data_YVO
# 
_chem_comp.id                                    YVO 
_chem_comp.name                                  "7-[(1~{S})-1-[2-(aminomethyl)-6-oxidanylidene-5-oxa-7-azaspiro[3.4]octan-7-yl]ethyl]-3-(2-oxidanylidene-1,3-dihydroindol-5-yl)-1~{H}-indole-2-carboxylic acid" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C26 H26 N4 O5" 
_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                        474.508 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YVO 
_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        8PH0 
_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 
YVO C12  C1  C 0 1 N N N N N N -25.470 -11.415 13.510 -3.642 -1.202 -1.111 C12  YVO 1  
YVO C01  C2  C 0 1 N N N N N N -22.583 -12.614 15.784 -3.447 -3.667 0.694  C01  YVO 2  
YVO C02  C3  C 0 1 N N S N N N -23.016 -12.127 14.373 -2.678 -2.358 0.881  C02  YVO 3  
YVO C04  C4  C 0 1 N N N N N N -25.386 -13.355 14.928 -3.951 -0.076 0.860  C04  YVO 4  
YVO C05  C5  C 0 1 N N N N N N -26.883 -13.015 14.585 -4.572 0.706  -0.302 C05  YVO 5  
YVO C06  C6  C 0 1 N N N N N N -27.702 -12.651 15.776 -4.178 2.179  -0.394 C06  YVO 6  
YVO C07  C7  C 0 1 N N N N N N -28.746 -13.595 15.244 -5.627 2.449  -0.840 C07  YVO 7  
YVO C08  C8  C 0 1 N N N N N N -29.239 -14.530 16.323 -6.231 3.714  -0.226 C08  YVO 8  
YVO C10  C9  C 0 1 N N N N N N -27.802 -14.144 14.213 -6.017 1.158  -0.098 C10  YVO 9  
YVO C14  C10 C 0 1 Y N N N N N -22.562 -12.899 13.275 -1.299 -2.497 0.290  C14  YVO 10 
YVO C15  C11 C 0 1 Y N N N N N -22.343 -12.224 12.039 -0.301 -1.584 0.622  C15  YVO 11 
YVO C17  C12 C 0 1 Y N N N N N -22.189 -10.760 10.473 0.975  0.097  1.430  C17  YVO 12 
YVO C18  C13 C 0 1 N N N N N N -22.386 -9.298  9.789  1.369  1.291  2.180  C18  YVO 13 
YVO C21  C14 C 0 1 Y N N N N N -21.769 -11.917 9.917  1.800  -0.638 0.596  C21  YVO 14 
YVO C22  C15 C 0 1 Y N N N N N -21.251 -12.144 8.421  3.224  -0.371 0.300  C22  YVO 15 
YVO C23  C16 C 0 1 Y N N N N N -20.322 -11.227 7.876  4.207  -1.280 0.698  C23  YVO 16 
YVO C24  C17 C 0 1 Y N N N N N -19.867 -11.436 6.598  5.531  -1.032 0.423  C24  YVO 17 
YVO C25  C18 C 0 1 Y N N N N N -20.363 -12.585 5.886  5.905  0.129  -0.256 C25  YVO 18 
YVO C27  C19 C 0 1 N N N N N N -20.777 -14.188 4.308  7.098  1.774  -1.276 C27  YVO 19 
YVO C29  C20 C 0 1 N N N N N N -21.330 -14.571 5.430  5.637  2.163  -1.348 C29  YVO 20 
YVO C30  C21 C 0 1 Y N N N N N -21.295 -13.493 6.463  4.921  1.030  -0.650 C30  YVO 21 
YVO C31  C22 C 0 1 Y N N N N N -21.759 -13.302 7.733  3.595  0.789  -0.384 C31  YVO 22 
YVO C32  C23 C 0 1 Y N N N N N -21.846 -12.896 10.917 0.982  -1.735 0.064  C32  YVO 23 
YVO C33  C24 C 0 1 Y N N N N N -21.546 -14.285 10.981 1.242  -2.791 -0.812 C33  YVO 24 
YVO C34  C25 C 0 1 Y N N N N N -21.773 -14.962 12.215 0.247  -3.675 -1.124 C34  YVO 25 
YVO C35  C26 C 0 1 Y N N N N N -22.285 -14.270 13.348 -1.020 -3.531 -0.576 C35  YVO 26 
YVO N03  N1  N 0 1 N N N N N N -24.610 -12.292 14.320 -3.391 -1.271 0.206  N03  YVO 27 
YVO N09  N2  N 0 1 N N N N N N -30.584 -15.205 15.627 -7.562 3.949  -0.800 N09  YVO 28 
YVO N16  N3  N 0 1 Y N N N N N -22.524 -10.970 11.742 -0.281 -0.478 1.439  N16  YVO 29 
YVO N26  N4  N 0 1 N N N N N N -20.068 -13.125 4.437  7.162  0.594  -0.637 N26  YVO 30 
YVO O11  O1  O 0 1 N N N N N N -26.864 -11.991 13.613 -4.314 -0.100 -1.476 O11  YVO 31 
YVO O13  O2  O 0 1 N N N N N N -25.151 -10.508 12.863 -3.288 -2.056 -1.899 O13  YVO 32 
YVO O19  O3  O 0 1 N N N N N N -22.843 -9.304  8.586  2.507  1.712  2.099  O19  YVO 33 
YVO O20  O4  O 0 1 N N N N N N -22.296 -8.263  10.530 0.470  1.923  2.963  O20  YVO 34 
YVO O28  O5  O 0 1 N N N N N N -20.755 -14.821 3.322  8.035  2.405  -1.717 O28  YVO 35 
YVO H013 H1  H 0 0 N N N N N N -22.994 -11.938 16.548 -2.917 -4.476 1.197  H013 YVO 36 
YVO H012 H2  H 0 0 N N N N N N -22.963 -13.632 15.953 -4.445 -3.566 1.122  H012 YVO 37 
YVO H011 H3  H 0 0 N N N N N N -21.485 -12.617 15.850 -3.529 -3.892 -0.369 H011 YVO 38 
YVO H021 H4  H 0 0 N N N N N N -22.761 -11.063 14.254 -2.596 -2.133 1.944  H021 YVO 39 
YVO H041 H5  H 0 0 N N N N N N -25.104 -14.330 14.504 -3.162 0.507  1.336  H041 YVO 40 
YVO H042 H6  H 0 0 N N N N N N -25.233 -13.371 16.017 -4.713 -0.354 1.588  H042 YVO 41 
YVO H061 H7  H 0 0 N N N N N N -27.266 -12.943 16.743 -3.926 2.626  0.568  H061 YVO 42 
YVO H062 H8  H 0 0 N N N N N N -28.012 -11.596 15.818 -3.436 2.386  -1.165 H062 YVO 43 
YVO H071 H9  H 0 0 N N N N N N -29.579 -13.050 14.776 -5.769 2.394  -1.919 H071 YVO 44 
YVO H081 H10 H 0 0 N N N N N N -28.486 -15.297 16.559 -6.318 3.588  0.854  H081 YVO 45 
YVO H082 H11 H 0 0 N N N N N N -29.500 -13.978 17.238 -5.586 4.566  -0.442 H082 YVO 46 
YVO H101 H12 H 0 0 N N N N N N -28.177 -14.113 13.179 -6.746 0.549  -0.633 H101 YVO 47 
YVO H102 H13 H 0 0 N N N N N N -27.412 -15.149 14.432 -6.282 1.317  0.947  H102 YVO 48 
YVO H231 H14 H 0 0 N N N N N N -19.978 -10.381 8.453  3.926  -2.181 1.223  H231 YVO 49 
YVO H241 H15 H 0 0 N N N N N N -19.159 -10.760 6.141  6.287  -1.739 0.733  H241 YVO 50 
YVO H291 H16 H 0 0 N N N N N N -22.378 -14.844 5.235  5.465  3.101  -0.820 H291 YVO 51 
YVO H292 H17 H 0 0 N N N N N N -20.788 -15.448 5.813  5.314  2.244  -2.386 H292 YVO 52 
YVO H311 H18 H 0 0 N N N N N N -22.464 -13.978 8.193  2.842  1.498  -0.696 H311 YVO 53 
YVO H331 H19 H 0 0 N N N N N N -21.158 -14.811 10.121 2.225  -2.909 -1.242 H331 YVO 54 
YVO H341 H20 H 0 0 N N N N N N -21.553 -16.017 12.291 0.449  -4.491 -1.802 H341 YVO 55 
YVO H351 H21 H 0 0 N N N N N N -22.461 -14.805 14.270 -1.795 -4.240 -0.829 H351 YVO 56 
YVO H093 H22 H 0 0 N N N N N N -31.000 -15.853 16.265 -7.982 4.780  -0.410 H093 YVO 57 
YVO H091 H23 H 0 0 N N N N N N -31.242 -14.485 15.407 -7.517 4.005  -1.806 H091 YVO 58 
YVO H161 H25 H 0 0 N N N N N N -22.863 -10.271 12.372 -1.039 -0.149 1.947  H161 YVO 59 
YVO H261 H26 H 0 0 N N N N N N -19.455 -12.723 3.757  7.990  0.121  -0.458 H261 YVO 60 
YVO H1   H27 H 0 1 N N N N N N -22.617 -7.505  10.056 0.823  2.700  3.418  H1   YVO 61 
# 
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 
YVO O28 C27  DOUB N N 1  
YVO C27 N26  SING N N 2  
YVO C27 C29  SING N N 3  
YVO N26 C25  SING N N 4  
YVO C29 C30  SING N N 5  
YVO C25 C30  DOUB Y N 6  
YVO C25 C24  SING Y N 7  
YVO C30 C31  SING Y N 8  
YVO C24 C23  DOUB Y N 9  
YVO C31 C22  DOUB Y N 10 
YVO C23 C22  SING Y N 11 
YVO C22 C21  SING N N 12 
YVO O19 C18  DOUB N N 13 
YVO C18 C17  SING N N 14 
YVO C18 O20  SING N N 15 
YVO C21 C17  DOUB Y N 16 
YVO C21 C32  SING Y N 17 
YVO C17 N16  SING Y N 18 
YVO C32 C33  DOUB Y N 19 
YVO C32 C15  SING Y N 20 
YVO C33 C34  SING Y N 21 
YVO N16 C15  SING Y N 22 
YVO C15 C14  DOUB Y N 23 
YVO C34 C35  DOUB Y N 24 
YVO O13 C12  DOUB N N 25 
YVO C14 C35  SING Y N 26 
YVO C14 C02  SING N N 27 
YVO C12 O11  SING N N 28 
YVO C12 N03  SING N N 29 
YVO O11 C05  SING N N 30 
YVO C10 C05  SING N N 31 
YVO C10 C07  SING N N 32 
YVO N03 C02  SING N N 33 
YVO N03 C04  SING N N 34 
YVO C02 C01  SING N N 35 
YVO C05 C04  SING N N 36 
YVO C05 C06  SING N N 37 
YVO C07 C06  SING N N 38 
YVO C07 C08  SING N N 39 
YVO N09 C08  SING N N 40 
YVO C01 H013 SING N N 41 
YVO C01 H012 SING N N 42 
YVO C01 H011 SING N N 43 
YVO C02 H021 SING N N 44 
YVO C04 H041 SING N N 45 
YVO C04 H042 SING N N 46 
YVO C06 H061 SING N N 47 
YVO C06 H062 SING N N 48 
YVO C07 H071 SING N N 49 
YVO C08 H081 SING N N 50 
YVO C08 H082 SING N N 51 
YVO C10 H101 SING N N 52 
YVO C10 H102 SING N N 53 
YVO C23 H231 SING N N 54 
YVO C24 H241 SING N N 55 
YVO C29 H291 SING N N 56 
YVO C29 H292 SING N N 57 
YVO C31 H311 SING N N 58 
YVO C33 H331 SING N N 59 
YVO C34 H341 SING N N 60 
YVO C35 H351 SING N N 61 
YVO N09 H093 SING N N 62 
YVO N09 H091 SING N N 63 
YVO N16 H161 SING N N 64 
YVO N26 H261 SING N N 65 
YVO O20 H1   SING N N 66 
# 
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 
YVO InChI            InChI                1.06  "InChI=1S/C26H26N4O5/c1-13(30-12-26(35-25(30)34)9-14(10-26)11-27)17-3-2-4-18-21(23(24(32)33)29-22(17)18)15-5-6-19-16(7-15)8-20(31)28-19/h2-7,13-14,29H,8-12,27H2,1H3,(H,28,31)(H,32,33)/t13-,14-,26-/m0/s1" 
YVO InChIKey         InChI                1.06  DKNKWPRCQALROS-SYMLIENRSA-N                                                                                                                                                                                 
YVO SMILES_CANONICAL CACTVS               3.385 "C[C@H](N1C[C@@]2(C[C@H](CN)C2)OC1=O)c3cccc4c3[nH]c(C(O)=O)c4c5ccc6NC(=O)Cc6c5"                                                                                                                             
YVO SMILES           CACTVS               3.385 "C[CH](N1C[C]2(C[CH](CN)C2)OC1=O)c3cccc4c3[nH]c(C(O)=O)c4c5ccc6NC(=O)Cc6c5"                                                                                                                                 
YVO SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@@H](c1cccc2c1[nH]c(c2c3ccc4c(c3)CC(=O)N4)C(=O)O)N5CC6(CC(C6)CN)OC5=O"                                                                                                                                  
YVO SMILES           "OpenEye OEToolkits" 2.0.7 "CC(c1cccc2c1[nH]c(c2c3ccc4c(c3)CC(=O)N4)C(=O)O)N5CC6(CC(C6)CN)OC5=O"                                                                                                                                       
# 
_pdbx_chem_comp_identifier.comp_id           YVO 
_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-[2-(aminomethyl)-6-oxidanylidene-5-oxa-7-azaspiro[3.4]octan-7-yl]ethyl]-3-(2-oxidanylidene-1,3-dihydroindol-5-yl)-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 
YVO "Create component" 2023-06-21 PDBE 
YVO "Initial release"  2024-07-10 RCSB 
# 
