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  
##
