data_YKH
# 
_chem_comp.id                                    YKH 
_chem_comp.name                                  "7-[(1~{S})-1-[2-(aminomethyl)-6-oxidanylidene-5-oxa-7-azaspiro[3.4]octan-7-yl]ethyl]-3-(6-methoxy-5-oxidanyl-pyridin-3-yl)-1~{H}-indole-2-carboxylic acid" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C24 H26 N4 O6" 
_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                        466.486 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YKH 
_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        8PGY 
_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 
YKH C13  C1  C 0 1 Y N N N N N -22.343 -12.238 11.984 -0.049 -1.431 0.648  C13  YKH 1  
YKH O25  O1  O 0 1 N N N N N N -26.847 -11.978 13.713 -4.261 -0.454 -1.344 O25  YKH 2  
YKH C26  C2  C 0 1 N N N N N N -25.529 -11.469 13.541 -3.477 -1.465 -0.940 C26  YKH 3  
YKH C29  C3  C 0 1 Y N N N N N -21.694 -14.864 12.206 0.613  -3.580 -0.985 C29  YKH 4  
YKH C31  C4  C 0 1 Y N N N N N -21.789 -12.871 10.918 1.215  -1.504 0.035  C31  YKH 5  
YKH C24  C5  C 0 1 N N N N N N -27.835 -14.195 14.266 -6.017 0.736  0.030  C24  YKH 6  
YKH C30  C6  C 0 1 Y N N N N N -21.436 -14.224 11.006 1.533  -2.591 -0.783 C30  YKH 7  
YKH C14  C7  C 0 1 Y N N N N N -22.607 -12.848 13.207 -0.971 -2.452 0.428  C14  YKH 8  
YKH C15  C8  C 0 1 N N S N N N -23.233 -12.037 14.373 -2.331 -2.394 1.074  C15  YKH 9  
YKH C01  C9  C 0 1 N N N N N N -19.884 -14.006 4.174  8.193  0.091  -0.462 C01  YKH 10 
YKH C03  C10 C 0 1 Y N N N N N -19.982 -12.682 6.120  5.899  0.692  -0.606 C03  YKH 11 
YKH C05  C11 C 0 1 Y N N N N N -21.454 -13.293 7.771  4.411  -0.710 0.464  C05  YKH 12 
YKH C06  C12 C 0 1 Y N N N N N -21.101 -12.183 8.507  3.327  0.071  0.064  C06  YKH 13 
YKH C07  C13 C 0 1 Y N N N N N -21.691 -11.932 9.861  1.950  -0.303 0.451  C07  YKH 14 
YKH C08  C14 C 0 1 Y N N N N N -22.208 -10.752 10.426 1.098  0.411  1.276  C08  YKH 15 
YKH C09  C15 C 0 1 N N N N N N -22.452 -9.375  9.842  1.413  1.685  1.926  C09  YKH 16 
YKH C16  C16 C 0 1 N N N N N N -22.630 -12.364 15.724 -2.986 -3.775 1.009  C16  YKH 17 
YKH C18  C17 C 0 1 N N N N N N -25.353 -13.468 14.727 -3.808 -0.240 0.967  C18  YKH 18 
YKH C19  C18 C 0 1 N N N N N N -26.804 -13.113 14.615 -4.545 0.402  -0.212 C19  YKH 19 
YKH C20  C19 C 0 1 N N N N N N -27.683 -12.711 15.798 -4.293 1.896  -0.416 C20  YKH 20 
YKH C21  C20 C 0 1 N N N N N N -28.823 -13.604 15.293 -5.778 2.004  -0.810 C21  YKH 21 
YKH C22  C21 C 0 1 N N N N N N -29.426 -14.561 16.330 -6.470 3.248  -0.250 C22  YKH 22 
YKH C28  C22 C 0 1 Y N N N N N -22.266 -14.196 13.295 -0.637 -3.514 -0.382 C28  YKH 23 
YKH C32  C23 C 0 1 Y N N N N N -20.130 -11.296 8.037  3.562  1.216  -0.710 C32  YKH 24 
YKH C33  C24 C 0 1 Y N N N N N -19.571 -11.559 6.808  4.869  1.524  -1.046 C33  YKH 25 
YKH N04  N1  N 0 1 Y N N N N N -20.904 -13.496 6.592  5.640  -0.381 0.123  N04  YKH 26 
YKH N12  N2  N 0 1 Y N N N N N -22.582 -10.976 11.668 -0.098 -0.270 1.384  N12  YKH 27 
YKH N17  N3  N 0 1 N N N N N N -24.637 -12.302 14.283 -3.168 -1.423 0.364  N17  YKH 28 
YKH N23  N4  N 0 1 N N N N N N -30.399 -15.421 15.649 -6.284 4.372  -1.178 N23  YKH 29 
YKH O02  O2  O 0 1 N N N N N N -19.388 -12.905 4.890  7.183  0.983  -0.936 O02  YKH 30 
YKH O10  O3  O 0 1 N N N N N N -23.043 -9.415  8.690  2.501  2.201  1.757  O10  YKH 31 
YKH O11  O4  O 0 1 N N N N N N -22.252 -8.363  10.607 0.495  2.286  2.711  O11  YKH 32 
YKH O27  O5  O 0 1 N N N N N N -25.197 -10.562 12.845 -3.083 -2.338 -1.688 O27  YKH 33 
YKH O34  O6  O 0 1 N N N N N N -18.596 -10.706 6.266  5.146  2.625  -1.795 O34  YKH 34 
YKH H291 H1  H 0 0 N N N N N N -21.446 -15.911 12.305 0.859  -4.420 -1.617 H291 YKH 35 
YKH H241 H2  H 0 0 N N N N N N -28.192 -14.153 13.227 -6.707 0.029  -0.432 H241 YKH 36 
YKH H242 H3  H 0 0 N N N N N N -27.506 -15.218 14.500 -6.253 0.940  1.074  H242 YKH 37 
YKH H301 H4  H 0 0 N N N N N N -20.983 -14.744 10.175 2.503  -2.649 -1.254 H301 YKH 38 
YKH H151 H5  H 0 0 N N N N N N -23.054 -10.971 14.170 -2.226 -2.090 2.116  H151 YKH 39 
YKH H012 H6  H 0 0 N N N N N N -19.348 -14.094 3.218  8.170  0.061  0.628  H012 YKH 40 
YKH H011 H7  H 0 0 N N N N N N -19.736 -14.923 4.763  8.009  -0.909 -0.856 H011 YKH 41 
YKH H013 H8  H 0 0 N N N N N N -20.958 -13.864 3.981  9.171  0.438  -0.795 H013 YKH 42 
YKH H051 H9  H 0 0 N N N N N N -22.179 -13.993 8.159  4.240  -1.594 1.061  H051 YKH 43 
YKH H162 H10 H 0 0 N N N N N N -23.118 -11.756 16.501 -3.970 -3.733 1.477  H162 YKH 44 
YKH H161 H11 H 0 0 N N N N N N -22.782 -13.431 15.944 -3.091 -4.079 -0.032 H161 YKH 45 
YKH H163 H12 H 0 0 N N N N N N -21.553 -12.142 15.708 -2.364 -4.497 1.537  H163 YKH 46 
YKH H181 H13 H 0 0 N N N N N N -25.118 -14.331 14.086 -3.057 0.441  1.368  H181 YKH 47 
YKH H182 H14 H 0 0 N N N N N N -25.094 -13.704 15.770 -4.511 -0.536 1.745  H182 YKH 48 
YKH H201 H15 H 0 0 N N N N N N -27.280 -13.015 16.775 -4.045 2.427  0.503  H201 YKH 49 
YKH H202 H16 H 0 0 N N N N N N -27.934 -11.640 15.822 -3.605 2.116  -1.232 H202 YKH 50 
YKH H211 H17 H 0 0 N N N N N N -29.605 -13.011 14.796 -5.958 1.862  -1.875 H211 YKH 51 
YKH H221 H18 H 0 0 N N N N N N -28.631 -15.178 16.774 -7.535 3.048  -0.131 H221 YKH 52 
YKH H222 H19 H 0 0 N N N N N N -29.928 -13.985 17.121 -6.037 3.500  0.718  H222 YKH 53 
YKH H281 H20 H 0 0 N N N N N N -22.445 -14.732 14.215 -1.354 -4.304 -0.551 H281 YKH 54 
YKH H321 H21 H 0 0 N N N N N N -19.829 -10.436 8.617  2.744  1.842  -1.035 H321 YKH 55 
YKH H121 H22 H 0 0 N N N N N N -22.985 -10.296 12.280 -0.861 0.024  1.907  H121 YKH 56 
YKH H232 H23 H 0 0 N N N N N N -30.805 -16.054 16.309 -6.619 4.138  -2.100 H232 YKH 57 
YKH H1   H24 H 0 1 N N N N N N -31.118 -14.856 15.244 -6.733 5.206  -0.830 H1   YKH 58 
YKH H2   H26 H 0 1 N N N N N N -22.614 -7.583  10.203 0.794  3.122  3.096  H2   YKH 59 
YKH H341 H27 H 0 0 N N N N N N -18.433 -9.988  6.867  5.151  2.461  -2.748 H341 YKH 60 
# 
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 
YKH C01 O02  SING N N 1  
YKH O02 C03  SING N N 2  
YKH C03 N04  DOUB Y N 3  
YKH C03 C33  SING Y N 4  
YKH O34 C33  SING N N 5  
YKH N04 C05  SING Y N 6  
YKH C33 C32  DOUB Y N 7  
YKH C05 C06  DOUB Y N 8  
YKH C32 C06  SING Y N 9  
YKH C06 C07  SING N N 10 
YKH O10 C09  DOUB N N 11 
YKH C09 C08  SING N N 12 
YKH C09 O11  SING N N 13 
YKH C07 C08  DOUB Y N 14 
YKH C07 C31  SING Y N 15 
YKH C08 N12  SING Y N 16 
YKH C31 C30  DOUB Y N 17 
YKH C31 C13  SING Y N 18 
YKH C30 C29  SING Y N 19 
YKH N12 C13  SING Y N 20 
YKH C13 C14  DOUB Y N 21 
YKH C29 C28  DOUB Y N 22 
YKH O27 C26  DOUB N N 23 
YKH C14 C28  SING Y N 24 
YKH C14 C15  SING N N 25 
YKH C26 O25  SING N N 26 
YKH C26 N17  SING N N 27 
YKH O25 C19  SING N N 28 
YKH C24 C19  SING N N 29 
YKH C24 C21  SING N N 30 
YKH N17 C15  SING N N 31 
YKH N17 C18  SING N N 32 
YKH C15 C16  SING N N 33 
YKH C19 C18  SING N N 34 
YKH C19 C20  SING N N 35 
YKH C21 C20  SING N N 36 
YKH C21 C22  SING N N 37 
YKH N23 C22  SING N N 38 
YKH C29 H291 SING N N 39 
YKH C24 H241 SING N N 40 
YKH C24 H242 SING N N 41 
YKH C30 H301 SING N N 42 
YKH C15 H151 SING N N 43 
YKH C01 H012 SING N N 44 
YKH C01 H011 SING N N 45 
YKH C01 H013 SING N N 46 
YKH C05 H051 SING N N 47 
YKH C16 H162 SING N N 48 
YKH C16 H161 SING N N 49 
YKH C16 H163 SING N N 50 
YKH C18 H181 SING N N 51 
YKH C18 H182 SING N N 52 
YKH C20 H201 SING N N 53 
YKH C20 H202 SING N N 54 
YKH C21 H211 SING N N 55 
YKH C22 H221 SING N N 56 
YKH C22 H222 SING N N 57 
YKH C28 H281 SING N N 58 
YKH C32 H321 SING N N 59 
YKH N12 H121 SING N N 60 
YKH N23 H232 SING N N 61 
YKH N23 H1   SING N N 62 
YKH O11 H2   SING N N 63 
YKH O34 H341 SING N N 64 
# 
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 
YKH InChI            InChI                1.06  "InChI=1S/C24H26N4O6/c1-12(28-11-24(34-23(28)32)7-13(8-24)9-25)15-4-3-5-16-18(20(22(30)31)27-19(15)16)14-6-17(29)21(33-2)26-10-14/h3-6,10,12-13,27,29H,7-9,11,25H2,1-2H3,(H,30,31)/t12-,13-,24-/m0/s1" 
YKH InChIKey         InChI                1.06  QWLRMDNLVJGYPL-ORPWPGRKSA-N                                                                                                                                                                            
YKH SMILES_CANONICAL CACTVS               3.385 "COc1ncc(cc1O)c2c([nH]c3c(cccc23)[C@H](C)N4C[C@]5(C[C@@H](CN)C5)OC4=O)C(O)=O"                                                                                                                          
YKH SMILES           CACTVS               3.385 "COc1ncc(cc1O)c2c([nH]c3c(cccc23)[CH](C)N4C[C]5(C[CH](CN)C5)OC4=O)C(O)=O"                                                                                                                              
YKH SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@@H](c1cccc2c1[nH]c(c2c3cc(c(nc3)OC)O)C(=O)O)N4CC5(CC(C5)CN)OC4=O"                                                                                                                                 
YKH SMILES           "OpenEye OEToolkits" 2.0.7 "CC(c1cccc2c1[nH]c(c2c3cc(c(nc3)OC)O)C(=O)O)N4CC5(CC(C5)CN)OC4=O"                                                                                                                                      
# 
_pdbx_chem_comp_identifier.comp_id           YKH 
_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-(6-methoxy-5-oxidanyl-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 
YKH "Create component" 2023-06-19 PDBE 
YKH "Initial release"  2024-07-10 RCSB 
# 
