data_VL9
# 
_chem_comp.id                                    VL9 
_chem_comp.name                                  "[(1~{S})-2-[3,5-bis(chloranyl)-1-oxidanyl-pyridin-4-yl]-1-(3,4-dimethoxyphenyl)ethyl] 5-[[[(1~{R})-2-[[(3~{R})-1-azabicyclo[2.2.2]octan-3-yl]oxy]-2-oxidanylidene-1-phenyl-ethyl]amino]methyl]thiophene-2-carboxylate" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C36 H38 Cl2 N3 O7 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-03-10 
_chem_comp.pdbx_modified_date                    2023-04-21 
_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                        727.674 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     VL9 
_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   Y 
_chem_comp.pdbx_model_coordinates_db_code        8OEG 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
# 
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.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 
VL9 O2  O1  O  0 1 N N N 37.987 22.412 -11.610 ? ? ? O2  VL9 1  
VL9 C22 C1  C  0 1 N N N 40.739 21.337 -14.073 ? ? ? C22 VL9 2  
VL9 C1  C2  C  0 1 Y N N 38.809 16.560 -3.606  ? ? ? C1  VL9 3  
VL9 C   C3  C  0 1 Y N N 38.362 17.314 -4.673  ? ? ? C   VL9 4  
VL9 N2  N1  N  0 1 N N N 40.079 23.826 -13.911 ? ? ? N2  VL9 5  
VL9 C21 C4  C  0 1 N N N 40.820 22.749 -14.757 ? ? ? C21 VL9 6  
VL9 O1  O2  O  0 1 N N N 34.849 19.389 -4.485  ? ? ? O1  VL9 7  
VL9 N   N2  N  0 1 Y N N 30.369 20.688 -2.846  ? ? ? N   VL9 8  
VL9 C2  C5  C  0 1 Y N N 38.057 16.508 -2.468  ? ? ? C2  VL9 9  
VL9 C3  C6  C  0 1 Y N N 36.900 17.232 -2.323  ? ? ? C3  VL9 10 
VL9 C7  C7  C  0 1 N N N 33.872 18.132 -2.733  ? ? ? C7  VL9 11 
VL9 N1  N3  N  0 1 N N N 34.907 23.858 -9.977  ? ? ? N1  VL9 12 
VL9 C6  C8  C  0 1 N N S 35.208 18.870 -3.190  ? ? ? C6  VL9 13 
VL9 C5  C9  C  0 1 Y N N 37.219 18.076 -4.551  ? ? ? C5  VL9 14 
VL9 C4  C10 C  0 1 Y N N 36.450 18.057 -3.380  ? ? ? C4  VL9 15 
VL9 C8  C11 C  0 1 Y N N 32.677 19.005 -2.826  ? ? ? C8  VL9 16 
VL9 C9  C12 C  0 1 Y N N 31.729 18.928 -3.843  ? ? ? C9  VL9 17 
VL9 C14 C13 C  0 1 Y N N 34.619 21.128 -6.100  ? ? ? C14 VL9 18 
VL9 C13 C14 C  0 1 N N N 34.887 20.736 -4.690  ? ? ? C13 VL9 19 
VL9 C12 C15 C  0 1 Y N N 32.320 19.917 -1.747  ? ? ? C12 VL9 20 
VL9 C11 C16 C  0 1 Y N N 31.216 20.703 -1.798  ? ? ? C11 VL9 21 
VL9 C10 C17 C  0 1 Y N N 30.624 19.819 -3.858  ? ? ? C10 VL9 22 
VL9 O   O3  O  0 1 N N N 29.125 21.606 -2.963  ? ? ? O   VL9 23 
VL9 C15 C18 C  0 1 Y N N 34.238 22.743 -8.028  ? ? ? C15 VL9 24 
VL9 C20 C19 C  0 1 N N N 38.601 23.367 -13.850 ? ? ? C20 VL9 25 
VL9 C19 C20 C  0 1 N N R 38.548 22.093 -12.942 ? ? ? C19 VL9 26 
VL9 C18 C21 C  0 1 N N N 36.673 22.986 -11.288 ? ? ? C18 VL9 27 
VL9 C17 C22 C  0 1 N N R 36.350 23.480 -9.875  ? ? ? C17 VL9 28 
VL9 C16 C23 C  0 1 N N N 34.214 24.094 -8.759  ? ? ? C16 VL9 29 
VL9 O4  O4  O  0 1 N N N 35.143 21.556 -3.878  ? ? ? O4  VL9 30 
VL9 CL  CL1 CL 0 0 N N N 33.449 20.102 -0.428  ? ? ? CL  VL9 31 
VL9 CL1 CL2 CL 0 0 N N N 32.013 17.786 -5.148  ? ? ? CL1 VL9 32 
VL9 O5  O5  O  0 1 N N N 39.972 15.846 -3.765  ? ? ? O5  VL9 33 
VL9 C34 C24 C  0 1 N N N 40.366 14.979 -2.712  ? ? ? C34 VL9 34 
VL9 O6  O6  O  0 1 N N N 39.107 17.305 -5.811  ? ? ? O6  VL9 35 
VL9 C35 C25 C  0 1 N N N 38.958 18.225 -6.898  ? ? ? C35 VL9 36 
VL9 C33 C26 C  0 1 Y N N 34.221 20.486 -7.202  ? ? ? C33 VL9 37 
VL9 C32 C27 C  0 1 Y N N 33.989 21.438 -8.298  ? ? ? C32 VL9 38 
VL9 S   S1  S  0 1 Y N N 34.748 22.851 -6.363  ? ? ? S   VL9 39 
VL9 C26 C28 C  0 1 Y N N 37.388 24.501 -9.649  ? ? ? C26 VL9 40 
VL9 C31 C29 C  0 1 Y N N 37.205 25.835 -10.032 ? ? ? C31 VL9 41 
VL9 C30 C30 C  0 1 Y N N 38.237 26.770 -9.876  ? ? ? C30 VL9 42 
VL9 C29 C31 C  0 1 Y N N 39.478 26.321 -9.400  ? ? ? C29 VL9 43 
VL9 C28 C32 C  0 1 Y N N 39.673 24.981 -9.038  ? ? ? C28 VL9 44 
VL9 C27 C33 C  0 1 Y N N 38.640 24.068 -9.180  ? ? ? C27 VL9 45 
VL9 O3  O7  O  0 1 N N N 35.878 23.091 -12.157 ? ? ? O3  VL9 46 
VL9 C23 C34 C  0 1 N N N 40.015 21.548 -12.714 ? ? ? C23 VL9 47 
VL9 C24 C35 C  0 1 N N N 40.874 22.588 -11.861 ? ? ? C24 VL9 48 
VL9 C25 C36 C  0 1 N N N 40.779 23.991 -12.569 ? ? ? C25 VL9 49 
VL9 H1  H1  H  0 1 N N N 40.167 20.641 -14.704 ? ? ? H1  VL9 50 
VL9 H2  H2  H  0 1 N N N 41.750 20.936 -13.907 ? ? ? H2  VL9 51 
VL9 H4  H4  H  0 1 N N N 41.876 23.038 -14.860 ? ? ? H4  VL9 52 
VL9 H5  H5  H  0 1 N N N 40.356 22.693 -15.753 ? ? ? H5  VL9 53 
VL9 H6  H6  H  0 1 N N N 38.383 15.876 -1.655  ? ? ? H6  VL9 54 
VL9 H7  H7  H  0 1 N N N 36.335 17.172 -1.405  ? ? ? H7  VL9 55 
VL9 H8  H8  H  0 1 N N N 33.717 17.253 -3.377  ? ? ? H8  VL9 56 
VL9 H9  H9  H  0 1 N N N 33.989 17.806 -1.689  ? ? ? H9  VL9 57 
VL9 H10 H10 H  0 1 N N N 34.852 24.695 -10.522 ? ? ? H10 VL9 58 
VL9 H12 H12 H  0 1 N N N 35.408 19.693 -2.488  ? ? ? H12 VL9 59 
VL9 H13 H13 H  0 1 N N N 36.910 18.701 -5.376  ? ? ? H13 VL9 60 
VL9 H14 H14 H  0 1 N N N 31.008 21.364 -0.970  ? ? ? H14 VL9 61 
VL9 H15 H15 H  0 1 N N N 29.959 19.805 -4.709  ? ? ? H15 VL9 62 
VL9 H16 H16 H  0 1 N N N 29.066 22.159 -2.193  ? ? ? H16 VL9 63 
VL9 H17 H17 H  0 1 N N N 37.977 24.163 -13.419 ? ? ? H17 VL9 64 
VL9 H18 H18 H  0 1 N N N 38.240 23.125 -14.860 ? ? ? H18 VL9 65 
VL9 H19 H19 H  0 1 N N N 37.947 21.316 -13.438 ? ? ? H19 VL9 66 
VL9 H20 H20 H  0 1 N N N 36.470 22.651 -9.162  ? ? ? H20 VL9 67 
VL9 H21 H21 H  0 1 N N N 34.726 24.866 -8.165  ? ? ? H21 VL9 68 
VL9 H22 H22 H  0 1 N N N 33.179 24.410 -8.957  ? ? ? H22 VL9 69 
VL9 H23 H23 H  0 1 N N N 41.308 14.479 -2.981  ? ? ? H23 VL9 70 
VL9 H24 H24 H  0 1 N N N 40.510 15.563 -1.791  ? ? ? H24 VL9 71 
VL9 H25 H25 H  0 1 N N N 39.584 14.223 -2.548  ? ? ? H25 VL9 72 
VL9 H26 H26 H  0 1 N N N 39.689 17.986 -7.684  ? ? ? H26 VL9 73 
VL9 H27 H27 H  0 1 N N N 37.940 18.147 -7.308  ? ? ? H27 VL9 74 
VL9 H28 H28 H  0 1 N N N 39.130 19.250 -6.537  ? ? ? H28 VL9 75 
VL9 H29 H29 H  0 1 N N N 34.088 19.417 -7.277  ? ? ? H29 VL9 76 
VL9 H30 H30 H  0 1 N N N 33.639 21.115 -9.267  ? ? ? H30 VL9 77 
VL9 H31 H31 H  0 1 N N N 36.260 26.146 -10.452 ? ? ? H31 VL9 78 
VL9 H32 H32 H  0 1 N N N 38.081 27.811 -10.116 ? ? ? H32 VL9 79 
VL9 H33 H33 H  0 1 N N N 40.297 27.020 -9.311  ? ? ? H33 VL9 80 
VL9 H34 H34 H  0 1 N N N 40.628 24.660 -8.649  ? ? ? H34 VL9 81 
VL9 H35 H35 H  0 1 N N N 38.796 23.029 -8.931  ? ? ? H35 VL9 82 
VL9 H36 H36 H  0 1 N N N 39.966 20.593 -12.171 ? ? ? H36 VL9 83 
VL9 H37 H37 H  0 1 N N N 40.471 22.657 -10.840 ? ? ? H37 VL9 84 
VL9 H38 H38 H  0 1 N N N 41.923 22.261 -11.820 ? ? ? H38 VL9 85 
VL9 H39 H39 H  0 1 N N N 41.791 24.392 -12.728 ? ? ? H39 VL9 86 
VL9 H40 H40 H  0 1 N N N 40.205 24.684 -11.937 ? ? ? H40 VL9 87 
# 
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 
VL9 C21 C22 SING N N 1  
VL9 C21 N2  SING N N 2  
VL9 C22 C23 SING N N 3  
VL9 N2  C20 SING N N 4  
VL9 N2  C25 SING N N 5  
VL9 C20 C19 SING N N 6  
VL9 C19 C23 SING N N 7  
VL9 C19 O2  SING N N 8  
VL9 C23 C24 SING N N 9  
VL9 C25 C24 SING N N 10 
VL9 O3  C18 DOUB N N 11 
VL9 O2  C18 SING N N 12 
VL9 C18 C17 SING N N 13 
VL9 C31 C30 DOUB Y N 14 
VL9 C31 C26 SING Y N 15 
VL9 N1  C17 SING N N 16 
VL9 N1  C16 SING N N 17 
VL9 C30 C29 SING Y N 18 
VL9 C17 C26 SING N N 19 
VL9 C26 C27 DOUB Y N 20 
VL9 C29 C28 DOUB Y N 21 
VL9 C27 C28 SING Y N 22 
VL9 C16 C15 SING N N 23 
VL9 C32 C15 DOUB Y N 24 
VL9 C32 C33 SING Y N 25 
VL9 C15 S   SING Y N 26 
VL9 C33 C14 DOUB Y N 27 
VL9 C35 O6  SING N N 28 
VL9 S   C14 SING Y N 29 
VL9 C14 C13 SING N N 30 
VL9 O6  C   SING N N 31 
VL9 CL1 C9  SING N N 32 
VL9 C13 O1  SING N N 33 
VL9 C13 O4  DOUB N N 34 
VL9 C   C5  DOUB Y N 35 
VL9 C   C1  SING Y N 36 
VL9 C5  C4  SING Y N 37 
VL9 O1  C6  SING N N 38 
VL9 C10 C9  DOUB Y N 39 
VL9 C10 N   SING Y N 40 
VL9 C9  C8  SING Y N 41 
VL9 O5  C1  SING N N 42 
VL9 O5  C34 SING N N 43 
VL9 C1  C2  DOUB Y N 44 
VL9 C4  C6  SING N N 45 
VL9 C4  C3  DOUB Y N 46 
VL9 C6  C7  SING N N 47 
VL9 O   N   SING N N 48 
VL9 N   C11 DOUB Y N 49 
VL9 C8  C7  SING N N 50 
VL9 C8  C12 DOUB Y N 51 
VL9 C2  C3  SING Y N 52 
VL9 C11 C12 SING Y N 53 
VL9 C12 CL  SING N N 54 
VL9 C22 H1  SING N N 55 
VL9 C22 H2  SING N N 56 
VL9 C21 H4  SING N N 57 
VL9 C21 H5  SING N N 58 
VL9 C2  H6  SING N N 59 
VL9 C3  H7  SING N N 60 
VL9 C7  H8  SING N N 61 
VL9 C7  H9  SING N N 62 
VL9 N1  H10 SING N N 63 
VL9 C6  H12 SING N N 64 
VL9 C5  H13 SING N N 65 
VL9 C11 H14 SING N N 66 
VL9 C10 H15 SING N N 67 
VL9 O   H16 SING N N 68 
VL9 C20 H17 SING N N 69 
VL9 C20 H18 SING N N 70 
VL9 C19 H19 SING N N 71 
VL9 C17 H20 SING N N 72 
VL9 C16 H21 SING N N 73 
VL9 C16 H22 SING N N 74 
VL9 C34 H23 SING N N 75 
VL9 C34 H24 SING N N 76 
VL9 C34 H25 SING N N 77 
VL9 C35 H26 SING N N 78 
VL9 C35 H27 SING N N 79 
VL9 C35 H28 SING N N 80 
VL9 C33 H29 SING N N 81 
VL9 C32 H30 SING N N 82 
VL9 C31 H31 SING N N 83 
VL9 C30 H32 SING N N 84 
VL9 C29 H33 SING N N 85 
VL9 C28 H34 SING N N 86 
VL9 C27 H35 SING N N 87 
VL9 C23 H36 SING N N 88 
VL9 C24 H37 SING N N 89 
VL9 C24 H38 SING N N 90 
VL9 C25 H39 SING N N 91 
VL9 C25 H40 SING N N 92 
# 
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 
VL9 InChI            InChI                1.06  "InChI=1S/C36H38Cl2N3O7S/c1-45-29-10-8-24(16-31(29)46-2)30(17-26-27(37)19-41(44)20-28(26)38)47-35(42)33-11-9-25(49-33)18-39-34(23-6-4-3-5-7-23)36(43)48-32-21-40-14-12-22(32)13-15-40/h3-11,16,19-20,22,30,32,34,39,44H,12-15,17-18,21H2,1-2H3/t30-,32-,34+/m0/s1" 
VL9 InChIKey         InChI                1.06  IMHXWUGXDHLPGY-LEEDBYTESA-N                                                                                                                                                                                                                                        
VL9 SMILES_CANONICAL CACTVS               3.385 "COc1ccc(cc1OC)[C@H](Cc2c(Cl)c[n](O)cc2Cl)OC(=O)c3sc(CN[C@@H](C(=O)O[C@H]4CN5CCC4CC5)c6ccccc6)cc3"                                                                                                                                                                 
VL9 SMILES           CACTVS               3.385 "COc1ccc(cc1OC)[CH](Cc2c(Cl)c[n](O)cc2Cl)OC(=O)c3sc(CN[CH](C(=O)O[CH]4CN5CCC4CC5)c6ccccc6)cc3"                                                                                                                                                                     
VL9 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "COc1ccc(cc1OC)[C@H](CC2=C(C=[N](C=C2Cl)O)Cl)OC(=O)c3ccc(s3)CN[C@H](c4ccccc4)C(=O)O[C@H]5CN6CCC5CC6"                                                                                                                                                               
VL9 SMILES           "OpenEye OEToolkits" 2.0.7 "COc1ccc(cc1OC)C(CC2=C(C=[N](C=C2Cl)O)Cl)OC(=O)c3ccc(s3)CNC(c4ccccc4)C(=O)OC5CN6CCC5CC6"                                                                                                                                                                           
# 
_pdbx_chem_comp_identifier.comp_id           VL9 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           "OpenEye OEToolkits" 
_pdbx_chem_comp_identifier.program_version   2.0.7 
_pdbx_chem_comp_identifier.identifier        "[(1~{S})-2-[3,5-bis(chloranyl)-1-oxidanyl-pyridin-4-yl]-1-(3,4-dimethoxyphenyl)ethyl] 5-[[[(1~{R})-2-[[(3~{R})-1-azabicyclo[2.2.2]octan-3-yl]oxy]-2-oxidanylidene-1-phenyl-ethyl]amino]methyl]thiophene-2-carboxylate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
VL9 "Create component" 2023-03-10 PDBE 
VL9 "Initial release"  2023-04-26 RCSB 
# 
