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                    2024-09-27 
_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 
_chem_comp.pdbx_pcm                              Y 
# 
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 
SI3 O1A O1A O 0 1 N N N 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 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 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 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 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 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 N N N 26.759 25.874 22.622 -1.141 -0.788 0.048  C4  SI3 7  
SI3 O4  O4  O 0 1 N N N 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 N N N 27.283 26.719 21.432 0.100  0.078  -0.175 C5  SI3 9  
SI3 N5  N5  N 0 1 N N N 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 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 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 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 N N N 28.518 26.044 20.936 1.357  -0.758 0.076  C6  SI3 14 
SI3 O6  O6  O 0 1 N N N 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 N N N 29.289 26.662 19.747 2.599  0.108  -0.147 C7  SI3 16 
SI3 O7  O7  O 0 1 N N N 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 N N N 30.319 25.747 19.113 3.854  -0.757 -0.018 C8  SI3 18 
SI3 O8  O8  O 0 1 N N N 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 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 
SI3 "Modify PCM"       2024-09-27 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         ? 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            SI3 
_pdbx_chem_comp_pcm.modified_residue_id                LYS 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           Carbohydrate 
_pdbx_chem_comp_pcm.position                           "Amino-acid side chain" 
_pdbx_chem_comp_pcm.polypeptide_position               "Any position" 
_pdbx_chem_comp_pcm.comp_id_linking_atom               C2 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   NZ 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
