data_Y98 # _chem_comp.id Y98 _chem_comp.name "5-amino-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid" _chem_comp.type "L-saccharide, beta linking" _chem_comp.pdbx_type ATOMS _chem_comp.formula "C9 H17 N O8" _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 267.233 _chem_comp.one_letter_code ? _chem_comp.three_letter_code Y98 _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 Y98 C8 C1 C 0 1 N N R N N N 52.797 -21.063 33.968 -2.537 -0.200 -0.044 C8 Y98 1 Y98 C5 C2 C 0 1 N N R N N N 53.861 -21.947 37.544 0.833 1.660 -0.017 C5 Y98 2 Y98 C6 C3 C 0 1 N N R N N N 53.345 -22.127 36.117 -0.138 0.487 -0.174 C6 Y98 3 Y98 C2 C4 C 0 1 N N R N N N 52.117 -24.107 36.990 1.453 -1.053 0.746 C2 Y98 4 Y98 C9 C5 C 0 1 N N N N N N 51.424 -21.718 33.813 -3.973 0.301 0.119 C9 Y98 5 Y98 C3 C6 C 0 1 N N N N N N 52.750 -23.965 38.287 2.489 0.058 0.940 C3 Y98 6 Y98 C1 C7 C 0 1 N N N N N N 52.952 -25.046 36.087 1.649 -1.692 -0.604 C1 Y98 7 Y98 C4 C8 C 0 1 N N S N N N 54.011 -23.268 38.186 2.270 1.140 -0.122 C4 Y98 8 Y98 C7 C9 C 0 1 N N R N N N 53.134 -20.838 35.468 -1.574 0.989 -0.011 C7 Y98 9 Y98 N5 N1 N 0 1 N N N N N N 55.165 -21.266 37.506 0.589 2.645 -1.079 N5 Y98 10 Y98 O1A O1 O 0 1 N N N N N N 52.694 -25.106 34.837 1.811 -2.886 -0.690 O1A Y98 11 Y98 O1B O2 O 0 1 N N N N N N 53.869 -25.727 36.552 1.642 -0.935 -1.713 O1B Y98 12 Y98 O4 O3 O 0 1 N N N N N N 54.584 -23.109 39.551 3.185 2.216 0.097 O4 Y98 13 Y98 O6 O4 O 0 1 N N N N N N 52.027 -22.828 36.267 0.139 -0.497 0.824 O6 Y98 14 Y98 O7 O5 O 0 1 N N N N N N 52.053 -20.172 36.119 -1.702 1.671 1.238 O7 Y98 15 Y98 O8 O6 O 0 1 N N N N N N 52.802 -19.865 33.305 -2.410 -0.882 -1.293 O8 Y98 16 Y98 O9 O7 O 0 1 N N N N N N 51.386 -22.415 32.552 -4.861 -0.815 0.206 O9 Y98 17 Y98 O1 O8 O 0 1 N Y N N N N 50.856 -24.647 36.918 1.615 -2.039 1.768 O1 Y98 18 Y98 H81 H1 H 0 1 N N N N N N 53.554 -21.741 33.547 -2.296 -0.885 0.770 H81 Y98 19 Y98 H51 H2 H 0 1 N N N N N N 53.141 -21.339 38.111 0.685 2.128 0.956 H51 Y98 20 Y98 H61 H3 H 0 1 N N N N N N 54.045 -22.748 35.540 -0.018 0.045 -1.163 H61 Y98 21 Y98 H91 H4 H 0 1 N N N N N N 51.258 -22.430 34.635 -4.049 0.897 1.029 H91 Y98 22 Y98 H92 H5 H 0 1 N N N N N N 50.641 -20.946 33.833 -4.244 0.915 -0.740 H92 Y98 23 Y98 H32 H6 H 0 1 N N N N N N 52.081 -23.399 38.952 2.374 0.493 1.933 H32 Y98 24 Y98 H31 H7 H 0 1 N N N N N N 52.927 -24.965 38.710 3.491 -0.357 0.837 H31 Y98 25 Y98 H41 H8 H 0 1 N N N N N N 54.707 -23.872 37.585 2.433 0.716 -1.113 H41 Y98 26 Y98 H71 H9 H 0 1 N N N N N N 54.050 -20.233 35.534 -1.815 1.673 -0.825 H71 Y98 27 Y98 H53 H10 H 0 1 N N N N N N 55.506 -21.146 38.438 1.219 3.429 -0.997 H53 Y98 28 Y98 H52 H11 H 0 1 N N N N N N 55.814 -21.818 36.982 0.660 2.219 -1.991 H52 Y98 29 Y98 H2 H13 H 0 1 N N N N N N 54.274 -26.231 35.856 1.771 -1.390 -2.556 H2 Y98 30 Y98 H42 H14 H 0 1 N N N N N N 54.677 -23.963 39.957 4.115 1.957 0.045 H42 Y98 31 Y98 H72 H15 H 0 1 N N N N N N 52.268 -20.039 37.035 -1.502 1.121 2.008 H72 Y98 32 Y98 H82 H16 H 0 1 N N N N N N 53.653 -19.454 33.399 -2.609 -0.333 -2.063 H82 Y98 33 Y98 H93 H17 H 0 1 N N N N N N 50.537 -22.827 32.443 -5.791 -0.571 0.311 H93 Y98 34 Y98 H3 H18 H 0 1 N N N N N N 50.768 -25.141 36.112 0.990 -2.775 1.707 H3 Y98 35 # 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 Y98 C8 C9 SING N N 1 Y98 C8 C7 SING N N 2 Y98 C8 O8 SING N N 3 Y98 C5 C6 SING N N 4 Y98 C5 C4 SING N N 5 Y98 C5 N5 SING N N 6 Y98 C6 C7 SING N N 7 Y98 C6 O6 SING N N 8 Y98 C2 C3 SING N N 9 Y98 C2 C1 SING N N 10 Y98 C2 O6 SING N N 11 Y98 C9 O9 SING N N 12 Y98 C3 C4 SING N N 13 Y98 C1 O1A DOUB N N 14 Y98 C1 O1B SING N N 15 Y98 C4 O4 SING N N 16 Y98 C7 O7 SING N N 17 Y98 C2 O1 SING N N 18 Y98 C8 H81 SING N N 19 Y98 C5 H51 SING N N 20 Y98 C6 H61 SING N N 21 Y98 C9 H91 SING N N 22 Y98 C9 H92 SING N N 23 Y98 C3 H32 SING N N 24 Y98 C3 H31 SING N N 25 Y98 C4 H41 SING N N 26 Y98 C7 H71 SING N N 27 Y98 N5 H53 SING N N 28 Y98 N5 H52 SING N N 29 Y98 O1B H2 SING N N 30 Y98 O4 H42 SING N N 31 Y98 O7 H72 SING N N 32 Y98 O8 H82 SING N N 33 Y98 O9 H93 SING N N 34 Y98 O1 H3 SING N N 35 # 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 Y98 SMILES ACDLabs 14.52 "OC(=O)C1(O)CC(O)C(N)C(O1)C(O)C(O)CO" Y98 InChI InChI 1.06 "InChI=1S/C9H17NO8/c10-5-3(12)1-9(17,8(15)16)18-7(5)6(14)4(13)2-11/h3-7,11-14,17H,1-2,10H2,(H,15,16)/t3-,4+,5+,6+,7+,9+/m0/s1" Y98 InChIKey InChI 1.06 CERZMXAJYMMUDR-LSRLBZCKSA-N Y98 SMILES_CANONICAL CACTVS 3.385 "N[C@@H]1[C@@H](O)C[C@@](O)(O[C@H]1[C@H](O)[C@H](O)CO)C(O)=O" Y98 SMILES CACTVS 3.385 "N[CH]1[CH](O)C[C](O)(O[CH]1[CH](O)[CH](O)CO)C(O)=O" Y98 SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "C1[C@@H]([C@H]([C@@H](O[C@]1(C(=O)O)O)[C@@H]([C@@H](CO)O)O)N)O" Y98 SMILES "OpenEye OEToolkits" 3.1.0.0 "C1C(C(C(OC1(C(=O)O)O)C(C(CO)O)O)N)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 Y98 "SYSTEMATIC NAME" ACDLabs 14.52 "5-amino-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid" Y98 "SYSTEMATIC NAME" "OpenEye OEToolkits" 3.1.0.0 "(2~{R},4~{S},5~{R},6~{R})-5-azanyl-2,4-bis(oxidanyl)-6-[(1~{R},2~{R})-1,2,3-tris(oxidanyl)propyl]oxane-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 Y98 "Create component" 2023-11-28 RCSB Y98 "Modify linking type" 2025-09-30 RCSB Y98 "Initial release" 2026-03-18 RCSB #