data_YKO
# 
_chem_comp.id                                    YKO 
_chem_comp.name                                  "7-[(1~{S})-1-[2-(aminomethyl)-6-oxidanylidene-5-oxa-7-azaspiro[3.4]octan-7-yl]ethyl]-3-(5-fluoranyl-6-oxidanylidene-1~{H}-pyridin-3-yl)-1~{H}-indole-2-carboxylic acid" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C23 H23 F N4 O5" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-06-19 
_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                        454.451 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YKO 
_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        8PGX 
_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 
YKO C12  C1  C 0 1 N N N N N N -20.164 -12.806 6.034  -6.196 -0.793 -0.609 C12  YKO 1  
YKO C26  C2  C 0 1 N N N N N N -27.680 -12.734 15.777 4.004  -1.922 -0.477 C26  YKO 2  
YKO C27  C3  C 0 1 N N N N N N -28.791 -13.640 15.216 5.487  -2.016 -0.876 C27  YKO 3  
YKO C24  C4  C 0 1 N N N N N N -25.452 -13.417 14.883 3.514  0.178  0.963  C24  YKO 4  
YKO C30  C5  C 0 1 N N N N N N -27.847 -14.101 14.145 5.725  -0.768 -0.006 C30  YKO 5  
YKO C10  C6  C 0 1 N N N N N N -21.536 -13.313 7.872  -4.692 0.260  0.858  C10  YKO 6  
YKO C14  C7  C 0 1 N N N N N N -19.770 -11.651 6.731  -5.132 -1.212 -1.431 C14  YKO 7  
YKO C01  C8  C 0 1 N N N N N N -22.709 -12.435 15.798 2.683  3.708  1.095  C01  YKO 8  
YKO C02  C9  C 0 1 N N S N N N -23.220 -12.065 14.418 2.032  2.324  1.129  C02  YKO 9  
YKO C03  C10 C 0 1 Y N N N N N -22.631 -12.861 13.303 0.669  2.394  0.489  C03  YKO 10 
YKO C04  C11 C 0 1 Y N N N N N -22.336 -14.230 13.352 0.329  3.475  -0.292 C04  YKO 11 
YKO C05  C12 C 0 1 Y N N N N N -21.774 -14.900 12.251 -0.923 3.553  -0.888 C05  YKO 12 
YKO C06  C13 C 0 1 Y N N N N N -21.480 -14.279 11.080 -1.839 2.556  -0.707 C06  YKO 13 
YKO C07  C14 C 0 1 Y N N N N N -21.793 -12.886 10.961 -1.516 1.450  0.082  C07  YKO 14 
YKO C08  C15 C 0 1 Y N N N N N -21.653 -11.949 9.904  -2.246 0.237  0.471  C08  YKO 15 
YKO C09  C16 C 0 1 N N N N N N -21.149 -12.182 8.604  -3.624 -0.130 0.081  C09  YKO 16 
YKO C16  C17 C 0 1 N N N N N N -20.220 -11.305 7.978  -3.854 -0.886 -1.093 C16  YKO 17 
YKO C17  C18 C 0 1 Y N N N N N -22.139 -10.762 10.471 -1.389 -0.495 1.276  C17  YKO 18 
YKO C18  C19 C 0 1 N N N N N N -22.302 -9.423  9.798  -1.698 -1.784 1.894  C18  YKO 19 
YKO C22  C20 C 0 1 Y N N N N N -22.345 -12.251 12.062 -0.247 1.363  0.684  C22  YKO 20 
YKO C25  C21 C 0 1 N N N N N N -26.841 -13.042 14.581 4.249  -0.433 -0.235 C25  YKO 21 
YKO C28  C22 C 0 1 N N N N N N -29.325 -14.752 16.047 6.185  -3.272 -0.348 C28  YKO 22 
YKO C32  C23 C 0 1 N N N N N N -25.462 -11.491 13.533 3.173  1.449  -0.912 C32  YKO 23 
YKO F15  F1  F 0 1 N N N N N N -18.816 -10.823 6.172  -5.377 -1.933 -2.547 F15  YKO 24 
YKO N11  N1  N 0 1 N N N N N N -21.101 -13.519 6.635  -5.957 -0.075 0.504  N11  YKO 25 
YKO N21  N2  N 0 1 Y N N N N N -22.500 -10.930 11.740 -0.195 0.190  1.400  N21  YKO 26 
YKO N23  N3  N 0 1 N N N N N N -24.707 -12.227 14.414 2.869  1.373  0.392  N23  YKO 27 
YKO N29  N4  N 0 1 N N N N N N -30.510 -14.307 16.712 7.554  -3.331 -0.878 N29  YKO 28 
YKO O13  O1  O 0 1 N N N N N N -19.780 -13.123 4.882  -7.344 -1.079 -0.910 O13  YKO 29 
YKO O19  O2  O 0 1 N N N N N N -22.275 -8.363  10.522 -0.776 -2.403 2.661  O19  YKO 30 
YKO O20  O3  O 0 1 N N N N N N -22.678 -9.457  8.632  -2.786 -2.299 1.717  O20  YKO 31 
YKO O31  O4  O 0 1 N N N N N N -26.741 -11.998 13.597 3.959  0.451  -1.343 O31  YKO 32 
YKO O33  O5  O 0 1 N N N N N N -25.142 -10.580 12.851 2.773  2.339  -1.636 O33  YKO 33 
YKO H262 H1  H 0 0 N N N N N N -27.253 -13.082 16.729 3.316  -2.124 -1.298 H262 YKO 34 
YKO H261 H2  H 0 0 N N N N N N -27.964 -11.675 15.868 3.758  -2.477 0.429  H261 YKO 35 
YKO H271 H3  H 0 0 N N N N N N -29.605 -13.034 14.791 5.665  -1.849 -1.938 H271 YKO 36 
YKO H241 H4  H 0 0 N N N N N N -25.152 -14.320 14.331 2.767  -0.515 1.349  H241 YKO 37 
YKO H242 H5  H 0 0 N N N N N N -25.307 -13.581 15.961 4.220  0.456  1.746  H242 YKO 38 
YKO H302 H6  H 0 0 N N N N N N -28.227 -13.966 13.122 5.965  -0.999 1.032  H302 YKO 39 
YKO H301 H7  H 0 0 N N N N N N -27.494 -15.135 14.271 6.411  -0.048 -0.450 H301 YKO 40 
YKO H101 H8  H 0 0 N N N N N N -22.203 -14.032 8.324  -4.521 0.836  1.755  H101 YKO 41 
YKO H013 H9  H 0 0 N N N N N N -23.196 -11.800 16.552 2.061  4.416  1.644  H013 YKO 42 
YKO H012 H10 H 0 0 N N N N N N -22.940 -13.491 16.003 3.669  3.657  1.558  H012 YKO 43 
YKO H011 H11 H 0 0 N N N N N N -21.620 -12.283 15.839 2.783  4.038  0.061  H011 YKO 44 
YKO H021 H12 H 0 0 N N N N N N -22.989 -11.004 14.244 1.932  1.994  2.163  H021 YKO 45 
YKO H041 H13 H 0 0 N N N N N N -22.545 -14.783 14.256 1.043  4.271  -0.444 H041 YKO 46 
YKO H051 H14 H 0 0 N N N N N N -21.567 -15.956 12.341 -1.174 4.408  -1.498 H051 YKO 47 
YKO H061 H15 H 0 0 N N N N N N -21.024 -14.819 10.263 -2.811 2.623  -1.173 H061 YKO 48 
YKO H161 H16 H 0 0 N N N N N N -19.883 -10.403 8.466  -3.027 -1.199 -1.713 H161 YKO 49 
YKO H281 H17 H 0 0 N N N N N N -29.564 -15.612 15.404 6.218  -3.238 0.741  H281 YKO 50 
YKO H282 H18 H 0 0 N N N N N N -28.573 -15.050 16.793 5.633  -4.155 -0.669 H282 YKO 51 
YKO H111 H19 H 0 0 N N N N N N -21.513 -14.270 6.119  -6.700 0.206  1.061  H111 YKO 52 
YKO H211 H20 H 0 0 N N N N N N -22.829 -10.213 12.354 0.570  -0.114 1.914  H211 YKO 53 
YKO H291 H21 H 0 0 N N N N N N -30.876 -15.049 17.274 8.035  -4.152 -0.544 H291 YKO 54 
YKO H1   H22 H 0 1 N N N N N N -30.291 -13.525 17.295 7.553  -3.297 -1.887 H1   YKO 55 
YKO H2   H24 H 0 1 N N N N N N -22.589 -7.624  10.014 -1.071 -3.248 3.026  H2   YKO 56 
# 
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 
YKO O13 C12  DOUB N N 1  
YKO C12 N11  SING N N 2  
YKO C12 C14  SING N N 3  
YKO F15 C14  SING N N 4  
YKO N11 C10  SING N N 5  
YKO C14 C16  DOUB N N 6  
YKO C10 C09  DOUB N N 7  
YKO C16 C09  SING N N 8  
YKO C09 C08  SING N N 9  
YKO O20 C18  DOUB N N 10 
YKO C18 C17  SING N N 11 
YKO C18 O19  SING N N 12 
YKO C08 C17  DOUB Y N 13 
YKO C08 C07  SING Y N 14 
YKO C17 N21  SING Y N 15 
YKO C07 C06  DOUB Y N 16 
YKO C07 C22  SING Y N 17 
YKO C06 C05  SING Y N 18 
YKO N21 C22  SING Y N 19 
YKO C22 C03  DOUB Y N 20 
YKO C05 C04  DOUB Y N 21 
YKO O33 C32  DOUB N N 22 
YKO C03 C04  SING Y N 23 
YKO C03 C02  SING N N 24 
YKO C32 O31  SING N N 25 
YKO C32 N23  SING N N 26 
YKO O31 C25  SING N N 27 
YKO C30 C25  SING N N 28 
YKO C30 C27  SING N N 29 
YKO N23 C02  SING N N 30 
YKO N23 C24  SING N N 31 
YKO C02 C01  SING N N 32 
YKO C25 C24  SING N N 33 
YKO C25 C26  SING N N 34 
YKO C27 C26  SING N N 35 
YKO C27 C28  SING N N 36 
YKO C28 N29  SING N N 37 
YKO C26 H262 SING N N 38 
YKO C26 H261 SING N N 39 
YKO C27 H271 SING N N 40 
YKO C24 H241 SING N N 41 
YKO C24 H242 SING N N 42 
YKO C30 H302 SING N N 43 
YKO C30 H301 SING N N 44 
YKO C10 H101 SING N N 45 
YKO C01 H013 SING N N 46 
YKO C01 H012 SING N N 47 
YKO C01 H011 SING N N 48 
YKO C02 H021 SING N N 49 
YKO C04 H041 SING N N 50 
YKO C05 H051 SING N N 51 
YKO C06 H061 SING N N 52 
YKO C16 H161 SING N N 53 
YKO C28 H281 SING N N 54 
YKO C28 H282 SING N N 55 
YKO N11 H111 SING N N 56 
YKO N21 H211 SING N N 57 
YKO N29 H291 SING N N 58 
YKO N29 H1   SING N N 59 
YKO O19 H2   SING N N 60 
# 
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 
YKO InChI            InChI                1.06  "InChI=1S/C23H23FN4O5/c1-11(28-10-23(33-22(28)32)6-12(7-23)8-25)14-3-2-4-15-17(19(21(30)31)27-18(14)15)13-5-16(24)20(29)26-9-13/h2-5,9,11-12,27H,6-8,10,25H2,1H3,(H,26,29)(H,30,31)/t11-,12-,23-/m0/s1" 
YKO InChIKey         InChI                1.06  PWIXGVSRGNKFLQ-RSPIHXBNSA-N                                                                                                                                                                             
YKO SMILES_CANONICAL CACTVS               3.385 "C[C@H](N1C[C@@]2(C[C@H](CN)C2)OC1=O)c3cccc4c3[nH]c(C(O)=O)c4C5=CNC(=O)C(=C5)F"                                                                                                                         
YKO SMILES           CACTVS               3.385 "C[CH](N1C[C]2(C[CH](CN)C2)OC1=O)c3cccc4c3[nH]c(C(O)=O)c4C5=CNC(=O)C(=C5)F"                                                                                                                             
YKO SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@@H](c1cccc2c1[nH]c(c2C3=CNC(=O)C(=C3)F)C(=O)O)N4CC5(CC(C5)CN)OC4=O"                                                                                                                                
YKO SMILES           "OpenEye OEToolkits" 2.0.7 "CC(c1cccc2c1[nH]c(c2C3=CNC(=O)C(=C3)F)C(=O)O)N4CC5(CC(C5)CN)OC4=O"                                                                                                                                     
# 
_pdbx_chem_comp_identifier.comp_id           YKO 
_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-(5-fluoranyl-6-oxidanylidene-1~{H}-pyridin-3-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 
YKO "Create component" 2023-06-19 PDBE 
YKO "Initial release"  2024-07-10 RCSB 
# 
