data_YVB
# 
_chem_comp.id                                    YVB 
_chem_comp.name                                  "(2P)-2-{3-[(2-amino-4,5-dimethylphenyl)carbamoyl]phenyl}-1H-benzimidazole-4-carboxamide" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C23 H21 N5 O2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-02-22 
_chem_comp.pdbx_modified_date                    2024-02-02 
_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                        399.445 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YVB 
_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        8FZ1 
_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 
YVB N1  N1  N 0 1 Y N N N N N 37.252 12.383 -8.339  -3.158 -0.081 -0.008 N1  YVB 1  
YVB C7  C1  C 0 1 Y N N N N N 40.848 10.914 -10.251 0.874  1.478  0.189  C7  YVB 2  
YVB C8  C2  C 0 1 Y N N N N N 39.800 11.335 -9.440  -0.405 0.931  0.123  C8  YVB 3  
YVB N2  N2  N 0 1 Y N N N N N 36.631 10.277 -7.920  -4.039 1.922  0.112  N2  YVB 4  
YVB C9  C3  C 0 1 Y N N N N N 38.616 10.606 -9.383  -1.517 1.770  0.157  C9  YVB 5  
YVB O1  O1  O 0 1 N N N N N N 35.384 15.735 -6.271  -3.512 -2.872 -0.210 O1  YVB 6  
YVB C1  C4  C 0 1 Y N N N N N 45.105 15.757 -10.926 6.644  -1.335 -0.165 C1  YVB 7  
YVB C5  C5  C 0 1 Y N N N N N 43.130 13.779 -11.077 4.421  0.300  0.089  C5  YVB 8  
YVB C6  C6  C 0 1 N N N N N N 42.109 11.717 -10.224 2.060  0.595  0.153  C6  YVB 9  
YVB N3  N3  N 0 1 N N N N N N 36.867 15.198 -7.849  -5.515 -3.825 -0.319 N3  YVB 10 
YVB C4  C7  C 0 1 Y N N N N N 42.878 14.970 -10.403 4.397  -0.991 0.594  C4  YVB 11 
YVB C3  C8  C 0 1 N N N N N N 43.563 17.208 -9.521  5.478  -3.207 1.016  C3  YVB 12 
YVB C2  C9  C 0 1 Y N N N N N 43.852 15.958 -10.310 5.508  -1.804 0.466  C2  YVB 13 
YVB N4  N4  N 0 1 N N N N N N 44.643 12.400 -12.347 5.596  2.072  -1.070 N4  YVB 14 
YVB N   N5  N 0 1 N N N N N N 42.166 12.749 -11.098 3.297  1.126  0.217  N   YVB 15 
YVB C   C10 C 0 1 N N N N N N 46.189 16.806 -10.855 7.851  -2.228 -0.301 C   YVB 16 
YVB O   O2  O 0 1 N N N N N N 43.006 11.464 -9.421  1.919  -0.609 0.066  O   YVB 17 
YVB C10 C11 C 0 1 Y N N N N N 38.492 9.444  -10.132 -1.342 3.152  0.257  C10 YVB 18 
YVB C11 C12 C 0 1 Y N N N N N 39.527 9.026  -10.948 -0.071 3.688  0.322  C11 YVB 19 
YVB C12 C13 C 0 1 Y N N N N N 40.698 9.761  -11.015 1.035  2.862  0.283  C12 YVB 20 
YVB C13 C14 C 0 1 Y N N N N N 37.504 11.098 -8.560  -2.879 1.198  0.087  C13 YVB 21 
YVB C14 C15 C 0 1 Y N N N N N 36.151 12.393 -7.493  -4.490 -0.255 -0.049 C14 YVB 22 
YVB C15 C16 C 0 1 Y N N N N N 35.748 11.086 -7.232  -5.082 1.019  0.027  C15 YVB 23 
YVB C16 C17 C 0 1 Y N N N N N 34.645 10.792 -6.445  -6.463 1.146  0.005  C16 YVB 24 
YVB C17 C18 C 0 1 Y N N N N N 33.933 11.857 -5.918  -7.262 0.023  -0.090 C17 YVB 25 
YVB C18 C19 C 0 1 Y N N N N N 34.329 13.169 -6.155  -6.701 -1.238 -0.165 C18 YVB 26 
YVB C19 C20 C 0 1 Y N N N N N 35.451 13.467 -6.926  -5.317 -1.395 -0.146 C19 YVB 27 
YVB C20 C21 C 0 1 N N N N N N 35.898 14.892 -7.007  -4.721 -2.740 -0.227 C20 YVB 28 
YVB C21 C22 C 0 1 Y N N N N N 44.374 13.568 -11.691 5.567  0.772  -0.553 C21 YVB 29 
YVB C22 C23 C 0 1 Y N N N N N 45.348 14.569 -11.609 6.676  -0.051 -0.677 C22 YVB 30 
YVB H2  H2  H 0 1 N N N N N N 39.906 12.234 -8.850  -0.535 -0.138 0.046  H2  YVB 31 
YVB H3  H3  H 0 1 N N N N N N 36.628 9.277  -7.943  -4.115 2.887  0.178  H3  YVB 32 
YVB H4  H4  H 0 1 N N N N N N 37.205 16.138 -7.903  -6.479 -3.721 -0.332 H4  YVB 33 
YVB H5  H5  H 0 1 N N N N N N 37.264 14.490 -8.433  -5.123 -4.711 -0.372 H5  YVB 34 
YVB H6  H6  H 0 1 N N N N N N 41.913 15.129 -9.946  3.512  -1.359 1.091  H6  YVB 35 
YVB H7  H7  H 0 1 N N N N N N 43.129 17.970 -10.186 5.828  -3.200 2.049  H7  YVB 36 
YVB H8  H8  H 0 1 N N N N N N 42.851 16.976 -8.715  4.459  -3.590 0.981  H8  YVB 37 
YVB H9  H9  H 0 1 N N N N N N 44.498 17.591 -9.086  6.128  -3.846 0.417  H9  YVB 38 
YVB H10 H10 H 0 1 N N N N N N 43.842 11.803 -12.308 6.394  2.398  -1.516 H10 YVB 39 
YVB H11 H11 H 0 1 N N N N N N 44.865 12.598 -13.302 4.820  2.646  -0.983 H11 YVB 40 
YVB H12 H12 H 0 1 N N N N N N 41.470 12.784 -11.815 3.409  2.080  0.352  H12 YVB 41 
YVB H13 H13 H 0 1 N N N N N N 46.094 17.491 -11.711 7.785  -2.789 -1.233 H13 YVB 42 
YVB H14 H14 H 0 1 N N N N N N 46.089 17.374 -9.918  8.755  -1.619 -0.306 H14 YVB 43 
YVB H15 H15 H 0 1 N N N N N N 47.174 16.318 -10.884 7.886  -2.922 0.539  H15 YVB 44 
YVB H16 H16 H 0 1 N N N N N N 37.583 8.864  -10.077 -2.204 3.803  0.283  H16 YVB 45 
YVB H17 H17 H 0 1 N N N N N N 39.422 8.125  -11.534 0.058  4.757  0.399  H17 YVB 46 
YVB H18 H18 H 0 1 N N N N N N 41.499 9.438  -11.663 2.026  3.288  0.335  H18 YVB 47 
YVB H19 H19 H 0 1 N N N N N N 34.352 9.771  -6.250  -6.914 2.125  0.063  H19 YVB 48 
YVB H20 H20 H 0 1 N N N N N N 33.058 11.666 -5.315  -8.337 0.132  -0.105 H20 YVB 49 
YVB H21 H21 H 0 1 N N N N N N 33.752 13.978 -5.731  -7.339 -2.107 -0.238 H21 YVB 50 
YVB H22 H22 H 0 1 N N N N N N 46.306 14.417 -12.084 7.564  0.311  -1.173 H22 YVB 51 
# 
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 
YVB N4  C21 SING N N 1  
YVB C21 C22 DOUB Y N 2  
YVB C21 C5  SING Y N 3  
YVB C22 C1  SING Y N 4  
YVB N   C5  SING N N 5  
YVB N   C6  SING N N 6  
YVB C5  C4  DOUB Y N 7  
YVB C12 C11 DOUB Y N 8  
YVB C12 C7  SING Y N 9  
YVB C11 C10 SING Y N 10 
YVB C1  C   SING N N 11 
YVB C1  C2  DOUB Y N 12 
YVB C4  C2  SING Y N 13 
YVB C2  C3  SING N N 14 
YVB C7  C6  SING N N 15 
YVB C7  C8  DOUB Y N 16 
YVB C6  O   DOUB N N 17 
YVB C10 C9  DOUB Y N 18 
YVB C8  C9  SING Y N 19 
YVB C9  C13 SING N N 20 
YVB C13 N1  DOUB Y N 21 
YVB C13 N2  SING Y N 22 
YVB N1  C14 SING Y N 23 
YVB N2  C15 SING Y N 24 
YVB N3  C20 SING N N 25 
YVB C14 C15 DOUB Y N 26 
YVB C14 C19 SING Y N 27 
YVB C15 C16 SING Y N 28 
YVB C20 C19 SING N N 29 
YVB C20 O1  DOUB N N 30 
YVB C19 C18 DOUB Y N 31 
YVB C16 C17 DOUB Y N 32 
YVB C18 C17 SING Y N 33 
YVB C8  H2  SING N N 34 
YVB N2  H3  SING N N 35 
YVB N3  H4  SING N N 36 
YVB N3  H5  SING N N 37 
YVB C4  H6  SING N N 38 
YVB C3  H7  SING N N 39 
YVB C3  H8  SING N N 40 
YVB C3  H9  SING N N 41 
YVB N4  H10 SING N N 42 
YVB N4  H11 SING N N 43 
YVB N   H12 SING N N 44 
YVB C   H13 SING N N 45 
YVB C   H14 SING N N 46 
YVB C   H15 SING N N 47 
YVB C10 H16 SING N N 48 
YVB C11 H17 SING N N 49 
YVB C12 H18 SING N N 50 
YVB C16 H19 SING N N 51 
YVB C17 H20 SING N N 52 
YVB C18 H21 SING N N 53 
YVB C22 H22 SING N N 54 
# 
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 
YVB SMILES           ACDLabs              12.01 "Cc1cc(NC(=O)c2cccc(c2)c2nc3c(cccc3[NH]2)C(N)=O)c(N)cc1C"                                                                                                          
YVB InChI            InChI                1.06  "InChI=1S/C23H21N5O2/c1-12-9-17(24)19(10-13(12)2)27-23(30)15-6-3-5-14(11-15)22-26-18-8-4-7-16(21(25)29)20(18)28-22/h3-11H,24H2,1-2H3,(H2,25,29)(H,26,28)(H,27,30)" 
YVB InChIKey         InChI                1.06  HJDGBHNQHCFQSJ-UHFFFAOYSA-N                                                                                                                                        
YVB SMILES_CANONICAL CACTVS               3.385 "Cc1cc(N)c(NC(=O)c2cccc(c2)c3[nH]c4cccc(C(N)=O)c4n3)cc1C"                                                                                                          
YVB SMILES           CACTVS               3.385 "Cc1cc(N)c(NC(=O)c2cccc(c2)c3[nH]c4cccc(C(N)=O)c4n3)cc1C"                                                                                                          
YVB SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1cc(c(cc1C)NC(=O)c2cccc(c2)c3[nH]c4cccc(c4n3)C(=O)N)N"                                                                                                          
YVB SMILES           "OpenEye OEToolkits" 2.0.7 "Cc1cc(c(cc1C)NC(=O)c2cccc(c2)c3[nH]c4cccc(c4n3)C(=O)N)N"                                                                                                          
# 
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 
YVB "SYSTEMATIC NAME" ACDLabs              12.01 "(2P)-2-{3-[(2-amino-4,5-dimethylphenyl)carbamoyl]phenyl}-1H-benzimidazole-4-carboxamide" 
YVB "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "2-[3-[(2-azanyl-4,5-dimethyl-phenyl)carbamoyl]phenyl]-1~{H}-benzimidazole-4-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 
YVB "Create component" 2023-02-22 RCSB 
YVB "Initial release"  2024-02-07 RCSB 
# 
