data_5N6 # _chem_comp.id 5N6 _chem_comp.name "9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid" _chem_comp.type "D-saccharide, alpha linking" _chem_comp.pdbx_type ATOMS _chem_comp.formula "C13 H21 N O10" _chem_comp.mon_nstd_parent_comp_id SIA _chem_comp.pdbx_synonyms ;(2~{R},4~{S},5~{R},6~{R})-5-acetamido-6-[(1~{R},2~{R})-3-acetyloxy-1,2-bis(oxidanyl)propyl]-2,4-bis(oxidanyl)oxane-2-ca rboxylic acid; 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulosonic acid; 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-D-galacto-non-2-ulosonic acid; 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-galacto-non-2-ulosonic acid ; _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2015-10-27 _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 351.307 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 5N6 _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 5E65 _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 5N6 ;(2~{R},4~{S},5~{R},6~{R})-5-acetamido-6-[(1~{R},2~{R})-3-acetyloxy-1,2-bis(oxidanyl)propyl]-2,4-bis(oxidanyl)oxane-2-ca rboxylic acid ; PDB ? 2 5N6 "9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulosonic acid" PDB ? 3 5N6 "9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-D-galacto-non-2-ulosonic acid" PDB ? 4 5N6 "9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-galacto-non-2-ulosonic 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 5N6 CAF CAF C 0 1 N N N -27.397 -38.640 -62.635 -6.842 0.535 -0.004 CAF 5N6 1 5N6 CAG CAG C 0 1 N N N -28.570 -38.481 -63.542 -5.600 -0.313 -0.098 CAG 5N6 2 5N6 C11 CAH C 0 1 N N N -24.362 -43.751 -64.093 2.514 -4.216 1.219 C11 5N6 3 5N6 C10 CAI C 0 1 N N N -25.150 -43.198 -65.249 2.444 -3.040 0.278 C10 5N6 4 5N6 C9 CAX C 0 1 N N N -28.444 -39.511 -65.451 -3.238 -0.629 -0.054 C9 5N6 5 5N6 C8 CAY C 0 1 N N R -27.439 -39.532 -66.541 -1.957 0.185 0.136 C8 5N6 6 5N6 C7 CAZ C 0 1 N N R -26.525 -40.681 -66.264 -0.741 -0.715 -0.094 C7 5N6 7 5N6 N5 NAB N 0 1 N N N -24.433 -42.752 -66.268 1.820 -1.908 0.659 N5 5N6 8 5N6 C5 CBA C 0 1 N N R -24.963 -42.200 -67.497 1.752 -0.766 -0.255 C5 5N6 9 5N6 C4 CBB C 0 1 N N S -23.770 -42.067 -68.414 3.026 0.074 -0.119 C4 5N6 10 5N6 C6 CBC C 0 1 N N R -25.435 -40.819 -67.296 0.540 0.100 0.097 C6 5N6 11 5N6 C3 CBD C 0 1 N N N -24.087 -41.461 -69.716 2.910 1.307 -1.022 C3 5N6 12 5N6 C2 CBE C 0 1 N N R -24.764 -40.179 -69.492 1.653 2.092 -0.641 C2 5N6 13 5N6 C1 CBF C 0 1 N N N -23.771 -39.163 -68.979 1.775 2.577 0.781 C1 5N6 14 5N6 OBJ OBJ O 0 1 N N N -29.694 -38.460 -63.093 -5.694 -1.500 -0.303 OBJ 5N6 15 5N6 O9 OBK O 0 1 N N N -28.258 -38.310 -64.814 -4.390 0.249 0.047 O9 5N6 16 5N6 O10 OBL O 0 1 N N N -26.359 -43.153 -65.186 2.950 -3.113 -0.821 O10 5N6 17 5N6 O7 OBW O 0 1 N N N -27.293 -41.844 -66.178 -0.780 -1.236 -1.424 O7 5N6 18 5N6 O8 OBX O 0 1 N N N -26.754 -38.354 -66.378 -1.918 0.707 1.466 O8 5N6 19 5N6 O4 OBY O 0 1 N N N -23.242 -43.304 -68.650 4.157 -0.705 -0.515 O4 5N6 20 5N6 O6 OBZ O 0 1 N N N -25.799 -40.287 -68.555 0.509 1.244 -0.759 O6 5N6 21 5N6 O1B OCA O 0 1 N N N -24.217 -38.312 -68.223 2.021 1.702 1.769 O1B 5N6 22 5N6 O1A OCB O 0 1 N N N -22.618 -39.212 -69.406 1.651 3.752 1.032 O1A 5N6 23 5N6 H1 H1 H 0 1 N N N -27.746 -38.723 -61.595 -7.722 -0.091 -0.147 H1 5N6 24 5N6 H2 H2 H 0 1 N N N -26.842 -39.549 -62.909 -6.886 1.007 0.977 H2 5N6 25 5N6 H3 H3 H 0 1 N N N -26.738 -37.765 -62.732 -6.814 1.305 -0.776 H3 5N6 26 5N6 H111 H4 H 0 0 N N N -25.051 -44.060 -63.293 3.053 -5.033 0.740 H111 5N6 27 5N6 H113 H5 H 0 0 N N N -23.778 -44.621 -64.430 3.034 -3.921 2.130 H113 5N6 28 5N6 H112 H6 H 0 0 N N N -23.680 -42.977 -63.711 1.504 -4.543 1.467 H112 5N6 29 5N6 H92 H7 H 0 1 N N N -29.462 -39.576 -65.863 -3.226 -1.100 -1.037 H92 5N6 30 5N6 H91 H8 H 0 1 N N N -28.276 -40.347 -64.756 -3.298 -1.398 0.716 H91 5N6 31 5N6 H8 H9 H 0 1 N N N -27.915 -39.627 -67.528 -1.940 1.009 -0.578 H8 5N6 32 5N6 H7 H10 H 0 1 N N N -26.042 -40.498 -65.293 -0.758 -1.538 0.620 H7 5N6 33 5N6 HN5 H11 H 0 1 N N N -23.438 -42.801 -66.182 1.415 -1.850 1.539 HN5 5N6 34 5N6 H5 H12 H 0 1 N N N -25.740 -42.839 -67.941 1.659 -1.124 -1.280 H5 5N6 35 5N6 H4 H13 H 0 1 N N N -23.026 -41.434 -67.909 3.145 0.391 0.917 H4 5N6 36 5N6 H6 H14 H 0 1 N N N -24.577 -40.239 -66.924 0.613 0.424 1.135 H6 5N6 37 5N6 H32 H15 H 0 1 N N N -24.747 -42.132 -70.285 3.789 1.939 -0.890 H32 5N6 38 5N6 H31 H16 H 0 1 N N N -23.158 -41.294 -70.281 2.841 0.991 -2.063 H31 5N6 39 5N6 HO7 H18 H 0 1 N Y N -26.821 -42.500 -65.679 -0.768 -0.558 -2.113 HO7 5N6 40 5N6 HO8 H19 H 0 1 N Y N -27.334 -37.623 -66.554 -1.930 0.029 2.155 HO8 5N6 41 5N6 HO4 H20 H 0 1 N Y N -23.027 -43.720 -67.823 4.999 -0.234 -0.454 HO4 5N6 42 5N6 HO1B H21 H 0 0 N N N -23.534 -37.687 -68.011 2.090 2.060 2.665 HO1B 5N6 43 5N6 O2 O1 O 0 1 N Y N -25.315 -39.787 -70.713 1.508 3.213 -1.515 O2 5N6 44 5N6 HO2 H17 H 0 1 N Y N -25.764 -38.957 -70.606 0.730 3.757 -1.331 HO2 5N6 45 # # 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 5N6 C3 C2 SING N N 1 5N6 C3 C4 SING N N 2 5N6 C2 C1 SING N N 3 5N6 C2 O6 SING N N 4 5N6 O1A C1 DOUB N N 5 5N6 C1 O1B SING N N 6 5N6 O4 C4 SING N N 7 5N6 O6 C6 SING N N 8 5N6 C4 C5 SING N N 9 5N6 C5 C6 SING N N 10 5N6 C5 N5 SING N N 11 5N6 C6 C7 SING N N 12 5N6 C8 O8 SING N N 13 5N6 C8 C7 SING N N 14 5N6 C8 C9 SING N N 15 5N6 N5 C10 SING N N 16 5N6 C7 O7 SING N N 17 5N6 C9 O9 SING N N 18 5N6 C10 O10 DOUB N N 19 5N6 C10 C11 SING N N 20 5N6 O9 CAG SING N N 21 5N6 CAG OBJ DOUB N N 22 5N6 CAG CAF SING N N 23 5N6 CAF H1 SING N N 24 5N6 CAF H2 SING N N 25 5N6 CAF H3 SING N N 26 5N6 C11 H111 SING N N 27 5N6 C11 H113 SING N N 28 5N6 C11 H112 SING N N 29 5N6 C9 H92 SING N N 30 5N6 C9 H91 SING N N 31 5N6 C8 H8 SING N N 32 5N6 C7 H7 SING N N 33 5N6 N5 HN5 SING N N 34 5N6 C5 H5 SING N N 35 5N6 C4 H4 SING N N 36 5N6 C6 H6 SING N N 37 5N6 C3 H32 SING N N 38 5N6 C3 H31 SING N N 39 5N6 O7 HO7 SING N N 40 5N6 O8 HO8 SING N N 41 5N6 O4 HO4 SING N N 42 5N6 O1B HO1B SING N N 43 5N6 C2 O2 SING N N 44 5N6 O2 HO2 SING N N 45 # # 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 5N6 InChI InChI 1.03 "InChI=1S/C13H21NO10/c1-5(15)14-9-7(17)3-13(22,12(20)21)24-11(9)10(19)8(18)4-23-6(2)16/h7-11,17-19,22H,3-4H2,1-2H3,(H,14,15)(H,20,21)/t7-,8+,9+,10+,11+,13+/m0/s1" 5N6 InChIKey InChI 1.03 NYWZBRWKDRMPAS-CTAKWSDESA-N 5N6 SMILES_CANONICAL CACTVS 3.385 "CC(=O)N[C@@H]1[C@@H](O)C[C@@](O)(O[C@H]1[C@H](O)[C@H](O)COC(C)=O)C(O)=O" 5N6 SMILES CACTVS 3.385 "CC(=O)N[CH]1[CH](O)C[C](O)(O[CH]1[CH](O)[CH](O)COC(C)=O)C(O)=O" 5N6 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.4 "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)O)O" 5N6 SMILES "OpenEye OEToolkits" 2.0.4 "CC(=O)NC1C(CC(OC1C(C(COC(=O)C)O)O)(C(=O)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 5N6 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.4 ;(2~{R},4~{S},5~{R},6~{R})-5-acetamido-6-[(1~{R},2~{R})-3-acetyloxy-1,2-bis(oxidanyl)propyl]-2,4-bis(oxidanyl)oxane-2-ca rboxylic acid ; 5N6 "IUPAC CARBOHYDRATE SYMBOL" PDB-CARE 1.0 a-D-Neup5Ac9Ac # _pdbx_chem_comp_related.comp_id 5N6 _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 5N6 C11 SIA C11 "Carbohydrate core" 2 5N6 C10 SIA C10 "Carbohydrate core" 3 5N6 C9 SIA C9 "Carbohydrate core" 4 5N6 C8 SIA C8 "Carbohydrate core" 5 5N6 C7 SIA C7 "Carbohydrate core" 6 5N6 C5 SIA C5 "Carbohydrate core" 7 5N6 C4 SIA C4 "Carbohydrate core" 8 5N6 C6 SIA C6 "Carbohydrate core" 9 5N6 C3 SIA C3 "Carbohydrate core" 10 5N6 C2 SIA C2 "Carbohydrate core" 11 5N6 C1 SIA C1 "Carbohydrate core" 12 5N6 N5 SIA N5 "Carbohydrate core" 13 5N6 O2 SIA O2 "Carbohydrate core" 14 5N6 O9 SIA O9 "Carbohydrate core" 15 5N6 O10 SIA O10 "Carbohydrate core" 16 5N6 O7 SIA O7 "Carbohydrate core" 17 5N6 O8 SIA O8 "Carbohydrate core" 18 5N6 O4 SIA O4 "Carbohydrate core" 19 5N6 O6 SIA O6 "Carbohydrate core" 20 5N6 O1B SIA O1B "Carbohydrate core" 21 5N6 O1A SIA O1A "Carbohydrate core" 22 5N6 H7 SIA H7 "Carbohydrate core" 23 5N6 HN5 SIA HN5 "Carbohydrate core" 24 5N6 H5 SIA H5 "Carbohydrate core" 25 5N6 H4 SIA H4 "Carbohydrate core" 26 5N6 H6 SIA H6 "Carbohydrate core" 27 5N6 H32 SIA H32 "Carbohydrate core" 28 5N6 H31 SIA H31 "Carbohydrate core" 29 5N6 HO2 SIA HO2 "Carbohydrate core" 30 5N6 HO7 SIA HO7 "Carbohydrate core" 31 5N6 HO8 SIA HO8 "Carbohydrate core" 32 5N6 HO4 SIA HO4 "Carbohydrate core" 33 5N6 HO1B SIA HO1B "Carbohydrate core" 34 5N6 H111 SIA H111 "Carbohydrate core" 35 5N6 H113 SIA H113 "Carbohydrate core" 36 5N6 H112 SIA H112 "Carbohydrate core" 37 5N6 H92 SIA H92 "Carbohydrate core" 38 5N6 H91 SIA H91 "Carbohydrate core" 39 5N6 H8 SIA H8 "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 5N6 "CARBOHYDRATE ISOMER" D PDB ? 5N6 "CARBOHYDRATE RING" pyranose PDB ? 5N6 "CARBOHYDRATE ANOMER" alpha PDB ? 5N6 "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 5N6 "Create component" 2015-10-27 RCSB 5N6 "Initial release" 2016-03-23 RCSB 5N6 "Other modification" 2020-07-03 RCSB 5N6 "Modify parent residue" 2020-07-17 RCSB 5N6 "Modify name" 2020-07-17 RCSB 5N6 "Modify synonyms" 2020-07-17 RCSB 5N6 "Modify internal type" 2020-07-17 RCSB 5N6 "Modify linking type" 2020-07-17 RCSB 5N6 "Modify atom id" 2020-07-17 RCSB 5N6 "Modify component atom id" 2020-07-17 RCSB 5N6 "Modify leaving atom flag" 2020-07-17 RCSB ##