data_YV3
# 
_chem_comp.id                                    YV3 
_chem_comp.name                                  "7-[(1~{S})-1-[3-(4-azanylbutyl)-2,5-bis(oxidanylidene)imidazolidin-1-yl]ethyl]-3-[3-fluoranyl-4-(methylsulfonylmethyl)phenyl]-1~{H}-indole-2-carboxylic acid" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C26 H29 F N4 O6 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-06-21 
_chem_comp.pdbx_modified_date                    2024-07-05 
_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                        544.595 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YV3 
_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        8PG7 
_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.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 
YV3 C13  C1  C 0 1 Y N N N N N -19.610 -11.104 6.651  4.958   0.320  -0.956 C13  YV3 1  
YV3 C12  C2  C 0 1 Y N N N N N -20.187 -11.024 7.905  3.611   0.460  -1.229 C12  YV3 2  
YV3 C11  C3  C 0 1 Y N N N N N -21.064 -11.997 8.357  2.702   0.610  -0.181 C11  YV3 3  
YV3 C16  C4  C 0 1 N N N N N N -19.230 -12.329 4.470  6.876   0.175  0.648  C16  YV3 4  
YV3 C15  C5  C 0 1 Y N N N N N -19.880 -12.209 5.853  5.405   0.328  0.356  C15  YV3 5  
YV3 C10  C6  C 0 1 Y N N N N N -21.656 -11.811 9.722  1.258   0.760  -0.466 C10  YV3 6  
YV3 C01  C7  C 0 1 N N N N N N -22.646 -12.345 15.531 -4.095  3.538  -1.065 C01  YV3 7  
YV3 C02  C8  C 0 1 N N S N N N -23.324 -12.060 14.180 -3.285  2.244  -0.954 C02  YV3 8  
YV3 C03  C9  C 0 1 Y N N N N N -22.677 -12.845 13.021 -1.888  2.563  -0.491 C03  YV3 9  
YV3 C04  C10 C 0 1 Y N N N N N -22.358 -12.173 11.829 -0.873  1.619  -0.628 C04  YV3 10 
YV3 C06  C11 C 0 1 Y N N N N N -22.185 -10.642 10.261 0.424   -0.184 -1.039 C06  YV3 11 
YV3 C07  C12 C 0 1 N N N N N N -22.396 -9.333  9.615  0.827   -1.523 -1.474 C07  YV3 12 
YV3 C18  C13 C 0 1 N N N N N N -20.531 -9.900  3.657  9.056   -1.530 1.179  C18  YV3 13 
YV3 C21  C14 C 0 1 Y N N N N N -20.733 -13.197 6.328  4.508   0.476  1.398  C21  YV3 14 
YV3 C22  C15 C 0 1 Y N N N N N -21.319 -13.113 7.582  3.160   0.617  1.137  C22  YV3 15 
YV3 C23  C16 C 0 1 Y N N N N N -21.776 -12.805 10.733 0.426   1.937  -0.190 C23  YV3 16 
YV3 C24  C17 C 0 1 Y N N N N N -21.453 -14.166 10.830 0.684   3.188  0.376  C24  YV3 17 
YV3 C25  C18 C 0 1 Y N N N N N -21.758 -14.861 12.008 -0.327  4.098  0.501  C25  YV3 18 
YV3 C26  C19 C 0 1 Y N N N N N -22.365 -14.212 13.111 -1.610  3.790  0.071  C26  YV3 19 
YV3 C28  C20 C 0 1 N N N N N N -25.631 -11.548 13.351 -4.090  1.634  1.317  C28  YV3 20 
YV3 C30  C21 C 0 1 N N N N N N -27.004 -12.093 13.500 -4.793  0.431  1.916  C30  YV3 21 
YV3 C32  C22 C 0 1 N N N N N N -27.956 -14.109 14.818 -5.587  -1.802 0.786  C32  YV3 22 
YV3 C33  C23 C 0 1 N N N N N N -28.324 -13.549 16.225 -7.084  -1.661 0.501  C33  YV3 23 
YV3 C34  C24 C 0 1 N N N N N N -28.497 -14.676 17.249 -7.738  -3.044 0.518  C34  YV3 24 
YV3 C35  C25 C 0 1 N N N N N N -27.813 -14.295 18.578 -9.235  -2.903 0.233  C35  YV3 25 
YV3 C37  C26 C 0 1 N N N N N N -25.464 -13.382 14.764 -4.424  0.144  -0.297 C37  YV3 26 
YV3 F14  F1  F 0 1 N N N N N N -18.767 -10.104 6.233  5.839   0.169  -1.969 F14  YV3 27 
YV3 N05  N1  N 0 1 Y N N N N N -22.565 -10.859 11.515 -0.849  0.340  -1.134 N05  YV3 28 
YV3 N27  N2  N 0 1 N N N N N N -24.769 -12.288 14.175 -3.927  1.347  0.011  N27  YV3 29 
YV3 N31  N3  N 0 1 N N N N N N -26.856 -13.230 14.387 -4.960  -0.478 0.769  N31  YV3 30 
YV3 N36  N4  N 0 1 N N N N N N -28.476 -14.834 19.766 -9.864  -4.231 0.250  N36  YV3 31 
YV3 O08  O1  O 0 1 N N N N N N -22.419 -8.295  10.339 -0.081  -2.357 -2.022 O08  YV3 32 
YV3 O09  O2  O 0 1 N N N N N N -22.781 -9.335  8.396  1.981   -1.884 -1.342 O09  YV3 33 
YV3 O19  O3  O 0 1 N N N N N N -19.577 -11.544 1.867  6.609   -2.075 1.997  O19  YV3 34 
YV3 O20  O4  O 0 1 N N N N N N -21.476 -12.349 3.029  7.070   -2.235 -0.405 O20  YV3 35 
YV3 O29  O5  O 0 1 N N N N N N -25.270 -10.626 12.662 -3.750  2.645  1.894  O29  YV3 36 
YV3 O38  O6  O 0 1 N N N N N N -24.981 -14.207 15.478 -4.394  -0.334 -1.414 O38  YV3 37 
YV3 S17  S1  S 0 1 N N N N N N -20.247 -11.579 3.156  7.274   -1.584 0.841  S17  YV3 38 
YV3 H121 H1  H 0 0 N N N N N N -19.950 -10.187 8.545  3.262   0.454  -2.251 H121 YV3 39 
YV3 H162 H2  H 0 0 N N N N N N -19.085 -13.395 4.239  7.455   0.590  -0.177 H162 YV3 40 
YV3 H161 H3  H 0 0 N N N N N N -18.254 -11.823 4.493  7.121   0.706  1.568  H161 YV3 41 
YV3 H011 H4  H 0 0 N N N N N N -23.143 -11.763 16.321 -3.617  4.204  -1.783 H011 YV3 42 
YV3 H012 H5  H 0 0 N N N N N N -22.724 -13.418 15.761 -5.106  3.306  -1.400 H012 YV3 43 
YV3 H013 H6  H 0 0 N N N N N N -21.585 -12.058 15.477 -4.137  4.024  -0.090 H013 YV3 44 
YV3 H021 H7  H 0 0 N N N N N N -23.158 -10.994 13.966 -3.243  1.758  -1.929 H021 YV3 45 
YV3 H182 H8  H 0 0 N N N N N N -21.039 -9.889  4.633  9.430   -2.544 1.319  H182 YV3 46 
YV3 H183 H9  H 0 0 N N N N N N -19.568 -9.374  3.739  9.571   -1.065 0.339  H183 YV3 47 
YV3 H181 H10 H 0 0 N N N N N N -21.162 -9.396  2.910  9.237   -0.948 2.083  H181 YV3 48 
YV3 H211 H11 H 0 0 N N N N N N -20.945 -14.053 5.704  4.863   0.481  2.418  H211 YV3 49 
YV3 H221 H12 H 0 0 N N N N N N -21.961 -13.902 7.945  2.461   0.733  1.952  H221 YV3 50 
YV3 H241 H13 H 0 0 N N N N N N -20.974 -14.673 10.006 1.680   3.434  0.714  H241 YV3 51 
YV3 H251 H14 H 0 0 N N N N N N -21.525 -15.913 12.076 -0.126  5.065  0.939  H251 YV3 52 
YV3 H261 H15 H 0 0 N N N N N N -22.586 -14.763 14.013 -2.399  4.520  0.176  H261 YV3 53 
YV3 H302 H16 H 0 0 N N N N N N -27.674 -11.341 13.942 -4.174  -0.031 2.685  H302 YV3 54 
YV3 H301 H17 H 0 0 N N N N N N -27.403 -12.411 12.525 -5.763  0.717  2.323  H301 YV3 55 
YV3 H322 H18 H 0 0 N N N N N N -28.811 -14.039 14.129 -5.445  -2.259 1.765  H322 YV3 56 
YV3 H321 H19 H 0 0 N N N N N N -27.623 -15.155 14.884 -5.129  -2.431 0.022  H321 YV3 57 
YV3 H332 H20 H 0 0 N N N N N N -27.521 -12.878 16.564 -7.541  -1.033 1.264  H332 YV3 58 
YV3 H331 H21 H 0 0 N N N N N N -29.266 -12.986 16.151 -7.225  -1.205 -0.479 H331 YV3 59 
YV3 H342 H22 H 0 0 N N N N N N -29.569 -14.844 17.427 -7.281  -3.673 -0.245 H342 YV3 60 
YV3 H341 H23 H 0 0 N N N N N N -28.042 -15.597 16.857 -7.597  -3.501 1.498  H341 YV3 61 
YV3 H351 H24 H 0 0 N N N N N N -26.781 -14.674 18.556 -9.693  -2.275 0.997  H351 YV3 62 
YV3 H352 H25 H 0 0 N N N N N N -27.799 -13.198 18.658 -9.377  -2.446 -0.747 H352 YV3 63 
YV3 H051 H26 H 0 0 N N N N N N -22.943 -10.169 12.132 -1.616  -0.126 -1.502 H051 YV3 64 
YV3 H1   H27 H 0 1 N N N N N N -27.979 -14.547 20.585 -10.853 -4.165 0.064  H1   YV3 65 
YV3 H362 H28 H 0 0 N N N N N N -29.414 -14.491 19.808 -9.413  -4.852 -0.405 H362 YV3 66 
YV3 H2   H30 H 0 1 N N N N N N -22.756 -7.564  9.835  0.278   -3.217 -2.277 H2   YV3 67 
# 
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 
YV3 O19 S17  DOUB N N 1  
YV3 O20 S17  DOUB N N 2  
YV3 S17 C18  SING N N 3  
YV3 S17 C16  SING N N 4  
YV3 C16 C15  SING N N 5  
YV3 C15 C21  DOUB Y N 6  
YV3 C15 C13  SING Y N 7  
YV3 F14 C13  SING N N 8  
YV3 C21 C22  SING Y N 9  
YV3 C13 C12  DOUB Y N 10 
YV3 C22 C11  DOUB Y N 11 
YV3 C12 C11  SING Y N 12 
YV3 C11 C10  SING N N 13 
YV3 O09 C07  DOUB N N 14 
YV3 C07 C06  SING N N 15 
YV3 C07 O08  SING N N 16 
YV3 C10 C06  DOUB Y N 17 
YV3 C10 C23  SING Y N 18 
YV3 C06 N05  SING Y N 19 
YV3 C23 C24  DOUB Y N 20 
YV3 C23 C04  SING Y N 21 
YV3 C24 C25  SING Y N 22 
YV3 N05 C04  SING Y N 23 
YV3 C04 C03  DOUB Y N 24 
YV3 C25 C26  DOUB Y N 25 
YV3 O29 C28  DOUB N N 26 
YV3 C03 C26  SING Y N 27 
YV3 C03 C02  SING N N 28 
YV3 C28 C30  SING N N 29 
YV3 C28 N27  SING N N 30 
YV3 C30 N31  SING N N 31 
YV3 N27 C02  SING N N 32 
YV3 N27 C37  SING N N 33 
YV3 C02 C01  SING N N 34 
YV3 N31 C37  SING N N 35 
YV3 N31 C32  SING N N 36 
YV3 C37 O38  DOUB N N 37 
YV3 C32 C33  SING N N 38 
YV3 C33 C34  SING N N 39 
YV3 C34 C35  SING N N 40 
YV3 C35 N36  SING N N 41 
YV3 C12 H121 SING N N 42 
YV3 C16 H162 SING N N 43 
YV3 C16 H161 SING N N 44 
YV3 C01 H011 SING N N 45 
YV3 C01 H012 SING N N 46 
YV3 C01 H013 SING N N 47 
YV3 C02 H021 SING N N 48 
YV3 C18 H182 SING N N 49 
YV3 C18 H183 SING N N 50 
YV3 C18 H181 SING N N 51 
YV3 C21 H211 SING N N 52 
YV3 C22 H221 SING N N 53 
YV3 C24 H241 SING N N 54 
YV3 C25 H251 SING N N 55 
YV3 C26 H261 SING N N 56 
YV3 C30 H302 SING N N 57 
YV3 C30 H301 SING N N 58 
YV3 C32 H322 SING N N 59 
YV3 C32 H321 SING N N 60 
YV3 C33 H332 SING N N 61 
YV3 C33 H331 SING N N 62 
YV3 C34 H342 SING N N 63 
YV3 C34 H341 SING N N 64 
YV3 C35 H351 SING N N 65 
YV3 C35 H352 SING N N 66 
YV3 N05 H051 SING N N 67 
YV3 N36 H1   SING N N 68 
YV3 N36 H362 SING N N 69 
YV3 O08 H2   SING N N 70 
# 
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 
YV3 InChI            InChI                1.06  "InChI=1S/C26H29FN4O6S/c1-15(31-21(32)13-30(26(31)35)11-4-3-10-28)18-6-5-7-19-22(24(25(33)34)29-23(18)19)16-8-9-17(20(27)12-16)14-38(2,36)37/h5-9,12,15,29H,3-4,10-11,13-14,28H2,1-2H3,(H,33,34)/t15-/m0/s1" 
YV3 InChIKey         InChI                1.06  CWLGVBVAKRPHNS-HNNXBMFYSA-N                                                                                                                                                                                  
YV3 SMILES_CANONICAL CACTVS               3.385 "C[C@H](N1C(=O)CN(CCCCN)C1=O)c2cccc3c2[nH]c(C(O)=O)c3c4ccc(C[S](C)(=O)=O)c(F)c4"                                                                                                                             
YV3 SMILES           CACTVS               3.385 "C[CH](N1C(=O)CN(CCCCN)C1=O)c2cccc3c2[nH]c(C(O)=O)c3c4ccc(C[S](C)(=O)=O)c(F)c4"                                                                                                                              
YV3 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@@H](c1cccc2c1[nH]c(c2c3ccc(c(c3)F)CS(=O)(=O)C)C(=O)O)N4C(=O)CN(C4=O)CCCCN"                                                                                                                              
YV3 SMILES           "OpenEye OEToolkits" 2.0.7 "CC(c1cccc2c1[nH]c(c2c3ccc(c(c3)F)CS(=O)(=O)C)C(=O)O)N4C(=O)CN(C4=O)CCCCN"                                                                                                                                   
# 
_pdbx_chem_comp_identifier.comp_id           YV3 
_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        "7-[(1~{S})-1-[3-(4-azanylbutyl)-2,5-bis(oxidanylidene)imidazolidin-1-yl]ethyl]-3-[3-fluoranyl-4-(methylsulfonylmethyl)phenyl]-1~{H}-indole-2-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 
YV3 "Create component" 2023-06-21 PDBE 
YV3 "Initial release"  2024-07-10 RCSB 
# 
