data_KDM # _chem_comp.id KDM _chem_comp.name "deamino-alpha-neuraminic acid" _chem_comp.type "D-saccharide, alpha linking" _chem_comp.pdbx_type ATOMS _chem_comp.formula "C9 H16 O9" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ;alpha-deaminoneuraminic acid; 3-deoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid; sialic acid; (2R,4S,5R,6R)-2,4,5-TRIHYDROXY-6-[(1R,2R)-1,2,3-TRIHYDROXYPROPYL]OXANE-2-CARBOXYLIC-ACID ; _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2010-11-26 _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 268.218 _chem_comp.one_letter_code ? _chem_comp.three_letter_code KDM _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 2XZI _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 KDM "alpha-deaminoneuraminic acid" PDB ? 2 KDM "3-deoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid" PDB ? 3 KDM "sialic acid" PDB ? 4 KDM "(2R,4S,5R,6R)-2,4,5-TRIHYDROXY-6-[(1R,2R)-1,2,3-TRIHYDROXYPROPYL]OXANE-2-CARBOXYLIC-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 KDM C2 C1 C 0 1 N N R 48.268 -3.011 104.820 1.449 1.064 -0.746 C2 KDM 1 KDM C1 C10 C 0 1 N N N 47.620 -3.161 103.418 1.643 1.705 0.604 C1 KDM 2 KDM C3 C2 C 0 1 N N N 49.469 -2.039 104.778 2.487 -0.045 -0.938 C3 KDM 3 KDM C4 C3 C 0 1 N N S 49.025 -0.567 104.715 2.270 -1.126 0.125 C4 KDM 4 KDM C5 C4 C 0 1 N N R 47.931 -0.254 105.761 0.834 -1.649 0.021 C5 KDM 5 KDM C6 C5 C 0 1 N N R 46.755 -1.249 105.641 -0.140 -0.477 0.176 C6 KDM 6 KDM C7 C6 C 0 1 N N R 45.548 -1.094 106.594 -1.575 -0.982 0.013 C7 KDM 7 KDM C8 C7 C 0 1 N N R 44.411 -2.100 106.272 -2.539 0.205 0.044 C8 KDM 8 KDM C9 C9 C 0 1 N N N 43.072 -1.730 106.931 -3.975 -0.299 -0.119 C9 KDM 9 KDM O5 O4 O 0 1 N N N 47.429 1.077 105.574 0.598 -2.606 1.055 O5 KDM 10 KDM O1A O8 O 0 1 N N N 48.394 -3.202 102.429 1.804 2.900 0.688 O1A KDM 11 KDM O1B O9 O 0 1 N N N 46.367 -3.231 103.372 1.638 0.949 1.713 O1B KDM 12 KDM O4 O3 O 0 1 N N N 50.180 0.258 104.922 3.187 -2.200 -0.092 O4 KDM 13 KDM O6 O5 O 0 1 N N N 47.292 -2.600 105.823 0.136 0.506 -0.824 O6 KDM 14 KDM O7 O6 O 0 1 N N N 46.007 -1.299 107.942 -1.701 -1.666 -1.235 O7 KDM 15 KDM O8 O7 O 0 1 N N N 44.215 -2.207 104.854 -2.414 0.889 1.293 O8 KDM 16 KDM O9 O10 O 0 1 N N N 42.367 -2.924 107.314 -4.864 0.816 -0.207 O9 KDM 17 KDM O2 O1 O 0 1 N Y N 48.736 -4.299 105.251 1.609 2.049 -1.769 O2 KDM 18 KDM H31 H21C H 0 1 N N N 50.069 -2.185 105.688 2.373 -0.482 -1.931 H31 KDM 19 KDM H32 H22C H 0 1 N N N 50.049 -2.257 103.869 3.489 0.372 -0.836 H32 KDM 20 KDM HO2 H1 H 0 1 N Y N 48.839 -4.867 104.497 0.983 2.784 -1.709 HO2 KDM 21 KDM HO1B H9 H 0 0 N N N 46.087 -3.321 102.469 1.766 1.405 2.556 HO1B KDM 22 KDM H4 H3 H 0 1 N N N 48.583 -0.362 103.729 2.432 -0.701 1.115 H4 KDM 23 KDM H5 H4 H 0 1 N N N 48.386 -0.346 106.758 0.687 -2.118 -0.952 H5 KDM 24 KDM HO4 HA H 0 1 N Y N 50.593 0.440 104.086 4.117 -1.939 -0.047 HO4 KDM 25 KDM H6 H5 H 0 1 N N N 46.334 -1.033 104.648 -0.020 -0.034 1.165 H6 KDM 26 KDM HO5 HB H 0 1 N Y N 47.318 1.496 106.419 1.184 -3.375 1.020 HO5 KDM 27 KDM H7 H6 H 0 1 N N N 45.132 -0.084 106.466 -1.814 -1.666 0.828 H7 KDM 28 KDM H8 H7 H 0 1 N N N 44.736 -3.065 106.689 -2.300 0.889 -0.770 H8 KDM 29 KDM HO7 HC H 0 1 N Y N 46.956 -1.344 107.950 -1.502 -1.117 -2.006 HO7 KDM 30 KDM H91 H91C H 0 1 N N N 43.263 -1.118 107.825 -4.049 -0.896 -1.028 H91 KDM 31 KDM H92 H92C H 0 1 N N N 42.460 -1.163 106.214 -4.244 -0.912 0.742 H92 KDM 32 KDM HO8 HD H 0 1 N Y N 43.285 -2.231 104.663 -2.612 0.340 2.064 HO8 KDM 33 KDM HO9 H10 H 0 1 N Y N 42.212 -3.461 106.546 -5.794 0.570 -0.311 HO9 KDM 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 KDM C2 C1 SING N N 1 KDM C2 C3 SING N N 2 KDM C2 O6 SING N N 3 KDM C2 O2 SING N N 4 KDM C1 O1B SING N N 5 KDM C1 O1A DOUB N N 6 KDM C3 C4 SING N N 7 KDM C4 C5 SING N N 8 KDM C4 O4 SING N N 9 KDM C5 C6 SING N N 10 KDM C5 O5 SING N N 11 KDM C6 C7 SING N N 12 KDM C6 O6 SING N N 13 KDM C7 C8 SING N N 14 KDM C7 O7 SING N N 15 KDM C8 C9 SING N N 16 KDM C8 O8 SING N N 17 KDM C9 O9 SING N N 18 KDM C3 H31 SING N N 19 KDM C3 H32 SING N N 20 KDM O2 HO2 SING N N 21 KDM O1B HO1B SING N N 22 KDM C4 H4 SING N N 23 KDM C5 H5 SING N N 24 KDM O4 HO4 SING N N 25 KDM C6 H6 SING N N 26 KDM O5 HO5 SING N N 27 KDM C7 H7 SING N N 28 KDM C8 H8 SING N N 29 KDM O7 HO7 SING N N 30 KDM C9 H91 SING N N 31 KDM C9 H92 SING N N 32 KDM O8 HO8 SING N N 33 KDM 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 KDM SMILES_CANONICAL CACTVS 3.352 "OC[C@@H](O)[C@@H](O)[C@@H]1O[C@](O)(C[C@H](O)[C@H]1O)C(O)=O" KDM SMILES CACTVS 3.352 "OC[CH](O)[CH](O)[CH]1O[C](O)(C[CH](O)[CH]1O)C(O)=O" KDM SMILES_CANONICAL "OpenEye OEToolkits" 1.6.1 "C1[C@@H]([C@H]([C@@H](O[C@]1(C(=O)O)O)[C@@H]([C@@H](CO)O)O)O)O" KDM SMILES "OpenEye OEToolkits" 1.6.1 "C1C(C(C(OC1(C(=O)O)O)C(C(CO)O)O)O)O" KDM 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" KDM InChIKey InChI 1.03 CLRLHXKNIYJWAW-LSRLBZCKSA-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 KDM "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.6.1 "(2R,4S,5R,6R)-2,4,5-trihydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]oxane-2-carboxylic acid" KDM "CONDENSED IUPAC CARBOHYDRATE SYMBOL" GMML 1.0 DKdnpa KDM "COMMON NAME" GMML 1.0 "2-keto-3-deoxy-a-D-nonulopyranosic acid" KDM "IUPAC CARBOHYDRATE SYMBOL" PDB-CARE 1.0 a-D-Kdnp KDM "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 KDM "CARBOHYDRATE ISOMER" D PDB ? KDM "CARBOHYDRATE RING" pyranose PDB ? KDM "CARBOHYDRATE ANOMER" alpha PDB ? KDM "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 KDM "Create component" 2010-11-26 EBI KDM "Modify descriptor" 2011-06-04 RCSB KDM "Other modification" 2019-08-12 RCSB KDM "Other modification" 2019-12-19 RCSB KDM "Other modification" 2020-07-03 RCSB KDM "Modify name" 2020-07-17 RCSB KDM "Modify synonyms" 2020-07-17 RCSB KDM "Modify atom id" 2020-07-17 RCSB KDM "Modify component atom id" 2020-07-17 RCSB ##