data_KDO # _chem_comp.id KDO _chem_comp.name "3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid" _chem_comp.type "D-saccharide, alpha linking" _chem_comp.pdbx_type ATOMS _chem_comp.formula "C8 H14 O8" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ;3-deoxy-d-manno-oct-2-ulopyranosonic acid; 2-keto-3-deoxy-D-mannooctanoic acid; 3-deoxy-alpha-D-manno-oct-2-ulosonic acid; 3-deoxy-D-manno-oct-2-ulosonic acid; 3-deoxy-manno-oct-2-ulosonic acid ; _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-08 _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 238.192 _chem_comp.one_letter_code ? _chem_comp.three_letter_code KDO _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1FCP _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # # 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 KDO "3-deoxy-d-manno-oct-2-ulopyranosonic acid" PDB ? 2 KDO "2-keto-3-deoxy-D-mannooctanoic acid" PDB ? 3 KDO "3-deoxy-alpha-D-manno-oct-2-ulosonic acid" PDB ? 4 KDO "3-deoxy-D-manno-oct-2-ulosonic acid" PDB ? 5 KDO "3-deoxy-manno-oct-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 KDO C1 C1 C 0 1 N N N 54.860 65.598 52.980 1.541 -0.269 -2.261 C1 KDO 1 KDO O1A O1A O 0 1 N N N 55.576 65.023 52.137 2.364 -1.061 -1.868 O1A KDO 2 KDO O1B O1B O 0 1 N N N 53.631 65.746 52.830 1.565 0.146 -3.537 O1B KDO 3 KDO C2 C2 C 0 1 N N R 55.510 66.151 54.235 0.486 0.251 -1.319 C2 KDO 4 KDO O2 O2 O 0 1 N Y N 55.212 67.494 54.366 0.602 1.671 -1.215 O2 KDO 5 KDO C3 C3 C 0 1 N N N 54.984 65.382 55.453 -0.899 -0.108 -1.859 C3 KDO 6 KDO C4 C4 C 0 1 N N R 55.773 65.751 56.715 -1.965 0.453 -0.913 C4 KDO 7 KDO O4 O4 O 0 1 N N N 55.299 64.977 57.839 -3.257 0.001 -1.323 O4 KDO 8 KDO C5 C5 C 0 1 N N R 57.265 65.480 56.463 -1.669 -0.043 0.506 C5 KDO 9 KDO O5 O5 O 0 1 N N N 57.460 64.078 56.108 -1.845 -1.460 0.563 O5 KDO 10 KDO C6 C6 C 0 1 N N R 57.657 66.392 55.298 -0.226 0.312 0.868 C6 KDO 11 KDO O6 O6 O 0 1 N N N 56.935 65.999 54.102 0.670 -0.335 -0.032 O6 KDO 12 KDO C7 C7 C 0 1 N N R 59.159 66.381 55.058 0.068 -0.147 2.297 C7 KDO 13 KDO O7 O7 O 0 1 N N N 59.791 67.072 56.121 -0.827 0.502 3.201 O7 KDO 14 KDO C8 C8 C 0 1 N N N 59.519 67.048 53.727 1.510 0.210 2.662 C8 KDO 15 KDO O8 O8 O 0 1 N N N 59.358 68.451 53.841 1.785 -0.219 3.997 O8 KDO 16 KDO HO1B H1B H 0 0 N N N 53.085 66.184 53.472 2.242 -0.187 -4.142 HO1B KDO 17 KDO HO2 HO2 H 0 1 N Y N 55.618 67.840 55.151 1.489 1.856 -0.876 HO2 KDO 18 KDO H31 H31 H 0 1 N N N 53.888 65.532 55.593 -1.027 0.325 -2.851 H31 KDO 19 KDO H32 H32 H 0 1 N N N 54.981 64.281 55.275 -0.997 -1.192 -1.918 H32 KDO 20 KDO H4 H4 H 0 1 N N N 55.628 66.830 56.951 -1.936 1.543 -0.933 H4 KDO 21 KDO HO4 HO4 H 0 1 N Y N 55.787 65.205 58.620 -3.394 0.325 -2.223 HO4 KDO 22 KDO H5 H5 H 0 1 N N N 57.888 65.682 57.365 -2.349 0.437 1.210 H5 KDO 23 KDO HO5 HO5 H 0 1 N Y N 58.382 63.910 55.952 -2.765 -1.637 0.323 HO5 KDO 24 KDO H6 H6 H 0 1 N N N 57.377 67.438 55.562 -0.091 1.392 0.800 H6 KDO 25 KDO H7 H7 H 0 1 N N N 59.507 65.322 55.013 -0.066 -1.227 2.366 H7 KDO 26 KDO HO7 HO7 H 0 1 N Y N 60.729 67.065 55.971 -0.676 1.453 3.109 HO7 KDO 27 KDO H81 H81 H 0 1 N N N 60.540 66.768 53.378 1.645 1.289 2.593 H81 KDO 28 KDO H82 H82 H 0 1 N N N 58.938 66.625 52.873 2.193 -0.285 1.973 H82 KDO 29 KDO HO8 HO8 H 0 1 N Y N 59.581 68.864 53.015 2.701 0.024 4.186 HO8 KDO 30 # # 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 KDO C1 O1A DOUB N N 1 KDO C1 O1B SING N N 2 KDO C1 C2 SING N N 3 KDO O1B HO1B SING N N 4 KDO C2 O2 SING N N 5 KDO C2 C3 SING N N 6 KDO C2 O6 SING N N 7 KDO O2 HO2 SING N N 8 KDO C3 C4 SING N N 9 KDO C3 H31 SING N N 10 KDO C3 H32 SING N N 11 KDO C4 O4 SING N N 12 KDO C4 C5 SING N N 13 KDO C4 H4 SING N N 14 KDO O4 HO4 SING N N 15 KDO C5 O5 SING N N 16 KDO C5 C6 SING N N 17 KDO C5 H5 SING N N 18 KDO O5 HO5 SING N N 19 KDO C6 O6 SING N N 20 KDO C6 C7 SING N N 21 KDO C6 H6 SING N N 22 KDO C7 O7 SING N N 23 KDO C7 C8 SING N N 24 KDO C7 H7 SING N N 25 KDO O7 HO7 SING N N 26 KDO C8 O8 SING N N 27 KDO C8 H81 SING N N 28 KDO C8 H82 SING N N 29 KDO O8 HO8 SING N N 30 # # 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 KDO SMILES ACDLabs 10.04 "O=C(O)C1(O)OC(C(O)CO)C(O)C(O)C1" KDO SMILES_CANONICAL CACTVS 3.341 "OC[C@@H](O)[C@H]1O[C@](O)(C[C@@H](O)[C@H]1O)C(O)=O" KDO SMILES CACTVS 3.341 "OC[CH](O)[CH]1O[C](O)(C[CH](O)[CH]1O)C(O)=O" KDO SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1[C@H]([C@H]([C@H](O[C@]1(C(=O)O)O)[C@@H](CO)O)O)O" KDO SMILES "OpenEye OEToolkits" 1.5.0 "C1C(C(C(OC1(C(=O)O)O)C(CO)O)O)O" KDO InChI InChI 1.03 "InChI=1S/C8H14O8/c9-2-4(11)6-5(12)3(10)1-8(15,16-6)7(13)14/h3-6,9-12,15H,1-2H2,(H,13,14)/t3-,4-,5-,6-,8-/m1/s1" KDO InChIKey InChI 1.03 NNLZBVFSCVTSLA-HXUQBWEZSA-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 KDO "SYSTEMATIC NAME" ACDLabs 10.04 "3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid" KDO "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2R,4R,5R,6R)-6-[(1R)-1,2-dihydroxyethyl]-2,4,5-trihydroxy-oxane-2-carboxylic acid" KDO "CONDENSED IUPAC CARBOHYDRATE SYMBOL" GMML 1.0 DKdopa KDO "IUPAC CARBOHYDRATE SYMBOL" PDB-CARE 1.0 a-D-Kdop KDO "SNFG CARBOHYDRATE SYMBOL" GMML 1.0 Kdo # # 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 KDO "CARBOHYDRATE ISOMER" D PDB ? KDO "CARBOHYDRATE RING" pyranose PDB ? KDO "CARBOHYDRATE ANOMER" alpha PDB ? KDO "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 KDO "Create component" 1999-07-08 EBI KDO "Modify descriptor" 2011-06-04 RCSB KDO "Other modification" 2019-08-12 RCSB KDO "Other modification" 2019-12-19 RCSB KDO "Other modification" 2020-07-03 RCSB KDO "Modify name" 2020-07-17 RCSB KDO "Modify synonyms" 2020-07-17 RCSB KDO "Modify atom id" 2020-07-17 RCSB KDO "Modify component atom id" 2020-07-17 RCSB ##