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 #