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.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _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 N N N 48.268 -3.011 104.820 1.449 1.064 -0.746 C2 KDM 1 KDM C1 C10 C 0 1 N N N 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 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 N N N 49.025 -0.567 104.715 2.270 -1.126 0.125 C4 KDM 4 KDM C5 C4 C 0 1 N N R N N N 47.931 -0.254 105.761 0.834 -1.649 0.021 C5 KDM 5 KDM C6 C5 C 0 1 N N R N N N 46.755 -1.249 105.641 -0.140 -0.477 0.176 C6 KDM 6 KDM C7 C6 C 0 1 N N R N N N 45.548 -1.094 106.594 -1.575 -0.982 0.013 C7 KDM 7 KDM C8 C7 C 0 1 N N R N N N 44.411 -2.100 106.272 -2.539 0.205 0.044 C8 KDM 8 KDM C9 C9 C 0 1 N N N 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 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 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 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 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 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 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 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 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 N N 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 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 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 N N 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 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 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 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 N N 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 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 N N 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 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 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 N N 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 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 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 N N 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 N N 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 # loop_ _pdbe_chem_comp_synonyms.comp_id _pdbe_chem_comp_synonyms.name _pdbe_chem_comp_synonyms.provenance _pdbe_chem_comp_synonyms.type KDM 'alpha-deaminoneuraminic acid' wwPDB ? KDM '3-deoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid' wwPDB ? KDM 'sialic acid' wwPDB ? KDM '(2R,4S,5R,6R)-2,4,5-TRIHYDROXY-6-[(1R,2R)-1,2,3-TRIHYDROXYPROPYL]OXANE-2-CARBOXYLIC-ACID' wwPDB ? # loop_ _software.name _software.version _software.description rdkit 2025.03.3 'Core functionality.' pdbeccdutils 1.0.0 'Wrapper to provide 2D templates and molecular fragments.' # loop_ _pdbe_chem_comp_atom_depiction.comp_id _pdbe_chem_comp_atom_depiction.atom_id _pdbe_chem_comp_atom_depiction.element _pdbe_chem_comp_atom_depiction.model_Cartn_x _pdbe_chem_comp_atom_depiction.model_Cartn_y _pdbe_chem_comp_atom_depiction.pdbx_ordinal KDM C2 C 6.404 -1.183 1 KDM C1 C 5.654 -2.482 2 KDM C3 C 5.104 -0.433 3 KDM C4 C 5.104 1.067 4 KDM C5 C 6.404 1.817 5 KDM C6 C 7.702 1.067 6 KDM C7 C 9.002 1.817 7 KDM C8 C 10.301 1.067 8 KDM C9 C 11.600 1.817 9 KDM O5 O 6.404 3.317 10 KDM O1A O 6.404 -3.781 11 KDM O1B O 4.154 -2.482 12 KDM O4 O 3.805 1.817 13 KDM O6 O 7.702 -0.433 14 KDM O7 O 9.002 3.317 15 KDM O8 O 10.301 -0.433 16 KDM O9 O 12.899 1.067 17 KDM O2 O 7.154 -2.482 18 # loop_ _pdbe_chem_comp_bond_depiction.comp_id _pdbe_chem_comp_bond_depiction.atom_id_1 _pdbe_chem_comp_bond_depiction.atom_id_2 _pdbe_chem_comp_bond_depiction.value_order _pdbe_chem_comp_bond_depiction.bond_dir _pdbe_chem_comp_bond_depiction.pdbx_ordinal KDM C2 C1 SINGLE NONE 1 KDM C2 C3 SINGLE NONE 2 KDM C2 O6 SINGLE NONE 3 KDM C2 O2 SINGLE BEGINDASH 4 KDM C1 O1B SINGLE NONE 5 KDM C1 O1A DOUBLE NONE 6 KDM C3 C4 SINGLE NONE 7 KDM C4 C5 SINGLE NONE 8 KDM C4 O4 SINGLE BEGINDASH 9 KDM C5 C6 SINGLE NONE 10 KDM C5 O5 SINGLE BEGINWEDGE 11 KDM C6 C7 SINGLE NONE 12 KDM C6 O6 SINGLE BEGINDASH 13 KDM C7 C8 SINGLE NONE 14 KDM C7 O7 SINGLE BEGINDASH 15 KDM C8 C9 SINGLE NONE 16 KDM C8 O8 SINGLE BEGINWEDGE 17 KDM C9 O9 SINGLE NONE 18 # loop_ _pdbe_chem_comp_substructure.comp_id _pdbe_chem_comp_substructure.substructure_name _pdbe_chem_comp_substructure.id _pdbe_chem_comp_substructure.substructure_type _pdbe_chem_comp_substructure.substructure_smiles _pdbe_chem_comp_substructure.substructure_inchis _pdbe_chem_comp_substructure.substructure_inchikeys KDM MurckoScaffold S1 scaffold C1CCOCC1 InChI=1S/C5H10O/c1-2-4-6-5-3-1/h1-5H2 DHXVGJBLRPWPCS-UHFFFAOYSA-N KDM pyranose F1 fragment OC1CCCCO1 InChI=1S/C5H10O2/c6-5-3-1-2-4-7-5/h5-6H,1-4H2 CELWCAITJAEQNL-UHFFFAOYSA-N # loop_ _pdbe_chem_comp_substructure_mapping.comp_id _pdbe_chem_comp_substructure_mapping.atom_id _pdbe_chem_comp_substructure_mapping.substructure_id _pdbe_chem_comp_substructure_mapping.substructure_ordinal KDM C2 S1 1 KDM C3 S1 1 KDM C4 S1 1 KDM C5 S1 1 KDM C6 S1 1 KDM O6 S1 1 KDM C5 F1 1 KDM C6 F1 1 KDM O6 F1 1 KDM C2 F1 1 KDM C3 F1 1 KDM C4 F1 1 KDM O2 F1 1 # _pdbe_chem_comp_rdkit_properties.comp_id KDM _pdbe_chem_comp_rdkit_properties.exactmw 268.079 _pdbe_chem_comp_rdkit_properties.amw 268.218 _pdbe_chem_comp_rdkit_properties.lipinskiHBA 9 _pdbe_chem_comp_rdkit_properties.lipinskiHBD 7 _pdbe_chem_comp_rdkit_properties.NumRotatableBonds 10 _pdbe_chem_comp_rdkit_properties.NumHBD 7 _pdbe_chem_comp_rdkit_properties.NumHBA 9 _pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 18 _pdbe_chem_comp_rdkit_properties.NumAtoms 34 _pdbe_chem_comp_rdkit_properties.NumHeteroatoms 9 _pdbe_chem_comp_rdkit_properties.NumAmideBonds 0 _pdbe_chem_comp_rdkit_properties.FractionCSP3 0.889 _pdbe_chem_comp_rdkit_properties.NumRings 1 _pdbe_chem_comp_rdkit_properties.NumAromaticRings 0 _pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1 _pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1 _pdbe_chem_comp_rdkit_properties.NumHeterocycles 1 _pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0 _pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1 _pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1 _pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0 _pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0 _pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 6 _pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0 _pdbe_chem_comp_rdkit_properties.labuteASA 124.574 _pdbe_chem_comp_rdkit_properties.tpsa 167.910 _pdbe_chem_comp_rdkit_properties.CrippenClogP -4.016 _pdbe_chem_comp_rdkit_properties.CrippenMR 53.189 _pdbe_chem_comp_rdkit_properties.chi0v 8.174 _pdbe_chem_comp_rdkit_properties.chi1v 4.041 _pdbe_chem_comp_rdkit_properties.chi2v 1.710 _pdbe_chem_comp_rdkit_properties.chi3v 1.710 _pdbe_chem_comp_rdkit_properties.chi4v 0.917 _pdbe_chem_comp_rdkit_properties.chi0n 24.174 _pdbe_chem_comp_rdkit_properties.chi1n 11.399 _pdbe_chem_comp_rdkit_properties.chi2n 1.710 _pdbe_chem_comp_rdkit_properties.chi3n 1.710 _pdbe_chem_comp_rdkit_properties.chi4n 0.917 _pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.810 _pdbe_chem_comp_rdkit_properties.kappa1 4.090 _pdbe_chem_comp_rdkit_properties.kappa2 5.446 _pdbe_chem_comp_rdkit_properties.kappa3 2.777 _pdbe_chem_comp_rdkit_properties.Phi 1.238 # loop_ _pdbe_chem_comp_external_mappings.comp_id _pdbe_chem_comp_external_mappings.source _pdbe_chem_comp_external_mappings.resource _pdbe_chem_comp_external_mappings.resource_id KDM UniChem ChEBI 71432 KDM UniChem ZINC ZINC000004521632 KDM UniChem eMolecules 524613 KDM UniChem PubChem 197508 KDM UniChem BRENDA 212398 KDM UniChem BRENDA 215838 KDM UniChem 'EPA CompTox Dashboard' DTXSID80162690 KDM UniChem ACTor 144383-50-6 KDM UniChem Nikkaji J2.592.345F # loop_ _pdbe_chem_comp_rdkit_conformer.comp_id _pdbe_chem_comp_rdkit_conformer.atom_id _pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit _pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit _pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit _pdbe_chem_comp_rdkit_conformer.rdkit_method _pdbe_chem_comp_rdkit_conformer.rdkit_ordinal KDM C2 -2.364 -0.613 -0.188 ETKDGv3 1 KDM C1 -2.520 -1.584 0.969 ETKDGv3 2 KDM C3 -2.616 0.871 0.242 ETKDGv3 3 KDM C4 -1.728 1.836 -0.555 ETKDGv3 4 KDM C5 -0.230 1.459 -0.399 ETKDGv3 5 KDM C6 -0.055 -0.060 -0.110 ETKDGv3 6 KDM C7 1.316 -0.620 -0.586 ETKDGv3 7 KDM C8 2.536 -0.020 0.171 ETKDGv3 8 KDM C9 3.836 -0.807 -0.101 ETKDGv3 9 KDM O5 0.319 2.190 0.669 ETKDGv3 10 KDM O1A -2.859 -2.777 0.741 ETKDGv3 11 KDM O1B -2.218 -1.202 2.274 ETKDGv3 12 KDM O4 -2.121 1.883 -1.906 ETKDGv3 13 KDM O6 -1.074 -0.800 -0.766 ETKDGv3 14 KDM O7 1.305 -2.023 -0.474 ETKDGv3 15 KDM O8 2.733 1.306 -0.248 ETKDGv3 16 KDM O9 3.834 -2.042 0.565 ETKDGv3 17 KDM O2 -3.303 -0.945 -1.185 ETKDGv3 18 KDM H31 -3.684 1.152 0.112 ETKDGv3 19 KDM H32 -2.383 1.024 1.318 ETKDGv3 20 KDM HO2 -4.211 -0.912 -0.782 ETKDGv3 21 KDM HO1B -2.295 -1.860 3.040 ETKDGv3 22 KDM H4 -1.889 2.857 -0.143 ETKDGv3 23 KDM H5 0.302 1.721 -1.344 ETKDGv3 24 KDM HO4 -1.833 1.042 -2.346 ETKDGv3 25 KDM H6 -0.115 -0.231 0.990 ETKDGv3 26 KDM HO5 0.497 3.106 0.331 ETKDGv3 27 KDM H7 1.431 -0.384 -1.667 ETKDGv3 28 KDM H8 2.325 -0.043 1.266 ETKDGv3 29 KDM HO7 1.160 -2.245 0.483 ETKDGv3 30 KDM H91 3.947 -0.985 -1.192 ETKDGv3 31 KDM H92 4.718 -0.211 0.227 ETKDGv3 32 KDM HO8 3.244 1.764 0.471 ETKDGv3 33 KDM HO9 3.992 -1.847 1.525 ETKDGv3 34 #