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.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 KDN C2 C1 C 0 1 N N S N N N 9.107 -8.937 -11.899 -1.565 0.823 -0.231 C2 KDN 1 KDN C1 C10 C 0 1 N N N 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 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 N N N 11.410 -7.968 -11.858 -2.029 -1.630 -0.250 C4 KDN 4 KDN C5 C4 C 0 1 N N R N N N 10.903 -6.928 -12.867 -0.585 -1.855 0.211 C5 KDN 5 KDN C6 C5 C 0 1 N N R N N N 9.741 -7.529 -13.694 0.287 -0.700 -0.286 C6 KDN 6 KDN C7 C6 C 0 1 N N R N N N 9.085 -6.560 -14.670 1.719 -0.887 0.221 C7 KDN 7 KDN C8 C7 C 0 1 N N R N N N 7.935 -7.287 -15.400 2.561 0.329 -0.170 C8 KDN 8 KDN C9 C9 C 0 1 N N N 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 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 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 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 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 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 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 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 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 N N 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 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 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 N N 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 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 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 N N 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 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 N N 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 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 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 N N 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 N N 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 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 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 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 N N 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 # loop_ _pdbe_chem_comp_synonyms.comp_id _pdbe_chem_comp_synonyms.name _pdbe_chem_comp_synonyms.provenance _pdbe_chem_comp_synonyms.type KDN 'beta-deaminoneuraminic acid' wwPDB ? KDN '3-deoxy-D-glycero-beta-D-galacto-non-2-ulopyranosonic acid' wwPDB ? KDN 'sialic 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 KDN C2 C 6.404 -1.183 1 KDN C1 C 5.654 -2.482 2 KDN C3 C 5.104 -0.433 3 KDN C4 C 5.104 1.067 4 KDN C5 C 6.404 1.817 5 KDN C6 C 7.702 1.067 6 KDN C7 C 9.002 1.817 7 KDN C8 C 10.301 1.067 8 KDN C9 C 11.600 1.817 9 KDN O5 O 6.404 3.317 10 KDN O1A O 6.404 -3.781 11 KDN O1B O 4.154 -2.482 12 KDN O4 O 3.805 1.817 13 KDN O6 O 7.702 -0.433 14 KDN O7 O 9.002 3.317 15 KDN O8 O 10.301 -0.433 16 KDN O9 O 12.899 1.067 17 KDN 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 KDN C2 C3 SINGLE NONE 1 KDN C2 O2 SINGLE BEGINWEDGE 2 KDN C2 O6 SINGLE NONE 3 KDN C2 C1 SINGLE NONE 4 KDN C3 C4 SINGLE NONE 5 KDN C4 C5 SINGLE NONE 6 KDN C4 O4 SINGLE BEGINDASH 7 KDN C5 C6 SINGLE NONE 8 KDN C5 O5 SINGLE BEGINWEDGE 9 KDN C6 C7 SINGLE NONE 10 KDN C6 O6 SINGLE BEGINDASH 11 KDN C7 C8 SINGLE NONE 12 KDN C7 O7 SINGLE BEGINDASH 13 KDN C8 O8 SINGLE BEGINWEDGE 14 KDN C8 C9 SINGLE NONE 15 KDN O1B C1 SINGLE NONE 16 KDN O1A C1 DOUBLE NONE 17 KDN O9 C9 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 KDN MurckoScaffold S1 scaffold C1CCOCC1 InChI=1S/C5H10O/c1-2-4-6-5-3-1/h1-5H2 DHXVGJBLRPWPCS-UHFFFAOYSA-N KDN 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 KDN C2 S1 1 KDN C3 S1 1 KDN C4 S1 1 KDN C5 S1 1 KDN C6 S1 1 KDN O6 S1 1 KDN C5 F1 1 KDN C6 F1 1 KDN O6 F1 1 KDN C2 F1 1 KDN C3 F1 1 KDN C4 F1 1 KDN O2 F1 1 # _pdbe_chem_comp_rdkit_properties.comp_id KDN _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 KDN UniChem ChEBI 131593 KDN UniChem ZINC ZINC000013436054 KDN UniChem 'PubChem TPHARMA' 15914032 KDN UniChem NMRShiftDB 70114093 KDN UniChem Nikkaji J1.013.965A KDN UniChem MetaboLights MTBLC131593 KDN UniChem BRENDA 215744 KDN UniChem BRENDA 227588 KDN UniChem PubChem 10869261 # 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 KDN C2 -1.242 0.626 -1.188 ETKDGv3 1 KDN C1 -2.121 1.851 -1.081 ETKDGv3 2 KDN C3 -2.136 -0.655 -1.294 ETKDGv3 3 KDN C4 -2.256 -1.393 0.050 ETKDGv3 4 KDN C5 -0.860 -1.667 0.676 ETKDGv3 5 KDN C6 0.201 -0.667 0.147 ETKDGv3 6 KDN C7 1.387 -0.547 1.135 ETKDGv3 7 KDN C8 2.665 0.054 0.486 ETKDGv3 8 KDN C9 2.504 1.529 0.080 ETKDGv3 9 KDN O5 -0.443 -2.974 0.368 ETKDGv3 10 KDN O1A -2.823 2.216 -2.063 ETKDGv3 11 KDN O1B -2.177 2.576 0.108 ETKDGv3 12 KDN O4 -3.090 -0.683 0.934 ETKDGv3 13 KDN O6 -0.400 0.603 -0.039 ETKDGv3 14 KDN O7 0.998 0.207 2.257 ETKDGv3 15 KDN O8 3.738 -0.051 1.387 ETKDGv3 16 KDN O9 3.729 2.052 -0.359 ETKDGv3 17 KDN O2 -0.428 0.753 -2.332 ETKDGv3 18 KDN H31 -1.678 -1.361 -2.022 ETKDGv3 19 KDN H32 -3.151 -0.421 -1.685 ETKDGv3 20 KDN HO2 -1.012 0.707 -3.135 ETKDGv3 21 KDN H4 -2.759 -2.365 -0.149 ETKDGv3 22 KDN H5 -0.943 -1.562 1.784 ETKDGv3 23 KDN HO4 -2.603 0.126 1.236 ETKDGv3 24 KDN H6 0.606 -1.054 -0.818 ETKDGv3 25 KDN HO5 -0.945 -3.586 0.968 ETKDGv3 26 KDN H7 1.648 -1.583 1.461 ETKDGv3 27 KDN H8 2.906 -0.526 -0.436 ETKDGv3 28 KDN HO7 1.614 -0.033 2.997 ETKDGv3 29 KDN HO8 4.034 -0.999 1.377 ETKDGv3 30 KDN H91 1.749 1.634 -0.730 ETKDGv3 31 KDN H92 2.161 2.128 0.950 ETKDGv3 32 KDN HO1B -2.769 3.393 0.191 ETKDGv3 33 KDN HO9 3.895 1.672 -1.261 ETKDGv3 34 #