data_Y8W # _chem_comp.id Y8W _chem_comp.name "3,5-dideoxy-5-propanamido-D-glycero-D-galacto-non-2-ulosonic acid" _chem_comp.type L-saccharide _chem_comp.pdbx_type ATOMS _chem_comp.formula "C12 H21 N O9" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2023-11-28 _chem_comp.pdbx_modified_date 2026-03-13 _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 323.296 _chem_comp.one_letter_code ? _chem_comp.three_letter_code Y8W _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 8FPA _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _chem_comp.pdbx_pcm ? # 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_n_terminal_atom_flag _chem_comp_atom.pdbx_backbone_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 Y8W O7 O1 O 0 1 N N N N N N 46.854 -26.849 37.806 -1.410 2.098 -0.777 O7 Y8W 1 Y8W O8 O2 O 0 1 N N N N N N 44.274 -27.604 37.852 -2.559 -0.440 -1.483 O8 Y8W 2 Y8W O9 O3 O 0 1 N N N N N N 44.807 -24.256 38.840 -3.927 1.479 1.322 O9 Y8W 3 Y8W O6 O4 O 0 1 N N N N N N 51.409 -28.138 40.169 5.093 -0.672 -0.525 O6 Y8W 4 Y8W C12 C1 C 0 1 N N N N N N 42.819 -25.083 37.879 -5.109 0.076 -0.252 C12 Y8W 5 Y8W C11 C2 C 0 1 N N R N N N 44.365 -25.281 38.049 -3.874 0.945 -0.002 C11 Y8W 6 Y8W O5 O5 O 0 1 N N N N N N 50.870 -26.994 41.942 6.042 1.296 -0.149 O5 Y8W 7 Y8W C9 C3 C 0 1 N N R N N N 46.181 -26.759 39.001 -1.378 0.962 0.091 C9 Y8W 8 Y8W C10 C4 C 0 1 N N S N N N 44.653 -26.617 38.730 -2.612 0.094 -0.159 C10 Y8W 9 Y8W O3 O6 O 0 1 N N N N N N 49.807 -29.726 42.596 3.464 2.245 0.201 O3 Y8W 10 Y8W C8 C5 C 0 1 N N N N N N 50.713 -28.007 41.215 4.959 0.504 -0.262 C8 Y8W 11 Y8W O2 O7 O 0 1 N N N N N N 48.212 -26.987 41.104 1.113 1.474 1.415 O2 Y8W 12 Y8W C7 C6 C 0 1 N N N N N N 49.663 -29.080 41.600 3.596 1.073 -0.062 C7 Y8W 13 Y8W C6 C7 C 0 1 N N N N N N 48.407 -29.319 40.724 2.384 0.187 -0.188 C6 Y8W 14 Y8W C5 C8 C 0 1 N N S N N N 47.957 -27.992 40.123 1.120 1.013 0.063 C5 Y8W 15 Y8W C4 C9 C 0 1 N N R N N N 46.475 -28.019 39.796 -0.114 0.145 -0.187 C4 Y8W 16 Y8W N1 N1 N 0 1 N N N N N N 45.729 -27.893 41.033 -0.081 -1.019 0.702 N1 Y8W 17 Y8W O10 O8 O 0 1 N N N N N N 42.292 -25.056 39.201 -6.280 0.894 -0.221 O10 Y8W 18 Y8W C3 C10 C 0 1 N N N N N N 44.820 -28.904 41.508 0.043 -2.258 0.186 C3 Y8W 19 Y8W O1 O9 O 0 1 N N N N N N 44.678 -29.881 40.868 0.036 -2.418 -1.016 O1 Y8W 20 Y8W C2 C11 C 0 1 N N N N N N 44.062 -28.660 42.819 0.191 -3.445 1.103 C2 Y8W 21 Y8W C1 C12 C 0 1 N N N N N N 42.715 -27.936 42.560 0.312 -4.721 0.269 C1 Y8W 22 Y8W H71 H1 H 0 1 N N N N N N 47.785 -26.936 37.972 -1.416 1.874 -1.717 H71 Y8W 23 Y8W H81 H2 H 0 1 N N N N N N 44.438 -28.455 38.241 -2.538 0.232 -2.178 H81 Y8W 24 Y8W H92 H3 H 0 1 N N N N N N 45.745 -24.337 38.970 -3.949 0.807 2.017 H92 Y8W 25 Y8W H122 H4 H 0 0 N N N N N N 42.607 -24.136 37.361 -5.025 -0.402 -1.228 H122 Y8W 26 Y8W H121 H5 H 0 0 N N N N N N 42.385 -25.918 37.309 -5.178 -0.687 0.522 H121 Y8W 27 Y8W H111 H6 H 0 0 N N N N N N 44.839 -25.266 37.056 -3.853 1.762 -0.724 H111 Y8W 28 Y8W H1 H7 H 0 1 N N N N N N 51.541 -26.435 41.567 6.905 0.881 -0.287 H1 Y8W 29 Y8W H91 H8 H 0 1 N N N N N N 46.516 -25.885 39.579 -1.373 1.298 1.128 H91 Y8W 30 Y8W H101 H9 H 0 0 N N N N N N 44.106 -26.676 39.682 -2.633 -0.723 0.562 H101 Y8W 31 Y8W H21 H10 H 0 1 N N N N N N 49.140 -26.971 41.308 1.051 0.767 2.072 H21 Y8W 32 Y8W H61 H11 H 0 1 N N N N N N 47.599 -29.735 41.344 2.347 -0.238 -1.190 H61 Y8W 33 Y8W H62 H12 H 0 1 N N N N N N 48.650 -30.025 39.917 2.444 -0.617 0.546 H62 Y8W 34 Y8W H51 H13 H 0 1 N N N N N N 48.531 -27.795 39.205 1.106 1.868 -0.613 H51 Y8W 35 Y8W H41 H14 H 0 1 N N N N N N 46.204 -28.923 39.231 -0.119 -0.190 -1.224 H41 Y8W 36 Y8W H14 H15 H 0 1 N N N N N N 45.851 -27.066 41.582 -0.147 -0.898 1.662 H14 Y8W 37 Y8W H102 H16 H 0 0 N N N N N N 41.350 -24.937 39.165 -7.103 0.409 -0.372 H102 Y8W 38 Y8W H22 H17 H 0 1 N N N N N N 43.862 -29.627 43.304 1.085 -3.323 1.714 H22 Y8W 39 Y8W H23 H18 H 0 1 N N N N N N 44.682 -28.039 43.482 -0.684 -3.515 1.750 H23 Y8W 40 Y8W H12 H19 H 0 1 N N N N N N 42.195 -27.775 43.516 -0.583 -4.843 -0.341 H12 Y8W 41 Y8W H11 H20 H 0 1 N N N N N N 42.907 -26.965 42.079 1.187 -4.651 -0.378 H11 Y8W 42 Y8W H13 H21 H 0 1 N N N N N N 42.088 -28.554 41.901 0.419 -5.580 0.932 H13 Y8W 43 # 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 Y8W O7 C9 SING N N 1 Y8W O8 C10 SING N N 2 Y8W C12 C11 SING N N 3 Y8W C12 O10 SING N N 4 Y8W C11 C10 SING N N 5 Y8W C11 O9 SING N N 6 Y8W C10 C9 SING N N 7 Y8W C9 C4 SING N N 8 Y8W C4 C5 SING N N 9 Y8W C4 N1 SING N N 10 Y8W C5 C6 SING N N 11 Y8W C5 O2 SING N N 12 Y8W O6 C8 DOUB N N 13 Y8W C6 C7 SING N N 14 Y8W O1 C3 DOUB N N 15 Y8W N1 C3 SING N N 16 Y8W C8 C7 SING N N 17 Y8W C8 O5 SING N N 18 Y8W C3 C2 SING N N 19 Y8W C7 O3 DOUB N N 20 Y8W C1 C2 SING N N 21 Y8W O7 H71 SING N N 22 Y8W O8 H81 SING N N 23 Y8W O9 H92 SING N N 24 Y8W C12 H122 SING N N 25 Y8W C12 H121 SING N N 26 Y8W C11 H111 SING N N 27 Y8W O5 H1 SING N N 28 Y8W C9 H91 SING N N 29 Y8W C10 H101 SING N N 30 Y8W O2 H21 SING N N 31 Y8W C6 H61 SING N N 32 Y8W C6 H62 SING N N 33 Y8W C5 H51 SING N N 34 Y8W C4 H41 SING N N 35 Y8W N1 H14 SING N N 36 Y8W O10 H102 SING N N 37 Y8W C2 H22 SING N N 38 Y8W C2 H23 SING N N 39 Y8W C1 H12 SING N N 40 Y8W C1 H11 SING N N 41 Y8W C1 H13 SING N N 42 # 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 Y8W SMILES ACDLabs 14.52 "OC(C(NC(=O)CC)C(O)CC(=O)C(=O)O)C(O)C(O)CO" Y8W InChI InChI 1.06 "InChI=1S/C12H21NO9/c1-2-8(18)13-9(5(15)3-6(16)12(21)22)11(20)10(19)7(17)4-14/h5,7,9-11,14-15,17,19-20H,2-4H2,1H3,(H,13,18)(H,21,22)/t5-,7+,9+,10+,11+/m0/s1" Y8W InChIKey InChI 1.06 GWCTWNPFMJSTMF-GGYVPPMGSA-N Y8W SMILES_CANONICAL CACTVS 3.385 "CCC(=O)N[C@H]([C@@H](O)CC(=O)C(O)=O)[C@@H](O)[C@H](O)[C@H](O)CO" Y8W SMILES CACTVS 3.385 "CCC(=O)N[CH]([CH](O)CC(=O)C(O)=O)[CH](O)[CH](O)[CH](O)CO" Y8W SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "CCC(=O)N[C@H]([C@H](CC(=O)C(=O)O)O)[C@H]([C@@H]([C@@H](CO)O)O)O" Y8W SMILES "OpenEye OEToolkits" 3.1.0.0 "CCC(=O)NC(C(CC(=O)C(=O)O)O)C(C(C(CO)O)O)O" # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier Y8W "SYSTEMATIC NAME" ACDLabs 14.52 "3,5-dideoxy-5-propanamido-D-glycero-D-galacto-non-2-ulosonic acid" Y8W "SYSTEMATIC NAME" "OpenEye OEToolkits" 3.1.0.0 "(4~{S},5~{R},6~{R},7~{S},8~{R})-4,6,7,8,9-pentakis(oxidanyl)-2-oxidanylidene-5-(propanoylamino)nonanoic 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 Y8W "Create component" 2023-11-28 RCSB Y8W "Modify linking type" 2025-10-01 RCSB Y8W "Initial release" 2026-03-18 RCSB #