data_PKM # _chem_comp.id PKM _chem_comp.name "4-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 ;4-O-acetyl-5-(acetylamino)-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid; 4-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulosonic acid; 4-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-D-galacto-non-2-ulosonic acid; 4-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 2019-08-14 _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 PKM _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 6TYO _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 PKM "4-O-acetyl-5-(acetylamino)-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid" PDB ? 2 PKM "4-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulosonic acid" PDB ? 3 PKM "4-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-D-galacto-non-2-ulosonic acid" PDB ? 4 PKM "4-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 PKM C1 C1 C 0 1 N N N 52.202 24.462 23.233 -0.105 -2.593 -0.726 C1 PKM 1 PKM C10 C10 C 0 1 N N N 54.139 24.939 17.355 1.521 2.825 -0.245 C10 PKM 2 PKM C11 C11 C 0 1 N N N 55.479 25.211 16.634 1.788 3.969 -1.190 C11 PKM 3 PKM O1A O1B O 0 1 N N N 52.947 23.506 23.564 -0.429 -3.730 -0.973 O1A PKM 4 PKM C2 C2 C 0 1 N N R 51.318 24.314 22.027 -0.139 -2.091 0.694 C2 PKM 5 PKM C3 C3 C 0 1 N N N 51.311 25.639 21.276 1.236 -1.531 1.070 C3 PKM 6 PKM C4 C4 C 0 1 N N S 52.527 25.839 20.406 1.558 -0.339 0.163 C4 PKM 7 PKM O4 O4 O 0 1 N N N 52.205 26.975 19.569 2.827 0.244 0.560 O4 PKM 8 PKM C5 C5 C 0 1 N N R 52.877 24.686 19.552 0.447 0.707 0.299 C5 PKM 9 PKM C6 C6 C 0 1 N N R 53.121 23.520 20.481 -0.897 0.060 -0.047 C6 PKM 10 PKM C7 C7 C 0 1 N N R 53.554 22.267 19.829 -2.019 1.083 0.144 C7 PKM 11 PKM C8 C8 C 0 1 N N R 53.503 21.128 20.906 -3.371 0.403 -0.081 C8 PKM 12 PKM C9 C9 C 0 1 N N N 54.180 19.910 20.311 -4.494 1.426 0.111 C9 PKM 13 PKM O10 O10 O 0 1 N N N 53.136 24.756 16.744 2.040 2.810 0.851 O10 PKM 14 PKM N5 N5 N 0 1 N N N 54.145 24.937 18.822 0.706 1.819 -0.619 N5 PKM 15 PKM C C C 0 1 N N N 53.100 28.064 19.650 3.931 -0.241 -0.029 C PKM 16 PKM O O O 0 1 N N N 54.173 27.922 20.156 3.840 -1.123 -0.850 O PKM 17 PKM CH3 CH3 C 0 1 N N N 52.644 29.420 19.064 5.285 0.315 0.332 CH3 PKM 18 PKM O1B O1 O 0 1 N N N 52.204 25.541 23.899 0.289 -1.777 -1.717 O1B PKM 19 PKM O6 O6 O 0 1 N N N 51.830 23.204 21.202 -1.121 -1.059 0.812 O6 PKM 20 PKM O7 O7 O 0 1 N N N 52.674 21.967 18.796 -1.964 1.607 1.472 O7 PKM 21 PKM O8 O8 O 0 1 N N N 54.138 21.507 22.096 -3.426 -0.121 -1.409 O8 PKM 22 PKM O9 O9 O 0 1 N N N 54.256 18.917 21.301 -5.759 0.767 0.016 O9 PKM 23 PKM H111 H113 H 0 0 N N N 55.319 25.200 15.546 1.048 4.752 -1.030 H111 PKM 24 PKM H113 H112 H 0 0 N N N 55.865 26.195 16.937 2.785 4.368 -1.005 H113 PKM 25 PKM H112 H111 H 0 0 N N N 56.206 24.432 16.906 1.725 3.613 -2.218 H112 PKM 26 PKM H32 H32 H 0 1 N N N 51.269 26.456 22.011 1.224 -1.205 2.110 H32 PKM 27 PKM H31 H31 H 0 1 N N N 50.416 25.674 20.638 1.992 -2.304 0.939 H31 PKM 28 PKM H4 H4 H 0 1 N N N 53.385 26.086 21.049 1.619 -0.674 -0.872 H4 PKM 29 PKM H5 H5 H 0 1 N N N 52.062 24.454 18.851 0.420 1.078 1.324 H5 PKM 30 PKM H6 H6 H 0 1 N N N 53.875 23.816 21.225 -0.883 -0.274 -1.084 H6 PKM 31 PKM H7 H7 H 0 1 N N N 54.587 22.367 19.463 -1.897 1.895 -0.572 H7 PKM 32 PKM H8 H8 H 0 1 N N N 52.447 20.887 21.097 -3.494 -0.409 0.636 H8 PKM 33 PKM H92 H92 H 0 1 N N N 53.594 19.539 19.457 -4.398 1.890 1.092 H92 PKM 34 PKM H91 H91 H 0 1 N N N 55.192 20.176 19.973 -4.423 2.191 -0.662 H91 PKM 35 PKM HN5 HN5 H 0 1 N N N 54.994 25.103 19.324 0.292 1.831 -1.496 HN5 PKM 36 PKM H14 H14 H 0 1 N N N 53.443 30.165 19.197 5.701 -0.253 1.164 H14 PKM 37 PKM H16 H16 H 0 1 N N N 52.428 29.302 17.992 5.950 0.239 -0.528 H16 PKM 38 PKM H15 H15 H 0 1 N N N 51.737 29.758 19.586 5.182 1.361 0.621 H15 PKM 39 PKM HO1B HOB1 H 0 0 N N N 52.822 25.469 24.617 0.298 -2.145 -2.611 HO1B PKM 40 PKM HO7 HO7 H 0 1 N Y N 52.946 21.162 18.371 -2.066 0.939 2.164 HO7 PKM 41 PKM HO8 HO8 H 0 1 N Y N 53.640 22.200 22.514 -3.324 0.547 -2.100 HO8 PKM 42 PKM HO9 HO9 H 0 1 N Y N 54.679 18.145 20.944 -6.517 1.356 0.127 HO9 PKM 43 PKM O2 O2 O 0 1 N Y N 49.972 23.995 22.450 -0.471 -3.168 1.572 O2 PKM 44 PKM HO2 H1 H 0 1 N Y N 49.631 24.704 22.983 -1.331 -3.572 1.392 HO2 PKM 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 PKM C11 C10 SING N N 1 PKM O10 C10 DOUB N N 2 PKM C10 N5 SING N N 3 PKM O7 C7 SING N N 4 PKM N5 C5 SING N N 5 PKM CH3 C SING N N 6 PKM C5 C4 SING N N 7 PKM C5 C6 SING N N 8 PKM O4 C SING N N 9 PKM O4 C4 SING N N 10 PKM C O DOUB N N 11 PKM C7 C6 SING N N 12 PKM C7 C8 SING N N 13 PKM C9 C8 SING N N 14 PKM C9 O9 SING N N 15 PKM C4 C3 SING N N 16 PKM C6 O6 SING N N 17 PKM C8 O8 SING N N 18 PKM O6 C2 SING N N 19 PKM C3 C2 SING N N 20 PKM C2 C1 SING N N 21 PKM C1 O1A DOUB N N 22 PKM C1 O1B SING N N 23 PKM C11 H111 SING N N 24 PKM C11 H113 SING N N 25 PKM C11 H112 SING N N 26 PKM C3 H32 SING N N 27 PKM C3 H31 SING N N 28 PKM C4 H4 SING N N 29 PKM C5 H5 SING N N 30 PKM C6 H6 SING N N 31 PKM C7 H7 SING N N 32 PKM C8 H8 SING N N 33 PKM C9 H92 SING N N 34 PKM C9 H91 SING N N 35 PKM N5 HN5 SING N N 36 PKM CH3 H14 SING N N 37 PKM CH3 H16 SING N N 38 PKM CH3 H15 SING N N 39 PKM O1B HO1B SING N N 40 PKM O7 HO7 SING N N 41 PKM O8 HO8 SING N N 42 PKM O9 HO9 SING N N 43 PKM C2 O2 SING N N 44 PKM 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 PKM SMILES ACDLabs 12.01 "C(=O)(O)C1(O)CC(OC(=O)C)C(C(O1)C(C(O)CO)O)NC(C)=O" PKM InChI InChI 1.03 "InChI=1S/C13H21NO10/c1-5(16)14-9-8(23-6(2)17)3-13(22,12(20)21)24-11(9)10(19)7(18)4-15/h7-11,15,18-19,22H,3-4H2,1-2H3,(H,14,16)(H,20,21)/t7-,8+,9-,10-,11-,13-/m1/s1" PKM InChIKey InChI 1.03 LVBIMVQYUKOENY-CYBLFPARSA-N PKM SMILES_CANONICAL CACTVS 3.385 "CC(=O)N[C@@H]1[C@H](C[C@@](O)(O[C@H]1[C@H](O)[C@H](O)CO)C(O)=O)OC(C)=O" PKM SMILES CACTVS 3.385 "CC(=O)N[CH]1[CH](C[C](O)(O[CH]1[CH](O)[CH](O)CO)C(O)=O)OC(C)=O" PKM SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(=O)N[C@@H]1[C@H](C[C@@](O[C@H]1[C@@H]([C@@H](CO)O)O)(C(=O)O)O)OC(=O)C" PKM SMILES "OpenEye OEToolkits" 2.0.7 "CC(=O)NC1C(CC(OC1C(C(CO)O)O)(C(=O)O)O)OC(=O)C" # # 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 PKM "SYSTEMATIC NAME" ACDLabs 12.01 "4-O-acetyl-5-(acetylamino)-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid" PKM "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 ;(2~{R},4~{S},5~{R},6~{R})-5-acetamido-4-acetyloxy-2-oxidanyl-6-[(1~{R},2~{R})-1,2,3-tris(oxidanyl)propyl]oxane-2-carbox ylic acid ; # _pdbx_chem_comp_related.comp_id PKM _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 PKM C1 SIA C1 "Carbohydrate core" 2 PKM C10 SIA C10 "Carbohydrate core" 3 PKM C11 SIA C11 "Carbohydrate core" 4 PKM C2 SIA C2 "Carbohydrate core" 5 PKM C3 SIA C3 "Carbohydrate core" 6 PKM C4 SIA C4 "Carbohydrate core" 7 PKM C5 SIA C5 "Carbohydrate core" 8 PKM C6 SIA C6 "Carbohydrate core" 9 PKM C7 SIA C7 "Carbohydrate core" 10 PKM C8 SIA C8 "Carbohydrate core" 11 PKM C9 SIA C9 "Carbohydrate core" 12 PKM N5 SIA N5 "Carbohydrate core" 13 PKM O1B SIA O1B "Carbohydrate core" 14 PKM O10 SIA O10 "Carbohydrate core" 15 PKM O1A SIA O1A "Carbohydrate core" 16 PKM O2 SIA O2 "Carbohydrate core" 17 PKM O4 SIA O4 "Carbohydrate core" 18 PKM O6 SIA O6 "Carbohydrate core" 19 PKM O7 SIA O7 "Carbohydrate core" 20 PKM O8 SIA O8 "Carbohydrate core" 21 PKM O9 SIA O9 "Carbohydrate core" 22 PKM HO2 SIA HO2 "Carbohydrate core" 23 PKM H112 SIA H112 "Carbohydrate core" 24 PKM H113 SIA H113 "Carbohydrate core" 25 PKM H111 SIA H111 "Carbohydrate core" 26 PKM H31 SIA H31 "Carbohydrate core" 27 PKM H32 SIA H32 "Carbohydrate core" 28 PKM H4 SIA H4 "Carbohydrate core" 29 PKM H5 SIA H5 "Carbohydrate core" 30 PKM H6 SIA H6 "Carbohydrate core" 31 PKM H7 SIA H7 "Carbohydrate core" 32 PKM H8 SIA H8 "Carbohydrate core" 33 PKM H91 SIA H91 "Carbohydrate core" 34 PKM H92 SIA H92 "Carbohydrate core" 35 PKM HN5 SIA HN5 "Carbohydrate core" 36 PKM HO7 SIA HO7 "Carbohydrate core" 37 PKM HO8 SIA HO8 "Carbohydrate core" 38 PKM HO9 SIA HO9 "Carbohydrate core" 39 PKM HO1B SIA HO1B "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 PKM "CARBOHYDRATE ISOMER" D PDB ? PKM "CARBOHYDRATE RING" pyranose PDB ? PKM "CARBOHYDRATE ANOMER" alpha PDB ? PKM "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 PKM "Create component" 2019-08-14 RCSB PKM "Initial release" 2020-02-12 RCSB PKM "Other modification" 2020-07-03 RCSB PKM "Modify name" 2020-07-17 RCSB PKM "Modify synonyms" 2020-07-17 RCSB PKM "Modify linking type" 2020-07-17 RCSB PKM "Modify atom id" 2020-07-17 RCSB PKM "Modify component atom id" 2020-07-17 RCSB PKM "Modify leaving atom flag" 2020-07-17 RCSB ##