data_YU6
# 
_chem_comp.id                                    YU6 
_chem_comp.name                                  "(5M)-2-[(4-benzylpiperazin-1-yl)methyl]-5-(2-chloro-4-methylphenyl)-1H-benzimidazole-7-carboxylic acid" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C27 H27 Cl N4 O2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-02-21 
_chem_comp.pdbx_modified_date                    2024-02-16 
_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                        474.982 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YU6 
_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        7FUM 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
# 
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 
YU6 C10  C1  C  0 1 Y N N N N N 0.004  -23.034 -22.748 7.551  -1.720 -0.190 C10  YU6 1  
YU6 C11  C2  C  0 1 Y N N N N N -0.975 -23.227 -21.781 7.767  -3.078 -0.325 C11  YU6 2  
YU6 C13  C3  C  0 1 Y N N N N N 0.720  -23.386 -20.101 6.124  -3.508 1.363  C13  YU6 3  
YU6 C15  C4  C  0 1 Y N N N N N 5.405  -17.150 -22.728 0.475  1.914  -1.119 C15  YU6 4  
YU6 C17  C5  C  0 1 Y N N N N N 6.648  -17.199 -20.913 -1.463 1.963  -0.068 C17  YU6 5  
YU6 C18  C6  C  0 1 Y N N N N N 5.636  -16.242 -20.790 -1.273 0.706  -0.665 C18  YU6 6  
YU6 C20  C7  C  0 1 Y N N N N N 5.560  -15.430 -19.655 -2.253 -0.278 -0.532 C20  YU6 7  
YU6 C21  C8  C  0 1 Y N N N N N 6.504  -15.577 -18.634 -3.411 -0.014 0.189  C21  YU6 8  
YU6 C22  C9  C  0 1 Y N N N N N 6.457  -14.683 -17.445 -4.450 -1.065 0.327  C22  YU6 9  
YU6 C23  C10 C  0 1 Y N N N N N 6.974  -13.372 -17.465 -4.916 -1.741 -0.800 C23  YU6 10 
YU6 C25  C11 C  0 1 Y N N N N N 6.937  -12.560 -16.348 -5.883 -2.718 -0.665 C25  YU6 11 
YU6 C26  C12 C  0 1 Y N N N N N 6.351  -13.014 -15.172 -6.389 -3.025 0.584  C26  YU6 12 
YU6 C27  C13 C  0 1 N N N N N N 6.304  -12.135 -13.941 -7.443 -4.092 0.725  C27  YU6 13 
YU6 C28  C14 C  0 1 Y N N N N N 5.834  -14.306 -15.142 -5.930 -2.357 1.706  C28  YU6 14 
YU6 C1   C15 C  0 1 N N N N N N 4.794  -17.639 -24.003 1.811  2.336  -1.672 C1   YU6 15 
YU6 C12  C16 C  0 1 Y N N N N N -0.617 -23.412 -20.459 7.053  -3.972 0.451  C12  YU6 16 
YU6 C14  C17 C  0 1 Y N N N N N 1.699  -23.180 -21.066 5.917  -2.148 1.507  C14  YU6 17 
YU6 C29  C18 C  0 1 Y N N N N N 5.882  -15.134 -16.254 -4.960 -1.383 1.584  C29  YU6 18 
YU6 C3   C19 C  0 1 N N N N N N 3.876  -19.625 -25.100 4.166  2.510  -1.131 C3   YU6 19 
YU6 C30  C20 C  0 1 Y N N N N N 7.586  -16.445 -18.820 -3.604 1.232  0.783  C30  YU6 20 
YU6 C31  C21 C  0 1 Y N N N N N 7.604  -17.348 -19.887 -2.635 2.224  0.659  C31  YU6 21 
YU6 C32  C22 C  0 1 N N N N N N 8.725  -18.355 -19.938 -2.838 3.542  1.288  C32  YU6 22 
YU6 C4   C23 C  0 1 N N N N N N 3.561  -21.111 -24.860 5.229  2.112  -0.105 C4   YU6 23 
YU6 C6   C24 C  0 1 N N N N N N 2.842  -20.497 -22.578 4.037  0.052  0.333  C6   YU6 24 
YU6 C7   C25 C  0 1 N N N N N N 3.120  -19.047 -22.933 2.973  0.450  -0.693 C7   YU6 25 
YU6 C8   C26 C  0 1 N N N N N N 2.412  -22.736 -23.446 6.391  0.226  0.874  C8   YU6 26 
YU6 C9   C27 C  0 1 Y N N N N N 1.354  -23.026 -22.405 6.626  -1.255 0.726  C9   YU6 27 
YU6 N16  N1  N  0 1 Y N N N N N 6.439  -17.797 -22.138 -0.345 2.703  -0.371 N16  YU6 28 
YU6 N19  N2  N  0 1 Y N N N N N 4.867  -16.231 -21.950 -0.068 0.744  -1.292 N19  YU6 29 
YU6 N2   N3  N  0 1 N N N N N N 4.267  -18.994 -23.837 2.876  1.915  -0.752 N2   YU6 30 
YU6 N5   N4  N  0 1 N N N N N N 2.543  -21.306 -23.788 5.326  0.647  -0.046 N5   YU6 31 
YU6 O33  O1  O  0 1 N N N N N N 8.792  -19.082 -20.949 -1.990 4.405  1.178  O33  YU6 32 
YU6 O34  O2  O  0 1 N N N N N N 9.555  -18.385 -18.986 -3.964 3.789  1.986  O34  YU6 33 
YU6 CL24 CL1 CL 0 0 N N N N N N 7.660  -12.734 -18.934 -4.282 -1.355 -2.370 CL24 YU6 34 
YU6 H47  H1  H  0 1 N N N N N N -0.285 -22.888 -23.778 8.109  -1.021 -0.796 H47  YU6 35 
YU6 H48  H2  H  0 1 N N N N N N -2.018 -23.232 -22.063 8.493  -3.441 -1.038 H48  YU6 36 
YU6 H50  H3  H  0 1 N N N N N N 1.003  -23.526 -19.068 5.570  -4.206 1.973  H50  YU6 37 
YU6 H53  H4  H  0 1 N N N N N N 4.776  -14.693 -19.567 -2.112 -1.247 -0.989 H53  YU6 38 
YU6 H54  H5  H  0 1 N N N N N N 7.365  -11.569 -16.389 -6.244 -3.243 -1.537 H54  YU6 39 
YU6 H56  H6  H  0 1 N N N N N N 5.373  -11.549 -13.944 -6.964 -5.059 0.882  H56  YU6 40 
YU6 H57  H7  H  0 1 N N N N N N 6.338  -12.765 -13.040 -8.082 -3.861 1.578  H57  YU6 41 
YU6 H55  H8  H  0 1 N N N N N N 7.167  -11.453 -13.945 -8.047 -4.129 -0.182 H55  YU6 42 
YU6 H58  H9  H  0 1 N N N N N N 5.385  -14.673 -14.231 -6.329 -2.601 2.679  H58  YU6 43 
YU6 H35  H10 H  0 1 N N N N N N 5.560  -17.644 -24.792 1.966  1.870  -2.645 H35  YU6 44 
YU6 H36  H11 H  0 1 N N N N N N 3.974  -16.965 -24.292 1.834  3.420  -1.781 H36  YU6 45 
YU6 H49  H12 H  0 1 N N N N N N -1.377 -23.576 -19.709 7.221  -5.034 0.345  H49  YU6 46 
YU6 H51  H13 H  0 1 N N N N N N 2.738  -23.139 -20.773 5.201  -1.785 2.229  H51  YU6 47 
YU6 H59  H14 H  0 1 N N N N N N 5.473  -16.132 -16.199 -4.600 -0.866 2.460  H59  YU6 48 
YU6 H38  H15 H  0 1 N N N N N N 2.983  -19.122 -25.499 4.072  3.596  -1.155 H38  YU6 49 
YU6 H37  H16 H  0 1 N N N N N N 4.700  -19.538 -25.823 4.458  2.148  -2.117 H37  YU6 50 
YU6 H60  H17 H  0 1 N N N N N N 8.417  -16.417 -18.131 -4.508 1.429  1.341  H60  YU6 51 
YU6 H39  H18 H  0 1 N N N N N N 3.179  -21.547 -25.795 6.193  2.529  -0.400 H39  YU6 52 
YU6 H40  H19 H  0 1 N N N N N N 4.487  -21.626 -24.567 4.951  2.498  0.876  H40  YU6 53 
YU6 H42  H20 H  0 1 N N N N N N 1.979  -20.539 -21.897 3.745  0.415  1.319  H42  YU6 54 
YU6 H41  H21 H  0 1 N N N N N N 3.726  -20.918 -22.076 4.130  -1.033 0.358  H41  YU6 55 
YU6 H44  H22 H  0 1 N N N N N N 3.344  -18.479 -22.018 3.251  0.064  -1.673 H44  YU6 56 
YU6 H43  H23 H  0 1 N N N N N N 2.239  -18.612 -23.428 2.010  0.033  -0.398 H43  YU6 57 
YU6 H45  H24 H  0 1 N N N N N N 2.156  -23.289 -24.362 6.093  0.447  1.899  H45  YU6 58 
YU6 H46  H25 H  0 1 N N N N N N 3.380  -23.090 -23.063 7.309  0.765  0.638  H46  YU6 59 
YU6 H52  H26 H  0 1 N N N N N N 6.954  -18.565 -22.519 -0.172 3.618  -0.102 H52  YU6 60 
YU6 H4   H30 H  0 1 N N N N N N 10.221 -19.038 -19.166 -4.053 4.667  2.380  H4   YU6 61 
# 
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 
YU6 C1  N2   SING N N 1  
YU6 C1  C15  SING N N 2  
YU6 N2  C3   SING N N 3  
YU6 N2  C7   SING N N 4  
YU6 C3  C4   SING N N 5  
YU6 C4  N5   SING N N 6  
YU6 N5  C6   SING N N 7  
YU6 N5  C8   SING N N 8  
YU6 C6  C7   SING N N 9  
YU6 C8  C9   SING N N 10 
YU6 C9  C10  DOUB Y N 11 
YU6 C9  C14  SING Y N 12 
YU6 C10 C11  SING Y N 13 
YU6 C11 C12  DOUB Y N 14 
YU6 C12 C13  SING Y N 15 
YU6 C13 C14  DOUB Y N 16 
YU6 C15 N16  SING Y N 17 
YU6 C15 N19  DOUB Y N 18 
YU6 N16 C17  SING Y N 19 
YU6 C17 C18  DOUB Y N 20 
YU6 C17 C31  SING Y N 21 
YU6 C18 N19  SING Y N 22 
YU6 C18 C20  SING Y N 23 
YU6 C20 C21  DOUB Y N 24 
YU6 C21 C22  SING N N 25 
YU6 C21 C30  SING Y N 26 
YU6 C22 C23  DOUB Y N 27 
YU6 C22 C29  SING Y N 28 
YU6 C23 CL24 SING N N 29 
YU6 C23 C25  SING Y N 30 
YU6 C25 C26  DOUB Y N 31 
YU6 C26 C27  SING N N 32 
YU6 C26 C28  SING Y N 33 
YU6 C28 C29  DOUB Y N 34 
YU6 C30 C31  DOUB Y N 35 
YU6 C31 C32  SING N N 36 
YU6 C32 O33  DOUB N N 37 
YU6 C32 O34  SING N N 38 
YU6 C10 H47  SING N N 39 
YU6 C11 H48  SING N N 40 
YU6 C13 H50  SING N N 41 
YU6 C20 H53  SING N N 42 
YU6 C25 H54  SING N N 43 
YU6 C27 H56  SING N N 44 
YU6 C27 H57  SING N N 45 
YU6 C27 H55  SING N N 46 
YU6 C28 H58  SING N N 47 
YU6 C1  H35  SING N N 48 
YU6 C1  H36  SING N N 49 
YU6 C12 H49  SING N N 50 
YU6 C14 H51  SING N N 51 
YU6 C29 H59  SING N N 52 
YU6 C3  H38  SING N N 53 
YU6 C3  H37  SING N N 54 
YU6 C30 H60  SING N N 55 
YU6 C4  H39  SING N N 56 
YU6 C4  H40  SING N N 57 
YU6 C6  H42  SING N N 58 
YU6 C6  H41  SING N N 59 
YU6 C7  H44  SING N N 60 
YU6 C7  H43  SING N N 61 
YU6 C8  H45  SING N N 62 
YU6 C8  H46  SING N N 63 
YU6 N16 H52  SING N N 64 
YU6 O34 H4   SING N N 65 
# 
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 
YU6 SMILES           ACDLabs              12.01 "Cc1ccc(c(Cl)c1)c1cc2nc([NH]c2c(c1)C(=O)O)CN1CCN(CC1)Cc1ccccc1"                                                                                                                      
YU6 InChI            InChI                1.06  "InChI=1S/C27H27ClN4O2/c1-18-7-8-21(23(28)13-18)20-14-22(27(33)34)26-24(15-20)29-25(30-26)17-32-11-9-31(10-12-32)16-19-5-3-2-4-6-19/h2-8,13-15H,9-12,16-17H2,1H3,(H,29,30)(H,33,34)" 
YU6 InChIKey         InChI                1.06  GFNSGOYZMZLPLR-UHFFFAOYSA-N                                                                                                                                                          
YU6 SMILES_CANONICAL CACTVS               3.385 "Cc1ccc(c(Cl)c1)c2cc3nc(CN4CCN(CC4)Cc5ccccc5)[nH]c3c(c2)C(O)=O"                                                                                                                      
YU6 SMILES           CACTVS               3.385 "Cc1ccc(c(Cl)c1)c2cc3nc(CN4CCN(CC4)Cc5ccccc5)[nH]c3c(c2)C(O)=O"                                                                                                                      
YU6 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1ccc(c(c1)Cl)c2cc(c3c(c2)nc([nH]3)CN4CCN(CC4)Cc5ccccc5)C(=O)O"                                                                                                                    
YU6 SMILES           "OpenEye OEToolkits" 2.0.7 "Cc1ccc(c(c1)Cl)c2cc(c3c(c2)nc([nH]3)CN4CCN(CC4)Cc5ccccc5)C(=O)O"                                                                                                                    
# 
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 
YU6 "SYSTEMATIC NAME" ACDLabs              12.01 "(5M)-2-[(4-benzylpiperazin-1-yl)methyl]-5-(2-chloro-4-methylphenyl)-1H-benzimidazole-7-carboxylic acid"           
YU6 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "6-(2-chloranyl-4-methyl-phenyl)-2-[[4-(phenylmethyl)piperazin-1-yl]methyl]-3~{H}-benzimidazole-4-carboxylic acid" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
YU6 "Create component" 2023-02-21 RCSB 
YU6 "Initial release"  2024-02-21 RCSB 
# 
