data_A1A3D
# 
_chem_comp.id                                    A1A3D 
_chem_comp.name                                  "1-[(1r,3r)-3-(methylcarbamoyl)cyclobutyl]-N-[(1-methylpiperidin-4-yl)methyl]-2-(3,4,5-trimethoxyphenyl)-1H-1,3-benzimidazole-6-carboxamide" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C30 H39 N5 O5" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2024-08-23 
_chem_comp.pdbx_modified_date                    2024-11-22 
_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                        549.661 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     A1A3D 
_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        9D8Z 
_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 
A1A3D C28  C1  C 0 1 Y N N N N N 0.977  -3.994 5.987  -3.741 1.913  -0.885 C28  A1A3D 1  
A1A3D C27  C2  C 0 1 Y N N N N N -0.422 -3.906 5.862  -3.133 1.404  0.265  C27  A1A3D 2  
A1A3D C26  C3  C 0 1 Y N N N N N -1.149 -4.101 4.563  -1.667 1.233  0.312  C26  A1A3D 3  
A1A3D C25  C4  C 0 1 N N N N N N -0.247 -7.684 3.534  -2.705 -1.662 0.803  C25  A1A3D 4  
A1A3D C23  C5  C 0 1 N N N N N N 4.798  -8.582 3.817  -3.497 -6.020 -0.408 C23  A1A3D 5  
A1A3D C21  C6  C 0 1 N N N N N N 2.356  -8.142 3.671  -3.189 -3.626 -0.746 C21  A1A3D 6  
A1A3D C18  C7  C 0 1 N N N N N N 0.096  -6.159 3.757  -1.613 -1.245 -0.197 C18  A1A3D 7  
A1A3D C16  C8  C 0 1 Y N N N N N -1.893 -5.003 2.578  0.346  0.318  0.236  C16  A1A3D 8  
A1A3D C15  C9  C 0 1 Y N N N N N -2.665 -3.871 2.949  0.450  1.694  0.523  C15  A1A3D 9  
A1A3D C14  C10 C 0 1 Y N N N N N -3.704 -3.460 2.082  1.714  2.269  0.711  C14  A1A3D 10 
A1A3D C12  C11 C 0 1 Y N N N N N -3.220 -5.279 0.519  2.737  0.131  0.334  C12  A1A3D 11 
A1A3D C11  C12 C 0 1 N N N N N N -3.817 -5.844 -4.077 8.868  -0.926 0.592  C11  A1A3D 12 
A1A3D C02  C13 C 0 1 N N N N N N -3.497 -6.119 -0.724 3.960  -0.689 0.236  C02  A1A3D 13 
A1A3D C04  C14 C 0 1 N N N N N N -5.123 -7.217 -2.435 6.383  -0.936 0.322  C04  A1A3D 14 
A1A3D C05  C15 C 0 1 N N N N N N -5.176 -6.491 -3.828 7.609  -0.055 0.570  C05  A1A3D 15 
A1A3D C06  C16 C 0 1 N N N N N N -5.504 -7.448 -4.992 7.732  0.979  -0.553 C06  A1A3D 16 
A1A3D C07  C17 C 0 1 N N N N N N -4.454 -7.452 -6.026 8.994  1.817  -0.332 C07  A1A3D 17 
A1A3D C09  C18 C 0 1 N N N N N N -3.333 -6.143 -7.634 10.334 0.259  -1.612 C09  A1A3D 18 
A1A3D C10  C19 C 0 1 N N N N N N -3.700 -5.202 -5.542 10.097 -0.033 0.780  C10  A1A3D 19 
A1A3D C13  C20 C 0 1 Y N N N N N -3.983 -4.163 0.927  2.835  1.500  0.618  C13  A1A3D 20 
A1A3D C19  C21 C 0 1 N N N N N N 1.071  -6.363 2.514  -2.724 -1.174 -1.259 C19  A1A3D 21 
A1A3D C20  C22 C 0 1 N N N N N N 1.122  -7.865 2.845  -3.497 -2.191 -0.404 C20  A1A3D 22 
A1A3D C29  C23 C 0 1 Y N N N N N 1.647  -3.882 7.222  -5.114 2.073  -0.926 C29  A1A3D 23 
A1A3D C31  C24 C 0 1 N N N N N N 3.737  -3.982 6.045  -4.849 2.912  -3.136 C31  A1A3D 24 
A1A3D C32  C25 C 0 1 Y N N N N N 0.939  -3.757 8.419  -5.891 1.723  0.174  C32  A1A3D 25 
A1A3D C34  C26 C 0 1 N N N N N N 1.620  -2.313 10.123 -8.008 0.777  -0.352 C34  A1A3D 26 
A1A3D C35  C27 C 0 1 Y N N N N N -0.469 -3.666 8.321  -5.288 1.211  1.319  C35  A1A3D 27 
A1A3D C37  C28 C 0 1 N N N N N N -2.490 -3.410 9.413  -6.122 -0.519 2.722  C37  A1A3D 28 
A1A3D C38  C29 C 0 1 Y N N N N N -1.132 -3.784 7.074  -3.914 1.059  1.370  C38  A1A3D 29 
A1A3D C40  C30 C 0 1 Y N N N N N -2.196 -5.682 1.367  1.487  -0.457 0.143  C40  A1A3D 30 
A1A3D N03  N1  N 0 1 N N N N N N -4.790 -6.338 -1.276 5.169  -0.121 0.419  N03  A1A3D 31 
A1A3D N08  N2  N 0 1 N N N N N N -4.311 -6.071 -6.594 10.170 0.938  -0.319 N08  A1A3D 32 
A1A3D N17  N3  N 0 1 Y N N N N N -0.953 -5.162 3.629  -1.005 0.053  0.106  N17  A1A3D 33 
A1A3D N22  N4  N 0 1 N N N N N N 3.579  -8.331 3.030  -3.796 -4.625 -0.075 N22  A1A3D 34 
A1A3D N39  N5  N 0 1 Y N N N N N -2.213 -3.346 4.191  -0.802 2.190  0.553  N39  A1A3D 35 
A1A3D O01  O1  O 0 1 N N N N N N -2.535 -6.759 -1.168 3.877  -1.877 -0.011 O01  A1A3D 36 
A1A3D O24  O2  O 0 1 N N N N N N 2.326  -8.149 4.892  -2.394 -3.882 -1.626 O24  A1A3D 37 
A1A3D O30  O3  O 0 1 N N N N N N 3.036  -3.984 7.284  -5.706 2.573  -2.044 O30  A1A3D 38 
A1A3D O33  O4  O 0 1 N N N N N N 1.621  -3.628 9.588  -7.240 1.881  0.131  O33  A1A3D 39 
A1A3D O36  O5  O 0 1 N N N N N N -1.146 -3.556 9.498  -6.049 0.870  2.394  O36  A1A3D 40 
A1A3D H281 H1  H 0 0 N N N N N N 1.565  -4.155 5.095  -3.139 2.185  -1.739 H281 A1A3D 41 
A1A3D H251 H2  H 0 0 N N N N N N -1.111 -7.862 2.877  -2.388 -2.443 1.494  H251 A1A3D 42 
A1A3D H252 H3  H 0 0 N N N N N N -0.366 -8.262 4.462  -3.182 -0.821 1.305  H252 A1A3D 43 
A1A3D H231 H4  H 0 0 N N N N N N 5.655  -8.704 3.138  -4.078 -6.680 0.235  H231 A1A3D 44 
A1A3D H233 H5  H 0 0 N N N N N N 4.982  -7.731 4.489  -3.754 -6.208 -1.450 H233 A1A3D 45 
A1A3D H232 H6  H 0 0 N N N N N N 4.668  -9.498 4.412  -2.434 -6.209 -0.257 H232 A1A3D 46 
A1A3D H181 H7  H 0 0 N N N N N N 0.681  -6.030 4.680  -0.875 -2.023 -0.388 H181 A1A3D 47 
A1A3D H141 H8  H 0 0 N N N N N N -4.287 -2.584 2.327  1.800  3.322  0.931  H141 A1A3D 48 
A1A3D H112 H9  H 0 0 N N N N N N -3.036 -6.610 -3.965 8.805  -1.636 1.416  H112 A1A3D 49 
A1A3D H111 H10 H 0 0 N N N N N N -3.662 -5.051 -3.331 8.952  -1.468 -0.350 H111 A1A3D 50 
A1A3D H041 H11 H 0 0 N N N N N N -6.108 -7.669 -2.248 6.446  -1.375 -0.674 H041 A1A3D 51 
A1A3D H042 H12 H 0 0 N N N N N N -4.362 -8.009 -2.492 6.348  -1.730 1.067  H042 A1A3D 52 
A1A3D H051 H13 H 0 0 N N N N N N -5.946 -5.706 -3.784 7.503  0.456  1.527  H051 A1A3D 53 
A1A3D H061 H14 H 0 0 N N N N N N -6.452 -7.133 -5.452 7.799  0.467  -1.513 H061 A1A3D 54 
A1A3D H062 H15 H 0 0 N N N N N N -5.611 -8.467 -4.592 6.857  1.629  -0.547 H062 A1A3D 55 
A1A3D H071 H16 H 0 0 N N N N N N -4.731 -8.152 -6.828 9.092  2.544  -1.137 H071 A1A3D 56 
A1A3D H072 H17 H 0 0 N N N N N N -3.499 -7.766 -5.579 8.920  2.339  0.622  H072 A1A3D 57 
A1A3D H093 H18 H 0 0 N N N N N N -3.197 -5.147 -8.080 10.460 1.002  -2.399 H093 A1A3D 58 
A1A3D H092 H19 H 0 0 N N N N N N -2.377 -6.491 -7.215 11.212 -0.385 -1.575 H092 A1A3D 59 
A1A3D H091 H20 H 0 0 N N N N N N -3.672 -6.847 -8.408 9.450  -0.344 -1.820 H091 A1A3D 60 
A1A3D H101 H21 H 0 0 N N N N N N -2.636 -5.054 -5.779 10.018 0.498  1.729  H101 A1A3D 61 
A1A3D H102 H22 H 0 0 N N N N N N -4.214 -4.230 -5.544 10.996 -0.648 0.781  H102 A1A3D 62 
A1A3D H131 H23 H 0 0 N N N N N N -4.814 -3.848 0.314  3.806  1.949  0.765  H131 A1A3D 63 
A1A3D H191 H24 H 0 0 N N N N N N 2.037  -5.845 2.605  -3.207 -0.199 -1.321 H191 A1A3D 64 
A1A3D H192 H25 H 0 0 N N N N N N 0.619  -6.128 1.539  -2.422 -1.561 -2.232 H192 A1A3D 65 
A1A3D H201 H26 H 0 0 N N N N N N 1.058  -8.496 1.946  -4.567 -1.990 -0.346 H201 A1A3D 66 
A1A3D H311 H27 H 0 0 N N N N N N 4.817  -4.067 6.234  -4.309 2.024  -3.463 H311 A1A3D 67 
A1A3D H313 H28 H 0 0 N N N N N N 3.404  -4.834 5.434  -5.447 3.299  -3.961 H313 A1A3D 68 
A1A3D H312 H29 H 0 0 N N N N N N 3.532  -3.044 5.509  -4.137 3.673  -2.816 H312 A1A3D 69 
A1A3D H341 H30 H 0 0 N N N N N N 2.191  -2.299 11.063 -9.067 1.035  -0.335 H341 A1A3D 70 
A1A3D H342 H31 H 0 0 N N N N N N 2.084  -1.624 9.402  -7.707 0.545  -1.374 H342 A1A3D 71 
A1A3D H343 H32 H 0 0 N N N N N N 0.584  -1.997 10.318 -7.835 -0.092 0.283  H343 A1A3D 72 
A1A3D H372 H33 H 0 0 N N N N N N -2.916 -3.333 10.424 -7.018 -0.705 3.314  H372 A1A3D 73 
A1A3D H371 H34 H 0 0 N N N N N N -2.724 -2.497 8.846  -6.163 -1.107 1.806  H371 A1A3D 74 
A1A3D H373 H35 H 0 0 N N N N N N -2.922 -4.282 8.899  -5.241 -0.803 3.298  H373 A1A3D 75 
A1A3D H381 H36 H 0 0 N N N N N N -2.212 -3.780 7.051  -3.446 0.665  2.260  H381 A1A3D 76 
A1A3D H401 H37 H 0 0 N N N N N N -1.607 -6.545 1.095  1.411  -1.512 -0.076 H401 A1A3D 77 
A1A3D H031 H38 H 0 0 N N N N N N -5.552 -5.855 -0.844 5.235  0.826  0.616  H031 A1A3D 78 
A1A3D H221 H40 H 0 0 N N N N N N 3.629  -8.296 2.032  -4.432 -4.420 0.628  H221 A1A3D 79 
# 
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 
A1A3D C09 N08  SING N N 1  
A1A3D N08 C07  SING N N 2  
A1A3D N08 C10  SING N N 3  
A1A3D C07 C06  SING N N 4  
A1A3D C10 C11  SING N N 5  
A1A3D C06 C05  SING N N 6  
A1A3D C11 C05  SING N N 7  
A1A3D C05 C04  SING N N 8  
A1A3D C04 N03  SING N N 9  
A1A3D N03 C02  SING N N 10 
A1A3D O01 C02  DOUB N N 11 
A1A3D C02 C12  SING N N 12 
A1A3D C12 C13  DOUB Y N 13 
A1A3D C12 C40  SING Y N 14 
A1A3D C13 C14  SING Y N 15 
A1A3D C40 C16  DOUB Y N 16 
A1A3D C14 C15  DOUB Y N 17 
A1A3D C19 C20  SING N N 18 
A1A3D C19 C18  SING N N 19 
A1A3D C16 C15  SING Y N 20 
A1A3D C16 N17  SING Y N 21 
A1A3D C20 C25  SING N N 22 
A1A3D C20 C21  SING N N 23 
A1A3D C15 N39  SING Y N 24 
A1A3D N22 C21  SING N N 25 
A1A3D N22 C23  SING N N 26 
A1A3D C25 C18  SING N N 27 
A1A3D N17 C18  SING N N 28 
A1A3D N17 C26  SING Y N 29 
A1A3D C21 O24  DOUB N N 30 
A1A3D N39 C26  DOUB Y N 31 
A1A3D C26 C27  SING N N 32 
A1A3D C27 C28  DOUB Y N 33 
A1A3D C27 C38  SING Y N 34 
A1A3D C28 C29  SING Y N 35 
A1A3D C31 O30  SING N N 36 
A1A3D C38 C35  DOUB Y N 37 
A1A3D C29 O30  SING N N 38 
A1A3D C29 C32  DOUB Y N 39 
A1A3D C35 C32  SING Y N 40 
A1A3D C35 O36  SING N N 41 
A1A3D C32 O33  SING N N 42 
A1A3D C37 O36  SING N N 43 
A1A3D O33 C34  SING N N 44 
A1A3D C28 H281 SING N N 45 
A1A3D C25 H251 SING N N 46 
A1A3D C25 H252 SING N N 47 
A1A3D C23 H231 SING N N 48 
A1A3D C23 H233 SING N N 49 
A1A3D C23 H232 SING N N 50 
A1A3D C18 H181 SING N N 51 
A1A3D C14 H141 SING N N 52 
A1A3D C11 H112 SING N N 53 
A1A3D C11 H111 SING N N 54 
A1A3D C04 H041 SING N N 55 
A1A3D C04 H042 SING N N 56 
A1A3D C05 H051 SING N N 57 
A1A3D C06 H061 SING N N 58 
A1A3D C06 H062 SING N N 59 
A1A3D C07 H071 SING N N 60 
A1A3D C07 H072 SING N N 61 
A1A3D C09 H093 SING N N 62 
A1A3D C09 H092 SING N N 63 
A1A3D C09 H091 SING N N 64 
A1A3D C10 H101 SING N N 65 
A1A3D C10 H102 SING N N 66 
A1A3D C13 H131 SING N N 67 
A1A3D C19 H191 SING N N 68 
A1A3D C19 H192 SING N N 69 
A1A3D C20 H201 SING N N 70 
A1A3D C31 H311 SING N N 71 
A1A3D C31 H313 SING N N 72 
A1A3D C31 H312 SING N N 73 
A1A3D C34 H341 SING N N 74 
A1A3D C34 H342 SING N N 75 
A1A3D C34 H343 SING N N 76 
A1A3D C37 H372 SING N N 77 
A1A3D C37 H371 SING N N 78 
A1A3D C37 H373 SING N N 79 
A1A3D C38 H381 SING N N 80 
A1A3D C40 H401 SING N N 81 
A1A3D N03 H031 SING N N 82 
A1A3D N22 H221 SING N N 83 
# 
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 
A1A3D SMILES           ACDLabs              14.52 "CN1CCC(CNC(=O)c2ccc3nc(c4cc(OC)c(OC)c(OC)c4)n(C4CC(C4)C(=O)NC)c3c2)CC1"                                                                                                                                              
A1A3D InChI            InChI                1.06  "InChI=1S/C30H39N5O5/c1-31-29(36)21-12-22(13-21)35-24-14-19(30(37)32-17-18-8-10-34(2)11-9-18)6-7-23(24)33-28(35)20-15-25(38-3)27(40-5)26(16-20)39-4/h6-7,14-16,18,21-22H,8-13,17H2,1-5H3,(H,31,36)(H,32,37)/t21-,22-" 
A1A3D InChIKey         InChI                1.06  UIZVBBVWCDAVED-HZCBDIJESA-N                                                                                                                                                                                           
A1A3D SMILES_CANONICAL CACTVS               3.385 "CNC(=O)[C@H]1C[C@@H](C1)n2c3cc(ccc3nc2c4cc(OC)c(OC)c(OC)c4)C(=O)NCC5CCN(C)CC5"                                                                                                                                       
A1A3D SMILES           CACTVS               3.385 "CNC(=O)[CH]1C[CH](C1)n2c3cc(ccc3nc2c4cc(OC)c(OC)c(OC)c4)C(=O)NCC5CCN(C)CC5"                                                                                                                                          
A1A3D SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CNC(=O)C1CC(C1)n2c3cc(ccc3nc2c4cc(c(c(c4)OC)OC)OC)C(=O)NCC5CCN(CC5)C"                                                                                                                                                
A1A3D SMILES           "OpenEye OEToolkits" 2.0.7 "CNC(=O)C1CC(C1)n2c3cc(ccc3nc2c4cc(c(c(c4)OC)OC)OC)C(=O)NCC5CCN(CC5)C"                                                                                                                                                
# 
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 
A1A3D "SYSTEMATIC NAME" ACDLabs              14.52 "1-[(1r,3r)-3-(methylcarbamoyl)cyclobutyl]-N-[(1-methylpiperidin-4-yl)methyl]-2-(3,4,5-trimethoxyphenyl)-1H-1,3-benzimidazole-6-carboxamide" 
A1A3D "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "3-[3-(methylcarbamoyl)cyclobutyl]-~{N}-[(1-methylpiperidin-4-yl)methyl]-2-(3,4,5-trimethoxyphenyl)benzimidazole-5-carboxamide"              
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
A1A3D "Create component" 2024-08-23 RCSB 
A1A3D "Initial release"  2024-11-27 RCSB 
# 
