data_KDB # _chem_comp.id KDB _chem_comp.name "3,4,5-trideoxy-alpha-D-erythro-oct-3-en-2-ulopyranosonic acid" _chem_comp.type "D-saccharide, alpha linking" _chem_comp.pdbx_type ATOMS _chem_comp.formula "C8 H12 O6" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ;3,4-dehydro-3,4,5-trideoxy-alpha-D-manno-oct-2-ulosonic acid; 3,4,5-trideoxy-alpha-D-erythro-oct-3-en-2-ulosonic acid; 3,4,5-trideoxy-D-erythro-oct-3-en-2-ulosonic acid; 3,4,5-trideoxy-erythro-oct-3-en-2-ulosonic acid ; _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2008-01-04 _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 204.177 _chem_comp.one_letter_code ? _chem_comp.three_letter_code KDB _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 2R1W _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 KDB "3,4-dehydro-3,4,5-trideoxy-alpha-D-manno-oct-2-ulosonic acid" PDB ? 2 KDB "3,4,5-trideoxy-alpha-D-erythro-oct-3-en-2-ulosonic acid" PDB ? 3 KDB "3,4,5-trideoxy-D-erythro-oct-3-en-2-ulosonic acid" PDB ? 4 KDB "3,4,5-trideoxy-erythro-oct-3-en-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 KDB O2 O2 O 0 1 N Y N -6.095 4.166 69.810 1.379 0.177 -1.737 O2 KDB 1 KDB C2 C2 C 0 1 N N R -5.976 4.617 71.275 1.401 -0.025 -0.322 C2 KDB 2 KDB C1 C1 C 0 1 N N N -5.540 6.103 71.282 2.450 0.866 0.292 C1 KDB 3 KDB O1B O1B O 0 1 N N N -4.599 6.402 70.541 3.747 0.676 0.001 O1B KDB 4 KDB O1A O1A O 0 1 N N N -6.140 6.906 72.054 2.124 1.751 1.048 O1A KDB 5 KDB C3 C3 C 0 1 N N N -4.977 3.848 71.931 1.733 -1.460 -0.029 C3 KDB 6 KDB C4 C4 C 0 1 N N N -5.261 3.009 73.032 0.844 -2.325 0.361 C4 KDB 7 KDB C5 C5 C 0 1 N N N -6.585 2.744 73.461 -0.601 -1.962 0.562 C5 KDB 8 KDB C6 C6 C 0 1 N N S -7.663 3.180 72.422 -0.899 -0.631 -0.135 C6 KDB 9 KDB O6 O6 O 0 1 N N N -7.270 4.489 71.940 0.122 0.303 0.224 O6 KDB 10 KDB C7 C7 C 0 1 N N R -9.112 3.257 72.926 -2.263 -0.106 0.318 C7 KDB 11 KDB O7 O7 O 0 1 N N N -9.201 4.243 73.961 -3.276 -1.055 -0.020 O7 KDB 12 KDB C8 C8 C 0 1 N N N -9.644 1.926 73.484 -2.555 1.223 -0.381 C8 KDB 13 KDB O8 O8 O 0 1 N N N -9.365 0.831 72.602 -3.773 1.771 0.128 O8 KDB 14 KDB HO2 HO2 H 0 1 N Y N -6.362 3.255 69.779 2.217 -0.023 -2.176 HO2 KDB 15 KDB H3 H3 H 0 1 N N N -3.960 3.907 71.574 2.756 -1.788 -0.147 H3 KDB 16 KDB H4 H4 H 0 1 N N N -4.440 2.554 73.565 1.155 -3.342 0.546 H4 KDB 17 KDB H51 H51 H 0 1 N N N -6.686 1.663 73.638 -1.234 -2.743 0.140 H51 KDB 18 KDB H52 H52 H 0 1 N N N -6.764 3.287 74.400 -0.806 -1.866 1.629 H52 KDB 19 KDB H6 H6 H 0 1 N N N -7.631 2.465 71.587 -0.902 -0.776 -1.215 H6 KDB 20 KDB H7 H7 H 0 1 N N N -9.752 3.553 72.082 -2.253 0.046 1.398 H7 KDB 21 KDB HO7 HO7 H 0 1 N N N -10.096 4.293 74.275 -3.342 -1.240 -0.967 HO7 KDB 22 KDB H8 H8 H 0 1 N N N -9.167 1.731 74.456 -1.738 1.919 -0.195 H8 KDB 23 KDB H8A H8A H 0 1 N N N -10.733 2.006 73.619 -2.653 1.055 -1.454 H8A KDB 24 KDB HO8 HO8 H 0 1 N N N -9.706 0.027 72.976 -4.021 2.616 -0.271 HO8 KDB 25 KDB HO1B HO1B H 0 0 N N N -4.397 7.325 70.641 4.383 1.273 0.420 HO1B KDB 26 # # 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 KDB O2 C2 SING N N 1 KDB O2 HO2 SING N N 2 KDB C2 C1 SING N N 3 KDB C2 C3 SING N N 4 KDB C2 O6 SING N N 5 KDB O1B C1 SING N N 6 KDB C1 O1A DOUB N N 7 KDB C3 C4 DOUB N N 8 KDB C3 H3 SING N N 9 KDB C4 C5 SING N N 10 KDB C4 H4 SING N N 11 KDB C6 C5 SING N N 12 KDB C5 H51 SING N N 13 KDB C5 H52 SING N N 14 KDB O6 C6 SING N N 15 KDB C6 C7 SING N N 16 KDB C6 H6 SING N N 17 KDB C7 C8 SING N N 18 KDB C7 O7 SING N N 19 KDB C7 H7 SING N N 20 KDB O7 HO7 SING N N 21 KDB O8 C8 SING N N 22 KDB C8 H8 SING N N 23 KDB C8 H8A SING N N 24 KDB O8 HO8 SING N N 25 KDB O1B HO1B SING N N 26 # # 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 KDB SMILES ACDLabs 12.01 "OC1(C(=O)O)C=CCC(C(CO)O)O1" KDB InChI InChI 1.03 "InChI=1S/C8H12O6/c9-4-5(10)6-2-1-3-8(13,14-6)7(11)12/h1,3,5-6,9-10,13H,2,4H2,(H,11,12)/t5-,6+,8-/m1/s1" KDB InChIKey InChI 1.03 ITFIFEKDEVIBCW-GKROBHDKSA-N KDB SMILES_CANONICAL CACTVS 3.385 "OC[C@@H](O)[C@@H]1CC=C[C@@](O)(O1)C(O)=O" KDB SMILES CACTVS 3.385 "OC[CH](O)[CH]1CC=C[C](O)(O1)C(O)=O" KDB SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1C=C[C@@](O[C@@H]1[C@@H](CO)O)(C(=O)O)O" KDB SMILES "OpenEye OEToolkits" 2.0.7 "C1C=CC(OC1C(CO)O)(C(=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 KDB "SYSTEMATIC NAME" ACDLabs 12.01 "3,4,5-trideoxy-alpha-D-erythro-oct-3-en-2-ulopyranosonic acid" KDB "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{S},6~{R})-2-[(1~{R})-1,2-bis(oxidanyl)ethyl]-6-oxidanyl-2,3-dihydropyran-6-carboxylic acid" # # 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 KDB "CARBOHYDRATE ISOMER" D PDB ? KDB "CARBOHYDRATE RING" dihydropyran PDB ? KDB "CARBOHYDRATE ANOMER" alpha PDB ? KDB "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 KDB "Create component" 2008-01-04 RCSB KDB "Modify descriptor" 2011-06-04 RCSB KDB "Other modification" 2020-04-11 RCSB KDB "Other modification" 2020-07-03 RCSB KDB "Modify synonyms" 2020-07-17 RCSB KDB "Modify linking type" 2020-07-17 RCSB KDB "Modify component atom id" 2020-07-17 RCSB ##