data_YBF
# 
_chem_comp.id                                    YBF 
_chem_comp.name                                  "(4M)-4-(1-benzyl-1H-pyrrolo[2,3-b]pyridin-3-yl)-3-nitro-N-phenylbenzamide" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C27 H20 N4 O3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-06-12 
_chem_comp.pdbx_modified_date                    2024-12-13 
_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                        448.473 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YBF 
_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        7G6Q 
_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_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 
YBF C10 C1  C 0  1 N N N N N N -13.311 6.437  43.654 4.817   -0.445 -1.498 C10 YBF 1  
YBF C11 C2  C 0  1 Y N N N N N -12.451 5.218  43.782 5.378   -1.592 -0.698 C11 YBF 2  
YBF C13 C3  C 0  1 Y N N N N N -10.500 3.920  43.054 5.453   -3.934 -0.202 C13 YBF 3  
YBF C15 C4  C 0  1 Y N N N N N -12.095 3.002  44.728 6.841   -2.408 1.013  C15 YBF 4  
YBF C16 C5  C 0  1 Y N N N N N -12.870 4.175  44.645 6.327   -1.355 0.279  C16 YBF 5  
YBF C17 C6  C 0  1 Y N N N N N -11.951 10.491 49.781 -1.952  -0.969 0.138  C17 YBF 6  
YBF C18 C7  C 0  1 Y N N N N N -11.769 9.932  48.491 -0.590  -0.876 0.119  C18 YBF 7  
YBF C19 C8  C 0  1 Y N N N N N -12.898 9.455  47.739 0.024   0.320  -0.262 C19 YBF 8  
YBF C20 C9  C 0  1 Y N N N N N -14.194 9.579  48.342 -0.755  1.422  -0.623 C20 YBF 9  
YBF C21 C10 C 0  1 Y N N N N N -14.376 10.121 49.590 -2.118  1.331  -0.604 C21 YBF 10 
YBF C22 C11 C 0  1 Y N N N N N -13.262 10.561 50.314 -2.733  0.134  -0.223 C22 YBF 11 
YBF C23 C12 C 0  1 N N N N N N -13.618 11.008 51.684 -4.205  0.034  -0.202 C23 YBF 12 
YBF C1  C13 C 0  1 Y N N N N N -10.115 10.497 44.110 3.143   2.841  2.175  C1  YBF 13 
YBF C2  C14 C 0  1 Y N N N N N -10.325 9.551  43.022 4.430   2.550  1.750  C2  YBF 14 
YBF N3  N1  N 0  1 Y N N N N N -11.202 8.491  43.087 4.657   1.676  0.792  N3  YBF 15 
YBF C4  C15 C 0  1 Y N N N N N -10.842 10.352 45.300 2.071   2.201  1.579  C4  YBF 16 
YBF C5  C16 C 0  1 Y N N N N N -11.774 9.305  45.407 2.337   1.280  0.567  C5  YBF 17 
YBF C6  C17 C 0  1 Y N N N N N -11.909 8.412  44.275 3.668   1.032  0.187  C6  YBF 18 
YBF N7  N2  N 0  1 Y N N N N N -12.889 7.467  44.574 3.636   0.093  -0.818 N7  YBF 19 
YBF C8  C18 C 0  1 Y N N N N N -13.375 7.717  45.874 2.349   -0.265 -1.092 C8  YBF 20 
YBF C9  C19 C 0  1 Y N N N N N -12.703 8.853  46.409 1.500   0.420  -0.284 C9  YBF 21 
YBF C12 C20 C 0  1 Y N N N N N -11.288 5.110  43.012 4.938   -2.881 -0.936 C12 YBF 22 
YBF C14 C21 C 0  1 Y N N N N N -10.896 2.871  43.919 6.407   -3.697 0.770  C14 YBF 23 
YBF N24 N3  N 0  1 N N N N N N -12.963 12.103 52.238 -4.797  -1.119 0.164  N24 YBF 24 
YBF O25 O1  O 0  1 N N N N N N -14.489 10.359 52.334 -4.883  0.993  -0.516 O25 YBF 25 
YBF N26 N4  N 1  1 N N N N N N -15.467 9.127  47.699 -0.104  2.688  -1.026 N26 YBF 26 
YBF O27 O2  O 0  1 N N N N N N -16.055 8.137  48.122 -0.783  3.649  -1.340 O27 YBF 27 
YBF O28 O3  O -1 1 N N N N N N -15.895 9.796  46.796 1.111   2.770  -1.043 O28 YBF 28 
YBF C29 C22 C 0  1 Y N N N N N -13.334 12.584 53.572 -6.188  -1.182 0.290  C29 YBF 29 
YBF C30 C23 C 0  1 Y N N N N N -12.958 11.830 54.731 -6.863  -2.357 -0.016 C30 YBF 30 
YBF C31 C24 C 0  1 Y N N N N N -14.216 13.451 56.145 -8.941  -1.306 0.540  C31 YBF 31 
YBF C32 C25 C 0  1 Y N N N N N -14.587 14.213 55.004 -8.272  -0.136 0.852  C32 YBF 32 
YBF C33 C26 C 0  1 Y N N N N N -13.398 12.266 56.012 -8.237  -2.415 0.110  C33 YBF 33 
YBF C34 C27 C 0  1 Y N N N N N -14.143 13.788 53.700 -6.898  -0.071 0.728  C34 YBF 34 
YBF H39 H1  H 0  1 N N N N N N -14.354 6.166  43.872 5.571   0.336  -1.590 H39 YBF 35 
YBF H40 H2  H 0  1 N N N N N N -13.239 6.822  42.626 4.536   -0.798 -2.490 H40 YBF 36 
YBF H42 H3  H 0  1 N N N N N N -9.619  3.822  42.438 5.114   -4.941 -0.392 H42 YBF 37 
YBF H44 H4  H 0  1 N N N N N N -12.391 2.203  45.391 7.583   -2.222 1.776  H44 YBF 38 
YBF H45 H5  H 0  1 N N N N N N -13.771 4.278  45.231 6.667   -0.348 0.468  H45 YBF 39 
YBF H46 H6  H 0  1 N N N N N N -11.107 10.856 50.347 -2.426  -1.894 0.429  H46 YBF 40 
YBF H47 H7  H 0  1 N N N N N N -10.777 9.864  48.071 0.014   -1.727 0.398  H47 YBF 41 
YBF H48 H8  H 0  1 N N N N N N -15.368 10.207 50.009 -2.720  2.182  -0.882 H48 YBF 42 
YBF H35 H9  H 0  1 N N N N N N -9.405  11.303 44.001 2.980   3.559  2.965  H35 YBF 43 
YBF H36 H10 H 0  1 N N N N N N -9.760  9.689  42.112 5.265   3.051  2.216  H36 YBF 44 
YBF H37 H11 H 0  1 N N N N N N -10.688 11.035 46.123 1.058   2.408  1.891  H37 YBF 45 
YBF H38 H12 H 0  1 N N N N N N -14.134 7.140  46.382 2.050   -0.985 -1.840 H38 YBF 46 
YBF H41 H13 H 0  1 N N N N N N -10.984 5.932  42.381 4.193   -3.066 -1.696 H41 YBF 47 
YBF H43 H14 H 0  1 N N N N N N -10.304 1.970  43.977 6.812   -4.520 1.340  H43 YBF 48 
YBF H49 H15 H 0  1 N N N N N N -12.238 12.563 51.725 -4.258  -1.907 0.340  H49 YBF 49 
YBF H50 H16 H 0  1 N N N N N N -12.349 10.943 54.634 -6.313  -3.223 -0.353 H50 YBF 50 
YBF H51 H17 H 0  1 N N N N N N -14.549 13.761 57.124 -10.016 -1.354 0.639  H51 YBF 51 
YBF H52 H18 H 0  1 N N N N N N -15.194 15.100 55.113 -8.825  0.729  1.188  H52 YBF 52 
YBF H53 H19 H 0  1 N N N N N N -13.119 11.707 56.893 -8.762  -3.328 -0.128 H53 YBF 53 
YBF H54 H20 H 0  1 N N N N N N -14.409 14.359 52.823 -6.376  0.843  0.971  H54 YBF 54 
# 
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 
YBF C1  C2  DOUB Y N 1  
YBF C1  C4  SING Y N 2  
YBF C2  N3  SING Y N 3  
YBF N3  C6  DOUB Y N 4  
YBF C4  C5  DOUB Y N 5  
YBF C5  C6  SING Y N 6  
YBF C5  C9  SING Y N 7  
YBF C6  N7  SING Y N 8  
YBF N7  C8  SING Y N 9  
YBF N7  C10 SING N N 10 
YBF C8  C9  DOUB Y N 11 
YBF C9  C19 SING N N 12 
YBF C10 C11 SING N N 13 
YBF C11 C12 DOUB Y N 14 
YBF C11 C16 SING Y N 15 
YBF C12 C13 SING Y N 16 
YBF C13 C14 DOUB Y N 17 
YBF C14 C15 SING Y N 18 
YBF C15 C16 DOUB Y N 19 
YBF C17 C18 DOUB Y N 20 
YBF C17 C22 SING Y N 21 
YBF C18 C19 SING Y N 22 
YBF C19 C20 DOUB Y N 23 
YBF C20 C21 SING Y N 24 
YBF C20 N26 SING N N 25 
YBF C21 C22 DOUB Y N 26 
YBF C22 C23 SING N N 27 
YBF C23 N24 SING N N 28 
YBF C23 O25 DOUB N N 29 
YBF N24 C29 SING N N 30 
YBF N26 O27 DOUB N N 31 
YBF N26 O28 SING N N 32 
YBF C29 C30 DOUB Y N 33 
YBF C29 C34 SING Y N 34 
YBF C30 C33 SING Y N 35 
YBF C31 C32 SING Y N 36 
YBF C31 C33 DOUB Y N 37 
YBF C32 C34 DOUB Y N 38 
YBF C10 H39 SING N N 39 
YBF C10 H40 SING N N 40 
YBF C13 H42 SING N N 41 
YBF C15 H44 SING N N 42 
YBF C16 H45 SING N N 43 
YBF C17 H46 SING N N 44 
YBF C18 H47 SING N N 45 
YBF C21 H48 SING N N 46 
YBF C1  H35 SING N N 47 
YBF C2  H36 SING N N 48 
YBF C4  H37 SING N N 49 
YBF C8  H38 SING N N 50 
YBF C12 H41 SING N N 51 
YBF C14 H43 SING N N 52 
YBF N24 H49 SING N N 53 
YBF C30 H50 SING N N 54 
YBF C31 H51 SING N N 55 
YBF C32 H52 SING N N 56 
YBF C33 H53 SING N N 57 
YBF C34 H54 SING N N 58 
# 
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 
YBF SMILES           ACDLabs              12.01 "[O-][N+](=O)c1cc(ccc1c1cn(Cc2ccccc2)c2ncccc21)C(=O)Nc1ccccc1"                                                                                              
YBF InChI            InChI                1.06  "InChI=1S/C27H20N4O3/c32-27(29-21-10-5-2-6-11-21)20-13-14-22(25(16-20)31(33)34)24-18-30(17-19-8-3-1-4-9-19)26-23(24)12-7-15-28-26/h1-16,18H,17H2,(H,29,32)" 
YBF InChIKey         InChI                1.06  AHZNVHKEQIDYLP-UHFFFAOYSA-N                                                                                                                                 
YBF SMILES_CANONICAL CACTVS               3.385 "[O-][N+](=O)c1cc(ccc1c2cn(Cc3ccccc3)c4ncccc24)C(=O)Nc5ccccc5"                                                                                              
YBF SMILES           CACTVS               3.385 "[O-][N+](=O)c1cc(ccc1c2cn(Cc3ccccc3)c4ncccc24)C(=O)Nc5ccccc5"                                                                                              
YBF SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)Cn2cc(c3c2nccc3)c4ccc(cc4[N+](=O)[O-])C(=O)Nc5ccccc5"                                                                                            
YBF SMILES           "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)Cn2cc(c3c2nccc3)c4ccc(cc4[N+](=O)[O-])C(=O)Nc5ccccc5"                                                                                            
# 
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 
YBF "SYSTEMATIC NAME" ACDLabs              12.01 "(4M)-4-(1-benzyl-1H-pyrrolo[2,3-b]pyridin-3-yl)-3-nitro-N-phenylbenzamide"   
YBF "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "3-nitro-~{N}-phenyl-4-[1-(phenylmethyl)pyrrolo[2,3-b]pyridin-3-yl]benzamide" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
YBF "Create component" 2023-06-12 RCSB 
YBF "Initial release"  2024-12-18 RCSB 
# 
