data_SI3 # _chem_comp.id SI3 _chem_comp.name "5-(acetylamino)-3,5-dideoxy-D-glycero-D-galacto-non-2-ulosonic acid" _chem_comp.type D-SACCHARIDE _chem_comp.pdbx_type ATOMS _chem_comp.formula "C11 H19 N O9" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "N-acetylneuraminic acid, ketone form" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2013-01-04 _chem_comp.pdbx_modified_date 2020-06-17 _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 309.270 _chem_comp.one_letter_code ? _chem_comp.three_letter_code SI3 _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 4IMF _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # # 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.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 SI3 O1A O1A O 0 1 N N N 22.588 27.935 22.882 -6.065 -1.025 -0.170 O1A SI3 1 SI3 C1 C1 C 0 1 N N N 23.819 28.116 22.628 -4.976 -0.239 -0.258 C1 SI3 2 SI3 O1B O1B O 0 1 N N N 24.060 29.006 21.863 -5.100 0.946 -0.485 O1B SI3 3 SI3 C2 C2 C 0 1 N N N 24.928 27.531 23.270 -3.617 -0.825 -0.077 C2 SI3 4 SI3 O2 O2 O 0 1 N N N 25.497 28.291 24.101 -3.494 -2.005 0.149 O2 SI3 5 SI3 C3 C3 C 0 1 N N N 25.291 26.109 22.913 -2.398 0.055 -0.176 C3 SI3 6 SI3 C4 C4 C 0 1 N N S 26.759 25.874 22.622 -1.141 -0.788 0.048 C4 SI3 7 SI3 O4 O4 O 0 1 N N N 27.421 26.321 23.833 -1.137 -1.291 1.385 O4 SI3 8 SI3 C5 C5 C 0 1 N N R 27.283 26.719 21.432 0.100 0.078 -0.175 C5 SI3 9 SI3 N5 N5 N 0 1 N N N 27.541 28.132 21.846 0.076 1.214 0.750 N5 SI3 10 SI3 C10 C10 C 0 1 N N N 27.260 29.183 21.055 -0.038 2.469 0.273 C10 SI3 11 SI3 C11 C11 C 0 1 N N N 27.332 30.571 21.660 -0.176 3.628 1.227 C11 SI3 12 SI3 O10 O10 O 0 1 N N N 26.937 28.987 19.841 -0.030 2.666 -0.923 O10 SI3 13 SI3 C6 C6 C 0 1 N N R 28.518 26.044 20.936 1.357 -0.758 0.076 C6 SI3 14 SI3 O6 O6 O 0 1 N N N 27.981 24.782 20.574 1.381 -1.865 -0.826 O6 SI3 15 SI3 C7 C7 C 0 1 N N S 29.289 26.662 19.747 2.599 0.108 -0.147 C7 SI3 16 SI3 O7 O7 O 0 1 N N N 28.305 27.053 18.807 2.549 0.684 -1.454 O7 SI3 17 SI3 C8 C8 C 0 1 N N R 30.319 25.747 19.113 3.854 -0.757 -0.018 C8 SI3 18 SI3 O8 O8 O 0 1 N N N 31.075 25.064 20.165 3.903 -1.333 1.289 O8 SI3 19 SI3 C9 C9 C 0 1 N N N 31.326 26.429 18.214 5.095 0.109 -0.241 C9 SI3 20 SI3 O9 O9 O 0 1 N N N 31.888 27.551 18.877 6.260 -0.718 -0.236 O9 SI3 21 SI3 H1 H1 H 0 1 N N N 22.068 28.566 22.398 -6.924 -0.600 -0.295 H1 SI3 22 SI3 H2 H2 H 0 1 N N N 24.717 25.825 22.019 -2.358 0.512 -1.165 H2 SI3 23 SI3 H3 H3 H 0 1 N N N 25.003 25.462 23.755 -2.451 0.836 0.583 H3 SI3 24 SI3 H4 H4 H 0 1 N N N 26.946 24.806 22.434 -1.133 -1.622 -0.654 H4 SI3 25 SI3 H5 H5 H 0 1 N N N 26.950 27.061 24.197 -1.069 -0.605 2.063 H5 SI3 26 SI3 H6 H6 H 0 1 N N N 26.522 26.709 20.637 0.108 0.446 -1.201 H6 SI3 27 SI3 H7 H7 H 0 1 N N N 27.939 28.303 22.748 0.142 1.062 1.706 H7 SI3 28 SI3 H8 H8 H 0 1 N N N 27.069 31.318 20.897 0.699 3.671 1.875 H8 SI3 29 SI3 H9 H9 H 0 1 N N N 26.626 30.641 22.501 -0.256 4.556 0.662 H9 SI3 30 SI3 H10 H10 H 0 1 N N N 28.353 30.761 22.022 -1.072 3.494 1.834 H10 SI3 31 SI3 H11 H11 H 0 1 N N N 29.219 25.925 21.775 1.350 -1.125 1.102 H11 SI3 32 SI3 H12 H12 H 0 1 N N N 27.510 24.414 21.313 1.388 -1.612 -1.760 H12 SI3 33 SI3 H13 H13 H 0 1 N N N 29.812 27.556 20.118 2.626 0.903 0.600 H13 SI3 34 SI3 H14 H14 H 0 1 N N N 27.788 27.765 19.166 2.522 0.035 -2.169 H14 SI3 35 SI3 H15 H15 H 0 1 N N N 29.784 24.993 18.517 3.826 -1.551 -0.764 H15 SI3 36 SI3 H16 H16 H 0 1 N N N 30.473 24.622 20.752 3.930 -0.683 2.005 H16 SI3 37 SI3 H17 H17 H 0 1 N N N 30.825 26.763 17.294 5.015 0.619 -1.201 H17 SI3 38 SI3 H18 H18 H 0 1 N N N 32.126 25.719 17.959 5.171 0.848 0.557 H18 SI3 39 SI3 H19 H19 H 0 1 N N N 32.519 27.973 18.306 7.087 -0.234 -0.372 H19 SI3 40 # # 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 SI3 C9 O9 SING N N 1 SI3 C9 C8 SING N N 2 SI3 O7 C7 SING N N 3 SI3 C8 C7 SING N N 4 SI3 C8 O8 SING N N 5 SI3 C7 C6 SING N N 6 SI3 O10 C10 DOUB N N 7 SI3 O6 C6 SING N N 8 SI3 C6 C5 SING N N 9 SI3 C10 C11 SING N N 10 SI3 C10 N5 SING N N 11 SI3 C5 N5 SING N N 12 SI3 C5 C4 SING N N 13 SI3 O1B C1 DOUB N N 14 SI3 C4 C3 SING N N 15 SI3 C4 O4 SING N N 16 SI3 C1 O1A SING N N 17 SI3 C1 C2 SING N N 18 SI3 C3 C2 SING N N 19 SI3 C2 O2 DOUB N N 20 SI3 O1A H1 SING N N 21 SI3 C3 H2 SING N N 22 SI3 C3 H3 SING N N 23 SI3 C4 H4 SING N N 24 SI3 O4 H5 SING N N 25 SI3 C5 H6 SING N N 26 SI3 N5 H7 SING N N 27 SI3 C11 H8 SING N N 28 SI3 C11 H9 SING N N 29 SI3 C11 H10 SING N N 30 SI3 C6 H11 SING N N 31 SI3 O6 H12 SING N N 32 SI3 C7 H13 SING N N 33 SI3 O7 H14 SING N N 34 SI3 C8 H15 SING N N 35 SI3 O8 H16 SING N N 36 SI3 C9 H17 SING N N 37 SI3 C9 H18 SING N N 38 SI3 O9 H19 SING N N 39 # # 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 SI3 SMILES ACDLabs 12.01 "O=C(O)C(=O)CC(O)C(NC(=O)C)C(O)C(O)C(O)CO" SI3 InChI InChI 1.03 "InChI=1S/C11H19NO9/c1-4(14)12-8(5(15)2-6(16)11(20)21)10(19)9(18)7(17)3-13/h5,7-10,13,15,17-19H,2-3H2,1H3,(H,12,14)(H,20,21)/t5-,7+,8+,9+,10+/m0/s1" SI3 InChIKey InChI 1.03 KBGAYAKRZNYFFG-BOHATCBPSA-N SI3 SMILES_CANONICAL CACTVS 3.370 "CC(=O)N[C@H]([C@@H](O)CC(=O)C(O)=O)[C@@H](O)[C@H](O)[C@H](O)CO" SI3 SMILES CACTVS 3.370 "CC(=O)N[CH]([CH](O)CC(=O)C(O)=O)[CH](O)[CH](O)[CH](O)CO" SI3 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CC(=O)N[C@H]([C@H](CC(=O)C(=O)O)O)[C@H]([C@@H]([C@@H](CO)O)O)O" SI3 SMILES "OpenEye OEToolkits" 1.7.6 "CC(=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 SI3 "SYSTEMATIC NAME" ACDLabs 12.01 "5-(acetylamino)-3,5-dideoxy-D-glycero-D-galacto-non-2-ulosonic acid" SI3 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(4S,5R,6R,7S,8R)-5-acetamido-4,6,7,8,9-pentakis(oxidanyl)-2-oxidanylidene-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 SI3 "Create component" 2013-01-04 RCSB SI3 "Initial release" 2013-11-06 RCSB SI3 "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id SI3 _pdbx_chem_comp_synonyms.name "N-acetylneuraminic acid, ketone form" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##