data_A1D47
# 
_chem_comp.id                                    A1D47 
_chem_comp.name                                  "(3~{Z})-3-(1~{H}-benzimidazol-5-ylmethylidene)-4-(oxan-4-yloxy)-1~{H}-indol-2-one" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C21 H19 N3 O3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "(Z)-3-((1H-benzo[d]imidazol-5-yl)methylene)-4-((tetrahydro-2H-pyran-4-yl)oxy)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                        361.394 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1D47 
_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        8XGA 
_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 
A1D47 C10 C1  C 0 1 N N N N N N -36.332 -29.832 59.648 5.606  1.658  1.271  C10 A1D47 1  
A1D47 C12 C2  C 0 1 N N N N N N -35.298 -30.706 57.715 5.202  2.674  -0.863 C12 A1D47 2  
A1D47 C13 C3  C 0 1 N N N N N N -35.373 -29.306 57.115 3.774  2.125  -0.909 C13 A1D47 3  
A1D47 C14 C4  C 0 1 Y N N N N N -32.768 -27.821 56.225 3.293  -1.858 0.049  C14 A1D47 4  
A1D47 C15 C5  C 0 1 Y N N N N N -32.187 -27.248 55.066 3.113  -3.230 0.075  C15 A1D47 5  
A1D47 C16 C6  C 0 1 Y N N N N N -32.244 -25.860 54.880 1.849  -3.776 -0.020 C16 A1D47 6  
A1D47 C17 C7  C 0 1 N N N N N N -34.064 -24.503 57.849 -0.431 -0.967 -0.306 C17 A1D47 7  
A1D47 C18 C8  C 0 1 N N N N N N -34.699 -24.699 59.017 -0.751 0.357  -0.374 C18 A1D47 8  
A1D47 C19 C9  C 0 1 Y N N N N N -35.553 -23.619 59.725 -2.156 0.776  -0.317 C19 A1D47 9  
A1D47 C20 C10 C 0 1 Y N N N N N -36.260 -22.656 58.999 -3.031 0.161  0.580  C20 A1D47 10 
A1D47 C21 C11 C 0 1 Y N N N N N -37.037 -21.670 59.661 -4.363 0.567  0.626  C21 A1D47 11 
A1D47 C22 C12 C 0 1 Y N N N N N -37.114 -21.663 61.020 -4.807 1.591  -0.231 C22 A1D47 12 
A1D47 C24 C13 C 0 1 Y N N N N N -38.333 -20.012 60.273 -6.476 0.879  1.027  C24 A1D47 13 
A1D47 C26 C14 C 0 1 Y N N N N N -36.408 -22.646 61.773 -3.922 2.193  -1.120 C26 A1D47 14 
A1D47 C27 C15 C 0 1 Y N N N N N -35.642 -23.609 61.120 -2.617 1.800  -1.161 C27 A1D47 15 
A1D47 O01 O1  O 0 1 N N N N N N -34.098 -22.122 57.421 -2.564 -2.059 -0.461 O01 A1D47 16 
A1D47 C02 C16 C 0 1 N N N N N N -33.798 -23.228 57.109 -1.353 -2.116 -0.352 C02 A1D47 17 
A1D47 N03 N1  N 0 1 N N N N N N -33.079 -23.556 55.887 -0.620 -3.238 -0.254 N03 A1D47 18 
A1D47 C04 C17 C 0 1 Y N N N N N -32.880 -25.061 55.846 0.736  -2.951 -0.143 C04 A1D47 19 
A1D47 C05 C18 C 0 1 Y N N N N N -33.465 -25.633 57.015 0.917  -1.563 -0.169 C05 A1D47 20 
A1D47 C06 C19 C 0 1 Y N N N N N -33.409 -27.040 57.209 2.197  -1.017 -0.073 C06 A1D47 21 
A1D47 O07 O2  O 0 1 N N N N N N -33.976 -27.702 58.327 2.369  0.330  -0.095 O07 A1D47 22 
A1D47 C08 C20 C 0 1 N N N N N N -35.301 -28.142 58.054 3.714  0.812  -0.120 C08 A1D47 23 
A1D47 C09 C21 C 0 1 N N N N N N -36.020 -28.370 59.332 4.194  1.068  1.312  C09 A1D47 24 
A1D47 O11 O3  O 0 1 N N N N N N -35.286 -30.719 59.170 5.597  2.859  0.497  O11 A1D47 25 
A1D47 N23 N2  N 0 1 Y N N N N N -37.917 -20.634 61.373 -6.146 1.764  0.047  N23 A1D47 26 
A1D47 N25 N3  N 0 1 Y N N N N N -37.806 -20.634 59.213 -5.434 0.178  1.367  N25 A1D47 27 
A1D47 H1  H1  H 0 1 N N N N N N -37.281 -30.107 59.165 5.936  1.882  2.286  H1  A1D47 28 
A1D47 H2  H2  H 0 1 N N N N N N -36.428 -29.949 60.738 6.288  0.938  0.818  H2  A1D47 29 
A1D47 H3  H3  H 0 1 N N N N N N -36.171 -31.279 57.370 5.878  1.967  -1.345 H3  A1D47 30 
A1D47 H4  H4  H 0 1 N N N N N N -34.377 -31.189 57.356 5.241  3.629  -1.387 H4  A1D47 31 
A1D47 H5  H5  H 0 1 N N N N N N -34.539 -29.208 56.405 3.091  2.848  -0.463 H5  A1D47 32 
A1D47 H6  H6  H 0 1 N N N N N N -36.327 -29.232 56.572 3.487  1.941  -1.944 H6  A1D47 33 
A1D47 H7  H7  H 0 1 N N N N N N -32.718 -28.891 56.359 4.286  -1.442 0.127  H7  A1D47 34 
A1D47 H8  H8  H 0 1 N N N N N N -31.704 -27.876 54.332 3.970  -3.879 0.170  H8  A1D47 35 
A1D47 H9  H9  H 0 1 N N N N N N -31.804 -25.409 54.003 1.723  -4.849 0.002  H9  A1D47 36 
A1D47 H10 H10 H 0 1 N N N N N N -34.608 -25.666 59.489 0.029  1.097  -0.470 H10 A1D47 37 
A1D47 H11 H11 H 0 1 N N N N N N -36.214 -22.662 57.920 -2.678 -0.624 1.233  H11 A1D47 38 
A1D47 H12 H12 H 0 1 N N N N N N -38.985 -19.152 60.241 -7.459 0.774  1.460  H12 A1D47 39 
A1D47 H13 H13 H 0 1 N N N N N N -36.467 -22.644 62.851 -4.269 2.978  -1.776 H13 A1D47 40 
A1D47 H14 H14 H 0 1 N N N N N N -35.113 -24.354 61.696 -1.935 2.276  -1.850 H14 A1D47 41 
A1D47 H15 H15 H 0 1 N N N N N N -32.770 -22.904 55.195 -0.990 -4.135 -0.258 H15 A1D47 42 
A1D47 H16 H16 H 0 1 N N N N N N -35.819 -27.312 57.552 4.358  0.072  -0.595 H16 A1D47 43 
A1D47 H17 H17 H 0 1 N N N N N N -35.400 -27.970 60.148 4.208  0.128  1.865  H17 A1D47 44 
A1D47 H18 H18 H 0 1 N N N N N N -36.972 -27.820 59.291 3.520  1.770  1.802  H18 A1D47 45 
A1D47 H19 H19 H 0 1 N N N N N N -38.159 -20.381 62.310 -6.743 2.400  -0.377 H19 A1D47 46 
# 
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 
A1D47 C16 C15 DOUB Y N 1  
A1D47 C16 C04 SING Y N 2  
A1D47 C15 C14 SING Y N 3  
A1D47 C04 N03 SING N N 4  
A1D47 C04 C05 DOUB Y N 5  
A1D47 N03 C02 SING N N 6  
A1D47 C14 C06 DOUB Y N 7  
A1D47 C05 C06 SING Y N 8  
A1D47 C05 C17 SING N N 9  
A1D47 C02 O01 DOUB N N 10 
A1D47 C02 C17 SING N N 11 
A1D47 C13 C12 SING N N 12 
A1D47 C13 C08 SING N N 13 
A1D47 C06 O07 SING N N 14 
A1D47 C12 O11 SING N N 15 
A1D47 C17 C18 DOUB N Z 16 
A1D47 C08 O07 SING N N 17 
A1D47 C08 C09 SING N N 18 
A1D47 C20 C21 DOUB Y N 19 
A1D47 C20 C19 SING Y N 20 
A1D47 C18 C19 SING N N 21 
A1D47 O11 C10 SING N N 22 
A1D47 N25 C21 SING Y N 23 
A1D47 N25 C24 DOUB Y N 24 
A1D47 C09 C10 SING N N 25 
A1D47 C21 C22 SING Y N 26 
A1D47 C19 C27 DOUB Y N 27 
A1D47 C24 N23 SING Y N 28 
A1D47 C22 N23 SING Y N 29 
A1D47 C22 C26 DOUB Y N 30 
A1D47 C27 C26 SING Y N 31 
A1D47 C10 H1  SING N N 32 
A1D47 C10 H2  SING N N 33 
A1D47 C12 H3  SING N N 34 
A1D47 C12 H4  SING N N 35 
A1D47 C13 H5  SING N N 36 
A1D47 C13 H6  SING N N 37 
A1D47 C14 H7  SING N N 38 
A1D47 C15 H8  SING N N 39 
A1D47 C16 H9  SING N N 40 
A1D47 C18 H10 SING N N 41 
A1D47 C20 H11 SING N N 42 
A1D47 C24 H12 SING N N 43 
A1D47 C26 H13 SING N N 44 
A1D47 C27 H14 SING N N 45 
A1D47 N03 H15 SING N N 46 
A1D47 C08 H16 SING N N 47 
A1D47 C09 H17 SING N N 48 
A1D47 C09 H18 SING N N 49 
A1D47 N23 H19 SING N N 50 
# 
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 
A1D47 InChI            InChI                1.06  "InChI=1S/C21H19N3O3/c25-21-15(10-13-4-5-16-18(11-13)23-12-22-16)20-17(24-21)2-1-3-19(20)27-14-6-8-26-9-7-14/h1-5,10-12,14H,6-9H2,(H,22,23)(H,24,25)/b15-10-" 
A1D47 InChIKey         InChI                1.06  MLNIWJTYHTVNRA-GDNBJRDFSA-N                                                                                                                                   
A1D47 SMILES_CANONICAL CACTVS               3.385 "O=C\1Nc2cccc(OC3CCOCC3)c2C\1=C/c4ccc5[nH]cnc5c4"                                                                                                             
A1D47 SMILES           CACTVS               3.385 "O=C1Nc2cccc(OC3CCOCC3)c2C1=Cc4ccc5[nH]cnc5c4"                                                                                                                
A1D47 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc2c(c(c1)OC3CCOCC3)/C(=C/c4ccc5c(c4)nc[nH]5)/C(=O)N2"                                                                                                     
A1D47 SMILES           "OpenEye OEToolkits" 2.0.7 "c1cc2c(c(c1)OC3CCOCC3)C(=Cc4ccc5c(c4)nc[nH]5)C(=O)N2"                                                                                                        
# 
_pdbx_chem_comp_identifier.comp_id           A1D47 
_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~{Z})-3-(1~{H}-benzimidazol-5-ylmethylidene)-4-(oxan-4-yloxy)-1~{H}-indol-2-one" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
A1D47 "Create component" 2023-12-21 PDBC 
A1D47 "Initial release"  2024-06-12 RCSB 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      A1D47 
_pdbx_chem_comp_synonyms.name         "(Z)-3-((1H-benzo[d]imidazol-5-yl)methylene)-4-((tetrahydro-2H-pyran-4-yl)oxy)indolin-2-one" 
_pdbx_chem_comp_synonyms.provenance   AUTHOR 
_pdbx_chem_comp_synonyms.type         ? 
# 
