  H 0 1 N N N N N N -17.994 -17.002 26.104 6.471  1.484  -1.562 H9  A1D46 34 
A1D46 H10 H10 H 0 1 N N N N N N -16.562 -18.035 25.773 6.392  0.854  0.101  H10 A1D46 35 
A1D46 H11 H11 H 0 1 N N N N N N -15.047 -16.211 26.266 4.613  -0.147 -1.298 H11 A1D46 36 
A1D46 H12 H12 H 0 1 N N N N N N -16.279 -15.630 25.095 3.999  1.478  -1.688 H12 A1D46 37 
A1D46 H13 H13 H 0 1 N N N N N N -17.300 -12.794 28.748 4.285  -1.386 0.372  H13 A1D46 38 
A1D46 H14 H14 H 0 1 N N N N N N -18.719 -10.723 28.910 3.987  -3.826 0.401  H14 A1D46 39 
A1D46 H15 H15 H 0 1 N N N N N N -18.808 -9.074  27.029 1.756  -4.812 0.142  H15 A1D46 40 
A1D46 H16 H16 H 0 1 N N N N N N -17.775 -8.527  24.304 -0.952 -4.119 -0.214 H16 A1D46 41 
A1D46 H17 H17 H 0 1 N N N N N N -15.575 -13.260 23.685 0.034  1.120  -0.390 H17 A1D46 42 
A1D46 H19 H19 H 0 1 N N N N N N -13.806 -13.717 22.060 -1.882 2.314  -1.806 H19 A1D46 43 
A1D46 H20 H20 H 0 1 N N N N N N -11.454 -13.721 21.377 -4.220 3.006  -1.804 H20 A1D46 44 
A1D46 H21 H21 H 0 1 N N N N N N -8.978  -12.423 21.932 -6.746 2.376  -0.524 H21 A1D46 45 
A1D46 H22 H22 H 0 1 N N N N N N -8.173  -10.569 23.502 -7.524 0.703  1.244  H22 A1D46 46 
A1D46 H24 H24 H 0 1 N N N N N N -13.031 -10.592 24.862 -2.729 -0.664 1.174  H24 A1D46 47 
# 
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 
A1D46 C21 C20 DOUB Y N 1  
A1D46 C21 C22 SING Y N 2  
A1D46 C20 C19 SING Y N 3  
A1D46 O01 C02 DOUB N N 4  
A1D46 N23 C22 SING Y N 5  
A1D46 N23 C24 SING Y N 6  
A1D46 C22 C26 DOUB Y N 7  
A1D46 C24 N25 DOUB Y N 8  
A1D46 C19 C18 SING N N 9  
A1D46 C19 C27 DOUB Y N 10 
A1D46 C02 C03 SING N N 11 
A1D46 C02 N17 SING N N 12 
A1D46 C26 C27 SING Y N 13 
A1D46 C26 N25 SING Y N 14 
A1D46 C18 C03 DOUB N Z 15 
A1D46 C03 C04 SING N N 16 
A1D46 N17 C16 SING N N 17 
A1D46 C04 C16 DOUB Y N 18 
A1D46 C04 C05 SING Y N 19 
A1D46 C16 C15 SING Y N 20 
A1D46 C12 C11 SING N N 21 
A1D46 C12 C07 SING N N 22 
A1D46 C11 N10 SING N N 23 
A1D46 O06 C05 SING N N 24 
A1D46 O06 C07 SING N N 25 
A1D46 C05 C13 DOUB Y N 26 
A1D46 C15 C14 DOUB Y N 27 
A1D46 C07 C08 SING N N 28 
A1D46 N10 C09 SING N N 29 
A1D46 C13 C14 SING Y N 30 
A1D46 C08 C09 SING N N 31 
A1D46 C07 H2  SING N N 32 
A1D46 C08 H3  SING N N 33 
A1D46 C08 H4  SING N N 34 
A1D46 C09 H5  SING N N 35 
A1D46 C09 H6  SING N N 36 
A1D46 N10 H7  SING N N 37 
A1D46 C11 H9  SING N N 38 
A1D46 C11 H10 SING N N 39 
A1D46 C12 H11 SING N N 40 
A1D46 C12 H12 SING N N 41 
A1D46 C13 H13 SING N N 42 
A1D46 C14 H14 SING N N 43 
A1D46 C15 H15 SING N N 44 
A1D46 N17 H16 SING N N 45 
A1D46 C18 H17 SING N N 46 
A1D46 C20 H19 SING N N 47 
A1D46 C21 H20 SING N N 48 
A1D46 N23 H21 SING N N 49 
A1D46 C24 H22 SING N N 50 
A1D46 C27 H24 SING N N 51 
# 
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 
A1D46 InChI            InChI                1.06  "InChI=1S/C21H20N4O2/c26-21-15(10-13-4-5-16-18(11-13)24-12-23-16)20-17(25-21)2-1-3-19(20)27-14-6-8-22-9-7-14/h1-5,10-12,14,22H,6-9H2,(H,23,24)(H,25,26)" 
A1D46 InChIKey         InChI                1.06  GEWYCLDNMSKZLN-UHFFFAOYSA-N                                                                                                                              
A1D46 SMILES_CANONICAL CACTVS               3.385 "O=C\1Nc2cccc(OC3CCNCC3)c2C\1=C/c4ccc5[nH]cnc5c4"                                                                                                        
A1D46 SMILES           CACTVS               3.385 "O=C1Nc2cccc(OC3CCNCC3)c2C1=Cc4ccc5[nH]cnc5c4"                                                                                                           
A1D46 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc2c(c(c1)OC3CCNCC3)C(=Cc4ccc5c(c4)nc[nH]5)C(=O)N2"                                                                                                   
A1D46 SMILES           "OpenEye OEToolkits" 2.0.7 "c1cc2c(c(c1)OC3CCNCC3)C(=Cc4ccc5c(c4)nc[nH]5)C(=O)N2"                                                                                                   
# 
_pdbx_chem_comp_identifier.comp_id           A1D46 
_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~{H}-benzimidazol-5-ylmethylidene)-4-piperidin-4-yloxy-1~{H}-indol-2-one" 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      A1D46 
_pdbx_chem_comp_synonyms.name         "(Z)-3-((1H-benzo[d]imidazol-5-yl)methylene)-4-(piperidin-4-yloxy)indolin-2-one" 
_pdbx_chem_comp_synonyms.provenance   AUTHOR 
_pdbx_chem_comp_synonyms.type         ? 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
A1D46 "Create component" 2023-12-21 PDBC 
A1D46 "Initial release"  2024-06-12 RCSB 
# 
