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 #