data_VO8
# 
_chem_comp.id                                    VO8 
_chem_comp.name                                  "5-(2-{2-[2-oxo-3-(prop-2-enoyl)-2,3-dihydro-1H-benzimidazol-1-yl]ethoxy}phenoxy)naphthalene-2-carbonitrile" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C29 H23 N3 O4" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-09-14 
_chem_comp.pdbx_modified_date                    2023-11-03 
_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                        477.511 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     VO8 
_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        8U6T 
_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 
VO8 C10 C1  C 0 1 Y N N N N N 48.029 5.307  18.710 2.568  -3.330 -2.260 C10 VO8 1  
VO8 C1  C2  C 0 1 N N N N N N 44.017 -2.553 19.137 -6.437 2.537  -2.090 C1  VO8 2  
VO8 C2  C3  C 0 1 N N N N N N 45.007 -2.844 19.937 -5.746 1.297  -1.518 C2  VO8 3  
VO8 C3  C4  C 0 1 N N N N N N 45.351 -2.106 21.004 -4.708 1.719  -0.511 C3  VO8 4  
VO8 O1  O1  O 0 1 N N N N N N 46.166 -2.554 21.788 -4.538 2.895  -0.273 O1  VO8 5  
VO8 N1  N1  N 0 1 N N N N N N 44.842 -0.831 21.238 -3.970 0.788  0.126  N1  VO8 6  
VO8 C4  C5  C 0 1 N N N N N N 43.998 -0.137 20.376 -4.057 -0.544 -0.050 C4  VO8 7  
VO8 O2  O2  O 0 1 N N N N N N 43.558 -0.514 19.294 -4.821 -1.100 -0.816 O2  VO8 8  
VO8 N2  N2  N 0 1 N N N N N N 43.746 1.072  20.985 -3.171 -1.166 0.749  N2  VO8 9  
VO8 C5  C6  C 0 1 N N N N N N 42.897 2.095  20.380 -2.968 -2.614 0.840  C5  VO8 10 
VO8 C6  C7  C 0 1 N N N N N N 43.676 2.967  19.461 -1.905 -3.045 -0.172 C6  VO8 11 
VO8 O3  O3  O 0 1 N N N N N N 44.534 3.758  20.267 -0.648 -2.464 0.181  O3  VO8 12 
VO8 C7  C8  C 0 1 Y N N N N N 45.654 4.271  19.680 0.411  -2.749 -0.623 C7  VO8 13 
VO8 C8  C9  C 0 1 Y N N N N N 45.767 4.626  18.346 0.247  -3.578 -1.721 C8  VO8 14 
VO8 C9  C10 C 0 1 Y N N N N N 46.962 5.144  17.866 1.323  -3.862 -2.540 C9  VO8 15 
VO8 C11 C11 C 0 1 Y N N N N N 47.920 4.956  20.048 2.742  -2.511 -1.160 C11 VO8 16 
VO8 C12 C12 C 0 1 Y N N N N N 46.746 4.435  20.525 1.666  -2.218 -0.338 C12 VO8 17 
VO8 O4  O4  O 0 1 N N N N N N 46.619 4.090  21.863 1.833  -1.404 0.738  O4  VO8 18 
VO8 C13 C13 C 0 1 Y N N N N N 46.496 5.125  22.765 3.043  -0.813 0.909  C13 VO8 19 
VO8 C14 C14 C 0 1 Y N N N N N 45.876 6.291  22.465 3.995  -1.400 1.712  C14 VO8 20 
VO8 C15 C15 C 0 1 Y N N N N N 45.790 7.308  23.426 5.240  -0.803 1.895  C15 VO8 21 
VO8 C16 C16 C 0 1 Y N N N N N 46.323 7.145  24.664 5.550  0.374  1.286  C16 VO8 22 
VO8 C17 C17 C 0 1 Y N N N N N 46.979 5.944  25.010 4.605  1.006  0.458  C17 VO8 23 
VO8 C18 C18 C 0 1 Y N N N N N 47.547 5.736  26.285 4.900  2.220  -0.181 C18 VO8 24 
VO8 C19 C19 C 0 1 Y N N N N N 48.179 4.552  26.591 3.945  2.814  -0.990 C19 VO8 25 
VO8 C20 C20 C 0 1 N N N N N N 48.762 4.357  27.891 4.240  4.053  -1.645 C20 VO8 26 
VO8 N3  N3  N 0 1 N N N N N N 49.264 4.225  28.912 4.473  5.036  -2.164 N3  VO8 27 
VO8 C21 C21 C 0 1 Y N N N N N 48.261 3.546  25.623 2.689  2.209  -1.173 C21 VO8 28 
VO8 C22 C22 C 0 1 Y N N N N N 47.726 3.716  24.381 2.387  1.034  -0.562 C22 VO8 29 
VO8 C23 C23 C 0 1 Y N N N N N 47.067 4.917  24.042 3.337  0.404  0.260  C23 VO8 30 
VO8 C24 C24 C 0 1 Y N N N N N 44.411 1.165  22.192 -2.479 -0.199 1.476  C24 VO8 31 
VO8 C25 C25 C 0 1 Y N N N N N 44.454 2.177  23.128 -1.474 -0.264 2.429  C25 VO8 32 
VO8 C26 C26 C 0 1 Y N N N N N 45.224 1.944  24.257 -0.977 0.899  2.985  C26 VO8 33 
VO8 C27 C27 C 0 1 Y N N N N N 45.917 0.760  24.432 -1.479 2.129  2.594  C27 VO8 34 
VO8 C28 C28 C 0 1 Y N N N N N 45.871 -0.256 23.492 -2.480 2.203  1.645  C28 VO8 35 
VO8 C29 C29 C 0 1 Y N N N N N 45.104 -0.027 22.369 -2.980 1.041  1.078  C29 VO8 36 
VO8 H10 H1  H 0 1 N N N N N N 48.957 5.710  18.333 3.408  -3.558 -2.900 H10 VO8 37 
VO8 H22 H2  H 0 1 N N N N N N 43.948 -3.314 18.346 -6.917 3.090  -1.282 H22 VO8 38 
VO8 H1  H3  H 0 1 N N N N N N 43.078 -2.532 19.709 -5.696 3.174  -2.575 H1  VO8 39 
VO8 H3  H5  H 0 1 N N N N N N 44.790 -3.849 20.327 -6.486 0.660  -1.033 H3  VO8 40 
VO8 H5  H7  H 0 1 N N N N N N 42.459 2.714  21.176 -2.638 -2.872 1.846  H5  VO8 41 
VO8 H4  H8  H 0 1 N N N N N N 42.093 1.604  19.813 -3.905 -3.126 0.623  H4  VO8 42 
VO8 H7  H9  H 0 1 N N N N N N 42.996 3.613  18.886 -1.818 -4.131 -0.168 H7  VO8 43 
VO8 H6  H10 H 0 1 N N N N N N 44.269 2.352  18.769 -2.194 -2.708 -1.168 H6  VO8 44 
VO8 H8  H11 H 0 1 N N N N N N 44.926 4.500  17.680 -0.724 -3.999 -1.939 H8  VO8 45 
VO8 H9  H12 H 0 1 N N N N N N 47.051 5.419  16.825 1.192  -4.501 -3.401 H9  VO8 46 
VO8 H11 H13 H 0 1 N N N N N N 48.760 5.093  20.713 3.717  -2.101 -0.942 H11 VO8 47 
VO8 H12 H14 H 0 1 N N N N N N 45.447 6.438  21.485 3.773  -2.334 2.207  H12 VO8 48 
VO8 H13 H15 H 0 1 N N N N N N 45.293 8.234  23.178 5.970  -1.282 2.530  H13 VO8 49 
VO8 H14 H16 H 0 1 N N N N N N 46.244 7.941  25.390 6.520  0.822  1.440  H14 VO8 50 
VO8 H15 H17 H 0 1 N N N N N N 47.485 6.515  27.030 5.864  2.688  -0.042 H15 VO8 51 
VO8 H16 H18 H 0 1 N N N N N N 48.757 2.618  25.864 1.955  2.684  -1.807 H16 VO8 52 
VO8 H17 H19 H 0 1 N N N N N N 47.807 2.925  23.650 1.418  0.581  -0.712 H17 VO8 53 
VO8 H18 H20 H 0 1 N N N N N N 43.916 3.103  22.989 -1.080 -1.222 2.737  H18 VO8 54 
VO8 H19 H21 H 0 1 N N N N N N 45.284 2.707  25.019 -0.194 0.849  3.727  H19 VO8 55 
VO8 H20 H22 H 0 1 N N N N N N 46.509 0.624  25.325 -1.087 3.034  3.033  H20 VO8 56 
VO8 H21 H23 H 0 1 N N N N N N 46.409 -1.182 23.632 -2.870 3.163  1.344  H21 VO8 57 
VO8 H2  H28 H 0 1 N N N N N N 44.191 -1.567 18.682 -7.187 2.232  -2.819 H2  VO8 58 
VO8 H23 H29 H 0 1 N N N N N N 45.903 -2.884 19.300 -5.266 0.744  -2.326 H23 VO8 59 
# 
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 
VO8 C9  C8  DOUB Y N 1  
VO8 C9  C10 SING Y N 2  
VO8 C8  C7  SING Y N 3  
VO8 C10 C11 DOUB Y N 4  
VO8 C1  C2  SING N N 5  
VO8 O2  C4  DOUB N N 6  
VO8 C6  O3  SING N N 7  
VO8 C6  C5  SING N N 8  
VO8 C7  O3  SING N N 9  
VO8 C7  C12 DOUB Y N 10 
VO8 C2  C3  SING N N 11 
VO8 C11 C12 SING Y N 12 
VO8 C4  N2  SING N N 13 
VO8 C4  N1  SING N N 14 
VO8 C5  N2  SING N N 15 
VO8 C12 O4  SING N N 16 
VO8 N2  C24 SING N N 17 
VO8 C3  N1  SING N N 18 
VO8 C3  O1  DOUB N N 19 
VO8 N1  C29 SING N N 20 
VO8 O4  C13 SING N N 21 
VO8 C24 C29 DOUB Y N 22 
VO8 C24 C25 SING Y N 23 
VO8 C29 C28 SING Y N 24 
VO8 C14 C13 DOUB Y N 25 
VO8 C14 C15 SING Y N 26 
VO8 C13 C23 SING Y N 27 
VO8 C25 C26 DOUB Y N 28 
VO8 C15 C16 DOUB Y N 29 
VO8 C28 C27 DOUB Y N 30 
VO8 C23 C22 DOUB Y N 31 
VO8 C23 C17 SING Y N 32 
VO8 C26 C27 SING Y N 33 
VO8 C22 C21 SING Y N 34 
VO8 C16 C17 SING Y N 35 
VO8 C17 C18 DOUB Y N 36 
VO8 C21 C19 DOUB Y N 37 
VO8 C18 C19 SING Y N 38 
VO8 C19 C20 SING N N 39 
VO8 C20 N3  TRIP N N 40 
VO8 C10 H10 SING N N 41 
VO8 C1  H22 SING N N 42 
VO8 C1  H1  SING N N 43 
VO8 C2  H3  SING N N 44 
VO8 C5  H5  SING N N 45 
VO8 C5  H4  SING N N 46 
VO8 C6  H7  SING N N 47 
VO8 C6  H6  SING N N 48 
VO8 C8  H8  SING N N 49 
VO8 C9  H9  SING N N 50 
VO8 C11 H11 SING N N 51 
VO8 C14 H12 SING N N 52 
VO8 C15 H13 SING N N 53 
VO8 C16 H14 SING N N 54 
VO8 C18 H15 SING N N 55 
VO8 C21 H16 SING N N 56 
VO8 C22 H17 SING N N 57 
VO8 C25 H18 SING N N 58 
VO8 C26 H19 SING N N 59 
VO8 C27 H20 SING N N 60 
VO8 C28 H21 SING N N 61 
VO8 C1  H2  SING N N 62 
VO8 C2  H23 SING N N 63 
# 
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 
VO8 SMILES           ACDLabs              12.01 "N#Cc1ccc2c(c1)cccc2Oc1ccccc1OCCN1c2ccccc2N(C(=O)CC)C1=O"                                                                                                        
VO8 InChI            InChI                1.06  "InChI=1S/C29H23N3O4/c1-2-28(33)32-24-10-4-3-9-23(24)31(29(32)34)16-17-35-26-11-5-6-12-27(26)36-25-13-7-8-21-18-20(19-30)14-15-22(21)25/h3-15,18H,2,16-17H2,1H3" 
VO8 InChIKey         InChI                1.06  LHEUAVBYYKCINL-UHFFFAOYSA-N                                                                                                                                      
VO8 SMILES_CANONICAL CACTVS               3.385 "CCC(=O)N1C(=O)N(CCOc2ccccc2Oc3cccc4cc(ccc34)C#N)c5ccccc15"                                                                                                      
VO8 SMILES           CACTVS               3.385 "CCC(=O)N1C(=O)N(CCOc2ccccc2Oc3cccc4cc(ccc34)C#N)c5ccccc15"                                                                                                      
VO8 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CCC(=O)N1c2ccccc2N(C1=O)CCOc3ccccc3Oc4cccc5c4ccc(c5)C#N"                                                                                                        
VO8 SMILES           "OpenEye OEToolkits" 2.0.7 "CCC(=O)N1c2ccccc2N(C1=O)CCOc3ccccc3Oc4cccc5c4ccc(c5)C#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 
VO8 "SYSTEMATIC NAME" ACDLabs              12.01 "5-{2-[2-(2-oxo-3-propanoyl-2,3-dihydro-1H-benzimidazol-1-yl)ethoxy]phenoxy}naphthalene-2-carbonitrile" 
VO8 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "5-[2-[2-(2-oxidanylidene-3-propanoyl-benzimidazol-1-yl)ethoxy]phenoxy]naphthalene-2-carbonitrile"      
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
VO8 "Create component" 2023-09-14 RCSB 
VO8 "Initial release"  2023-11-08 RCSB 
# 
