data_KDN # _chem_comp.id KDN _chem_comp.name "deamino-beta-neuraminic acid" _chem_comp.type "D-saccharide, beta linking" _chem_comp.pdbx_type ATOMS _chem_comp.formula "C9 H16 O9" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "beta-deaminoneuraminic acid; 3-deoxy-D-glycero-beta-D-galacto-non-2-ulopyranosonic acid; sialic acid" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2008-09-18 _chem_comp.pdbx_modified_date 2020-07-17 _chem_comp.pdbx_ambiguous_flag ? _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 268.218 _chem_comp.one_letter_code ? _chem_comp.three_letter_code KDN _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 2V4C _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 KDN "beta-deaminoneuraminic acid" PDB ? 2 KDN "3-deoxy-D-glycero-beta-D-galacto-non-2-ulopyranosonic acid" PDB ? 3 KDN "sialic 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 KDN C2 C1 C 0 1 N N S 9.107 -8.937 -11.899 -1.565 0.823 -0.231 C2 KDN 1 KDN C1 C10 C 0 1 N N N 7.819 -9.212 -11.082 -2.000 2.155 0.322 C1 KDN 2 KDN C3 C2 C 0 1 N N N 10.225 -8.406 -10.978 -2.512 -0.271 0.268 C3 KDN 3 KDN C4 C3 C 0 1 N N S 11.410 -7.968 -11.858 -2.029 -1.630 -0.250 C4 KDN 4 KDN C5 C4 C 0 1 N N R 10.903 -6.928 -12.867 -0.585 -1.855 0.211 C5 KDN 5 KDN C6 C5 C 0 1 N N R 9.741 -7.529 -13.694 0.287 -0.700 -0.286 C6 KDN 6 KDN C7 C6 C 0 1 N N R 9.085 -6.560 -14.670 1.719 -0.887 0.221 C7 KDN 7 KDN C8 C7 C 0 1 N N R 7.935 -7.287 -15.400 2.561 0.329 -0.170 C8 KDN 8 KDN C9 C9 C 0 1 N N N 7.251 -6.343 -16.420 3.993 0.142 0.337 C9 KDN 9 KDN O5 O4 O 0 1 N N N 11.981 -6.506 -13.756 -0.099 -3.087 -0.327 O5 KDN 10 KDN O1A O9 O 0 1 N N N 7.423 -10.411 -11.058 -1.218 2.836 0.944 O1A KDN 11 KDN O1B O8 O 0 1 N N N 7.232 -8.200 -10.561 -3.256 2.586 0.125 O1B KDN 12 KDN O4 O3 O 0 1 N N N 12.448 -7.390 -11.051 -2.864 -2.665 0.272 O4 KDN 13 KDN O6 O5 O 0 1 N N N 8.708 -7.996 -12.811 -0.235 0.536 0.206 O6 KDN 14 KDN O7 O6 O 0 1 N N N 8.544 -5.393 -14.003 1.707 -1.020 1.643 O7 KDN 15 KDN O8 O7 O 0 1 N N N 8.416 -8.493 -16.042 2.573 0.462 -1.593 O8 KDN 16 KDN O9 O10 O 0 1 N N N 8.209 -5.841 -17.386 4.749 1.325 0.074 O9 KDN 17 KDN O2 O1 O 0 1 N Y N 9.549 -10.124 -12.547 -1.598 0.866 -1.659 O2 KDN 18 KDN H31 H21C H 0 1 N N N 9.854 -7.549 -10.397 -2.518 -0.278 1.358 H31 KDN 19 KDN H32 H22C H 0 1 N N N 10.544 -9.193 -10.278 -3.519 -0.078 -0.101 H32 KDN 20 KDN HO2 H1 H 0 1 N Y N 9.648 -9.959 -13.477 -1.020 1.538 -2.046 HO2 KDN 21 KDN H4 H3 H 0 1 N N N 11.825 -8.842 -12.381 -2.070 -1.640 -1.339 H4 KDN 22 KDN H5 H4 H 0 1 N N N 10.542 -6.047 -12.316 -0.553 -1.894 1.300 H5 KDN 23 KDN HO4 HA H 0 1 N Y N 13.227 -7.262 -11.580 -3.795 -2.581 0.024 HO4 KDN 24 KDN H6 H5 H 0 1 N N N 10.202 -8.337 -14.281 0.287 -0.687 -1.376 H6 KDN 25 KDN HO5 HB H 0 1 N Y N 11.645 -6.414 -14.640 -0.609 -3.862 -0.056 HO5 KDN 26 KDN H7 H6 H 0 1 N N N 9.858 -6.221 -15.376 2.148 -1.785 -0.225 H7 KDN 27 KDN H8 H7 H 0 1 N N N 7.182 -7.581 -14.654 2.132 1.227 0.275 H8 KDN 28 KDN HO7 HC H 0 1 N Y N 8.426 -5.582 -13.080 1.337 -0.256 2.107 HO7 KDN 29 KDN HO8 HD H 0 1 N Y N 8.521 -8.336 -16.973 2.943 -0.302 -2.057 HO8 KDN 30 KDN H91 H91C H 0 1 N N N 6.465 -6.900 -16.952 3.976 -0.048 1.410 H91 KDN 31 KDN H92 H92C H 0 1 N N N 6.821 -5.490 -15.875 4.452 -0.704 -0.175 H92 KDN 32 KDN HO1B H8 H 0 0 N N N 6.429 -8.482 -10.138 -3.488 3.447 0.500 HO1B KDN 33 KDN HO9 H10 H 0 1 N Y N 7.783 -5.731 -18.228 5.669 1.278 0.370 HO9 KDN 34 # # 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 KDN C2 C3 SING N N 1 KDN C2 O2 SING N N 2 KDN C2 O6 SING N N 3 KDN C2 C1 SING N N 4 KDN C3 C4 SING N N 5 KDN C4 C5 SING N N 6 KDN C4 O4 SING N N 7 KDN C5 C6 SING N N 8 KDN C5 O5 SING N N 9 KDN C6 C7 SING N N 10 KDN C6 O6 SING N N 11 KDN C7 C8 SING N N 12 KDN C7 O7 SING N N 13 KDN C8 O8 SING N N 14 KDN C8 C9 SING N N 15 KDN O1B C1 SING N N 16 KDN O1A C1 DOUB N N 17 KDN O9 C9 SING N N 18 KDN C3 H31 SING N N 19 KDN C3 H32 SING N N 20 KDN O2 HO2 SING N N 21 KDN C4 H4 SING N N 22 KDN C5 H5 SING N N 23 KDN O4 HO4 SING N N 24 KDN C6 H6 SING N N 25 KDN O5 HO5 SING N N 26 KDN C7 H7 SING N N 27 KDN C8 H8 SING N N 28 KDN O7 HO7 SING N N 29 KDN O8 HO8 SING N N 30 KDN C9 H91 SING N N 31 KDN C9 H92 SING N N 32 KDN O1B HO1B SING N N 33 KDN O9 HO9 SING N N 34 # # 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 KDN SMILES ACDLabs 10.04 "O=C(O)C1(O)OC(C(O)C(O)CO)C(O)C(O)C1" KDN SMILES_CANONICAL CACTVS 3.341 "OC[C@@H](O)[C@@H](O)[C@@H]1O[C@@](O)(C[C@H](O)[C@H]1O)C(O)=O" KDN SMILES CACTVS 3.341 "OC[CH](O)[CH](O)[CH]1O[C](O)(C[CH](O)[CH]1O)C(O)=O" KDN SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1[C@@H]([C@H]([C@@H](O[C@@]1(C(=O)O)O)[C@@H]([C@@H](CO)O)O)O)O" KDN SMILES "OpenEye OEToolkits" 1.5.0 "C1C(C(C(OC1(C(=O)O)O)C(C(CO)O)O)O)O" KDN InChI InChI 1.03 "InChI=1S/C9H16O9/c10-2-4(12)6(14)7-5(13)3(11)1-9(17,18-7)8(15)16/h3-7,10-14,17H,1-2H2,(H,15,16)/t3-,4+,5+,6+,7+,9-/m0/s1" KDN InChIKey InChI 1.03 CLRLHXKNIYJWAW-YOQZMRDMSA-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 KDN "SYSTEMATIC NAME" ACDLabs 10.04 "3-deoxy-D-glycero-beta-D-galacto-non-2-ulopyranosonic acid" KDN "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2S,4S,5R,6R)-2,4,5-trihydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]oxane-2-carboxylic acid" KDN "CONDENSED IUPAC CARBOHYDRATE SYMBOL" GMML 1.0 DKdnpb KDN "COMMON NAME" GMML 1.0 "2-keto-3-deoxy-b-D-nonulopyranosic acid" KDN "IUPAC CARBOHYDRATE SYMBOL" PDB-CARE 1.0 b-D-Kdnp KDN "SNFG CARBOHYDRATE SYMBOL" GMML 1.0 Kdn # # 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 KDN "CARBOHYDRATE ISOMER" D PDB ? KDN "CARBOHYDRATE RING" pyranose PDB ? KDN "CARBOHYDRATE ANOMER" beta PDB ? KDN "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 KDN "Create component" 2008-09-18 EBI KDN "Modify descriptor" 2011-06-04 RCSB KDN "Other modification" 2019-08-12 RCSB KDN "Other modification" 2019-12-19 RCSB KDN "Other modification" 2020-07-03 RCSB KDN "Modify name" 2020-07-17 RCSB KDN "Modify synonyms" 2020-07-17 RCSB KDN "Modify atom id" 2020-07-17 RCSB KDN "Modify component atom id" 2020-07-17 RCSB ##