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  
##
