data_SIO # _chem_comp.id SIO _chem_comp.name "methyl 4,9-di-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid" _chem_comp.type "D-saccharide, alpha linking" _chem_comp.pdbx_type ATOMS _chem_comp.formula "C16 H25 N O11" _chem_comp.mon_nstd_parent_comp_id SIA _chem_comp.pdbx_synonyms ;methyl 4,9-di-O-acetyl-5-(acetylamino)-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid; methyl 4,9-di-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulosidonic acid; methyl 4,9-di-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-D-galacto-non-2-ulosidonic acid; methyl 4,9-di-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-galacto-non-2-ulosidonic acid ; _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2008-03-20 _chem_comp.pdbx_modified_date 2020-07-17 _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 407.370 _chem_comp.one_letter_code ? _chem_comp.three_letter_code SIO _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 3CL5 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # # loop_ _pdbx_chem_comp_synonyms.ordinal _pdbx_chem_comp_synonyms.comp_id _pdbx_chem_comp_synonyms.name _pdbx_chem_comp_synonyms.provenance _pdbx_chem_comp_synonyms.type 1 SIO "methyl 4,9-di-O-acetyl-5-(acetylamino)-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid" PDB ? 2 SIO "methyl 4,9-di-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulosidonic acid" PDB ? 3 SIO "methyl 4,9-di-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-D-galacto-non-2-ulosidonic acid" PDB ? 4 SIO "methyl 4,9-di-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-galacto-non-2-ulosidonic acid" PDB ? # # 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 SIO OA4 OA4 O 0 1 N N N 18.330 8.296 19.934 4.756 0.410 0.992 OA4 SIO 1 SIO CA4 CA4 C 0 1 N N N 19.494 8.417 19.588 4.709 -0.383 0.082 CA4 SIO 2 SIO CM4 CM4 C 0 1 N N N 20.592 8.711 20.553 5.961 -1.095 -0.363 CM4 SIO 3 SIO O4 O4 O 0 1 N N N 19.796 8.269 18.181 3.541 -0.634 -0.530 O4 SIO 4 SIO C4 C4 C 0 1 N N S 21.178 8.426 17.843 2.375 0.083 -0.045 C4 SIO 5 SIO C5 C5 C 0 1 N N R 21.385 9.723 17.049 1.122 -0.771 -0.260 C5 SIO 6 SIO N5 N5 N 0 1 N N N 21.358 10.775 18.063 1.223 -1.997 0.535 N5 SIO 7 SIO C10 C10 C 0 1 N N N 20.247 11.471 18.268 1.878 -3.067 0.042 C10 SIO 8 SIO O10 O10 O 0 1 N N N 19.243 11.289 17.594 2.384 -3.015 -1.059 O10 SIO 9 SIO C11 C11 C 0 1 N N N 20.303 12.517 19.358 1.982 -4.329 0.859 C11 SIO 10 SIO C3 C3 C 0 1 N N N 21.597 7.188 17.051 2.225 1.398 -0.817 C3 SIO 11 SIO C2 C2 C 0 1 N N R 22.924 7.333 16.304 0.951 2.109 -0.354 C2 SIO 12 SIO O2 O2 O 0 1 N N N 23.032 6.265 15.363 0.774 3.309 -1.110 O2 SIO 13 SIO CM2 CM2 C 0 1 N N N 24.076 6.516 14.445 0.538 3.090 -2.502 CM2 SIO 14 SIO C1 C1 C 0 1 N N N 24.078 7.265 17.284 1.068 2.449 1.109 C1 SIO 15 SIO O1B O1 O 0 1 N N N 23.907 6.642 18.350 1.323 1.482 2.004 O1B SIO 16 SIO O1A O3 O 0 1 N N N 25.168 7.823 16.998 0.932 3.592 1.477 O1A SIO 17 SIO O6 O6 O 0 1 N N N 22.934 8.567 15.579 -0.173 1.250 -0.555 O6 SIO 18 SIO C6 C6 C 0 1 N N R 22.761 9.737 16.377 -0.110 0.024 0.181 C6 SIO 19 SIO C7 C7 C 0 1 N N R 22.970 10.890 15.422 -1.371 -0.798 -0.088 C7 SIO 20 SIO O7 O7 O 0 1 N N N 21.838 11.008 14.565 -1.403 -1.185 -1.463 O7 SIO 21 SIO C8 C8 C 0 1 N N R 24.207 10.640 14.583 -2.608 0.043 0.234 C8 SIO 22 SIO O8 O8 O 0 1 N N N 25.255 10.246 15.474 -2.576 0.431 1.609 O8 SIO 23 SIO C9 C9 C 0 1 N N N 24.617 11.893 13.828 -3.869 -0.779 -0.036 C9 SIO 24 SIO O9 O9 O 0 1 N N N 24.803 12.927 14.796 -5.041 0.056 0.156 O9 SIO 25 SIO CA9 CA9 C 0 1 N N N 25.181 14.257 14.371 -6.238 -0.519 -0.043 CA9 SIO 26 SIO OA9 OA9 O 0 1 N N N 25.142 14.501 13.165 -6.304 -1.682 -0.366 OA9 SIO 27 SIO CM9 CM9 C 0 1 N N N 25.587 15.252 15.436 -7.500 0.285 0.137 CM9 SIO 28 SIO HM4 HM4 H 0 1 N N N 20.177 8.792 21.568 6.070 -2.023 0.199 HM4 SIO 29 SIO HM4A HM4A H 0 0 N N N 21.333 7.898 20.524 5.892 -1.321 -1.427 HM4A SIO 30 SIO HM4B HM4B H 0 0 N N N 21.077 9.659 20.279 6.826 -0.457 -0.182 HM4B SIO 31 SIO H4 H4 H 0 1 N N N 21.805 8.510 18.743 2.494 0.296 1.018 H4 SIO 32 SIO H5 H5 H 0 1 N N N 20.626 9.841 16.262 1.032 -1.027 -1.316 H5 SIO 33 SIO HN5 HN5 H 0 1 N N N 22.177 10.970 18.603 0.818 -2.040 1.415 HN5 SIO 34 SIO H111 H11 H 0 0 N N N 19.336 13.038 19.417 1.471 -4.188 1.812 H111 SIO 35 SIO H113 H11A H 0 0 N N N 20.516 12.031 20.322 1.518 -5.153 0.317 H113 SIO 36 SIO H112 H11B H 0 0 N N N 21.097 13.243 19.129 3.032 -4.559 1.041 H112 SIO 37 SIO H32 H3 H 0 1 N N N 21.699 6.353 17.760 3.088 2.034 -0.624 H32 SIO 38 SIO H31 H3A H 0 1 N N N 20.813 6.982 16.308 2.159 1.188 -1.884 H31 SIO 39 SIO HM2 HM2 H 0 1 N N N 24.144 5.684 13.729 -0.307 2.413 -2.625 HM2 SIO 40 SIO HM2A HM2A H 0 0 N N N 23.870 7.450 13.902 0.315 4.041 -2.987 HM2A SIO 41 SIO HM2B HM2B H 0 0 N N N 25.028 6.610 14.989 1.425 2.650 -2.956 HM2B SIO 42 SIO HO1B HO1 H 0 0 N N N 24.705 6.670 18.865 1.390 1.749 2.932 HO1B SIO 43 SIO H6 H6 H 0 1 N N N 23.472 9.811 17.213 -0.039 0.244 1.246 H6 SIO 44 SIO H7 H7 H 0 1 N N N 23.098 11.819 15.997 -1.365 -1.689 0.540 H7 SIO 45 SIO HO7 HO7 H 0 1 N Y N 21.969 11.733 13.965 -1.410 -0.442 -2.081 HO7 SIO 46 SIO H8 H8 H 0 1 N N N 24.003 9.857 13.838 -2.614 0.934 -0.394 H8 SIO 47 SIO HO8 HO8 H 0 1 N Y N 25.032 9.416 15.879 -2.568 -0.313 2.227 HO8 SIO 48 SIO H92 H9 H 0 1 N N N 25.552 11.716 13.276 -3.850 -1.149 -1.061 H92 SIO 49 SIO H91 H9A H 0 1 N N N 23.833 12.179 13.111 -3.907 -1.622 0.654 H91 SIO 50 SIO HM9 HM9 H 0 1 N N N 25.838 16.213 14.964 -7.243 1.304 0.427 HM9 SIO 51 SIO HM9A HM9A H 0 0 N N N 24.754 15.395 16.140 -8.056 0.303 -0.800 HM9A SIO 52 SIO HM9B HM9B H 0 0 N N N 26.465 14.870 15.979 -8.113 -0.170 0.915 HM9B SIO 53 # # 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 SIO CA4 OA4 DOUB N N 1 SIO O4 CA4 SING N N 2 SIO CA4 CM4 SING N N 3 SIO CM4 HM4 SING N N 4 SIO CM4 HM4A SING N N 5 SIO CM4 HM4B SING N N 6 SIO C4 O4 SING N N 7 SIO C5 C4 SING N N 8 SIO C3 C4 SING N N 9 SIO C4 H4 SING N N 10 SIO C6 C5 SING N N 11 SIO C5 N5 SING N N 12 SIO C5 H5 SING N N 13 SIO N5 C10 SING N N 14 SIO N5 HN5 SING N N 15 SIO O10 C10 DOUB N N 16 SIO C10 C11 SING N N 17 SIO C11 H111 SING N N 18 SIO C11 H113 SING N N 19 SIO C11 H112 SING N N 20 SIO C2 C3 SING N N 21 SIO C3 H32 SING N N 22 SIO C3 H31 SING N N 23 SIO O2 C2 SING N N 24 SIO O6 C2 SING N N 25 SIO C2 C1 SING N N 26 SIO CM2 O2 SING N N 27 SIO CM2 HM2 SING N N 28 SIO CM2 HM2A SING N N 29 SIO CM2 HM2B SING N N 30 SIO O1A C1 DOUB N N 31 SIO C1 O1B SING N N 32 SIO O1B HO1B SING N N 33 SIO O6 C6 SING N N 34 SIO C7 C6 SING N N 35 SIO C6 H6 SING N N 36 SIO O7 C7 SING N N 37 SIO C8 C7 SING N N 38 SIO C7 H7 SING N N 39 SIO O7 HO7 SING N N 40 SIO C9 C8 SING N N 41 SIO C8 O8 SING N N 42 SIO C8 H8 SING N N 43 SIO O8 HO8 SING N N 44 SIO C9 O9 SING N N 45 SIO C9 H92 SING N N 46 SIO C9 H91 SING N N 47 SIO CA9 O9 SING N N 48 SIO OA9 CA9 DOUB N N 49 SIO CA9 CM9 SING N N 50 SIO CM9 HM9 SING N N 51 SIO CM9 HM9A SING N N 52 SIO CM9 HM9B SING N N 53 # # 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 SIO SMILES ACDLabs 12.01 "O=C(OCC(O)C(O)C1OC(OC)(C(=O)O)CC(OC(=O)C)C1NC(=O)C)C" SIO SMILES_CANONICAL CACTVS 3.370 "CO[C@@]1(C[C@H](OC(C)=O)[C@@H](NC(C)=O)[C@@H](O1)[C@H](O)[C@H](O)COC(C)=O)C(O)=O" SIO SMILES CACTVS 3.370 "CO[C]1(C[CH](OC(C)=O)[CH](NC(C)=O)[CH](O1)[CH](O)[CH](O)COC(C)=O)C(O)=O" SIO SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "CC(=O)N[C@@H]1[C@H](C[C@@](O[C@H]1[C@@H]([C@@H](COC(=O)C)O)O)(C(=O)O)OC)OC(=O)C" SIO SMILES "OpenEye OEToolkits" 1.7.0 "CC(=O)NC1C(CC(OC1C(C(COC(=O)C)O)O)(C(=O)O)OC)OC(=O)C" SIO InChI InChI 1.03 "InChI=1S/C16H25NO11/c1-7(18)17-12-11(27-9(3)20)5-16(25-4,15(23)24)28-14(12)13(22)10(21)6-26-8(2)19/h10-14,21-22H,5-6H2,1-4H3,(H,17,18)(H,23,24)/t10-,11+,12-,13-,14-,16-/m1/s1" SIO InChIKey InChI 1.03 PJCATKAGSUTUJA-NVWMEEMDSA-N # # 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 SIO "SYSTEMATIC NAME" ACDLabs 12.01 "methyl 4,9-di-O-acetyl-5-(acetylamino)-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid" SIO "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.0 "(2R,4S,5R,6R)-5-acetamido-4-acetyloxy-6-[(1R,2R)-3-acetyloxy-1,2-dihydroxy-propyl]-2-methoxy-oxane-2-carboxylic acid" # _pdbx_chem_comp_related.comp_id SIO _pdbx_chem_comp_related.related_comp_id SIA _pdbx_chem_comp_related.relationship_type "Carbohydrate core" _pdbx_chem_comp_related.details ? # # loop_ _pdbx_chem_comp_atom_related.ordinal _pdbx_chem_comp_atom_related.comp_id _pdbx_chem_comp_atom_related.atom_id _pdbx_chem_comp_atom_related.related_comp_id _pdbx_chem_comp_atom_related.related_atom_id _pdbx_chem_comp_atom_related.related_type 1 SIO C1 SIA C1 "Carbohydrate core" 2 SIO C10 SIA C10 "Carbohydrate core" 3 SIO C11 SIA C11 "Carbohydrate core" 4 SIO C2 SIA C2 "Carbohydrate core" 5 SIO C3 SIA C3 "Carbohydrate core" 6 SIO C4 SIA C4 "Carbohydrate core" 7 SIO C5 SIA C5 "Carbohydrate core" 8 SIO C6 SIA C6 "Carbohydrate core" 9 SIO C7 SIA C7 "Carbohydrate core" 10 SIO C8 SIA C8 "Carbohydrate core" 11 SIO C9 SIA C9 "Carbohydrate core" 12 SIO N5 SIA N5 "Carbohydrate core" 13 SIO O1B SIA O1B "Carbohydrate core" 14 SIO O10 SIA O10 "Carbohydrate core" 15 SIO O2 SIA O2 "Carbohydrate core" 16 SIO O1A SIA O1A "Carbohydrate core" 17 SIO O4 SIA O4 "Carbohydrate core" 18 SIO O6 SIA O6 "Carbohydrate core" 19 SIO O7 SIA O7 "Carbohydrate core" 20 SIO O8 SIA O8 "Carbohydrate core" 21 SIO O9 SIA O9 "Carbohydrate core" 22 SIO H111 SIA H111 "Carbohydrate core" 23 SIO H113 SIA H113 "Carbohydrate core" 24 SIO H112 SIA H112 "Carbohydrate core" 25 SIO H32 SIA H32 "Carbohydrate core" 26 SIO H31 SIA H31 "Carbohydrate core" 27 SIO H4 SIA H4 "Carbohydrate core" 28 SIO H5 SIA H5 "Carbohydrate core" 29 SIO H6 SIA H6 "Carbohydrate core" 30 SIO H7 SIA H7 "Carbohydrate core" 31 SIO H8 SIA H8 "Carbohydrate core" 32 SIO H92 SIA H92 "Carbohydrate core" 33 SIO H91 SIA H91 "Carbohydrate core" 34 SIO HN5 SIA HN5 "Carbohydrate core" 35 SIO HO1B SIA HO1B "Carbohydrate core" 36 SIO HO7 SIA HO7 "Carbohydrate core" 37 SIO HO8 SIA HO8 "Carbohydrate core" # # loop_ _pdbx_chem_comp_feature.comp_id _pdbx_chem_comp_feature.type _pdbx_chem_comp_feature.value _pdbx_chem_comp_feature.source _pdbx_chem_comp_feature.support SIO "CARBOHYDRATE ISOMER" D PDB ? SIO "CARBOHYDRATE RING" pyranose PDB ? SIO "CARBOHYDRATE ANOMER" alpha PDB ? SIO "CARBOHYDRATE PRIMARY CARBONYL GROUP" ketose PDB ? # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site SIO "Create component" 2008-03-20 RCSB SIO "Modify synonyms" 2011-02-21 RCSB SIO "Modify descriptor" 2011-06-04 RCSB SIO "Other modification" 2020-07-03 RCSB SIO "Modify parent residue" 2020-07-17 RCSB SIO "Modify name" 2020-07-17 RCSB SIO "Modify synonyms" 2020-07-17 RCSB SIO "Modify linking type" 2020-07-17 RCSB SIO "Modify atom id" 2020-07-17 RCSB SIO "Modify component atom id" 2020-07-17 RCSB SIO "Modify leaving atom flag" 2020-07-17 RCSB ##