data_KDB
#

_chem_comp.id                                   KDB
_chem_comp.name                                 "3,4,5-trideoxy-alpha-D-erythro-oct-3-en-2-ulopyranosonic acid"
_chem_comp.type                                 "D-saccharide, alpha linking"
_chem_comp.pdbx_type                            ATOMS
_chem_comp.formula                              "C8 H12 O6"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        
;3,4-dehydro-3,4,5-trideoxy-alpha-D-manno-oct-2-ulosonic acid; 3,4,5-trideoxy-alpha-D-erythro-oct-3-en-2-ulosonic acid;
3,4,5-trideoxy-D-erythro-oct-3-en-2-ulosonic acid; 3,4,5-trideoxy-erythro-oct-3-en-2-ulosonic acid
;

_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2008-01-04
_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                       204.177
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    KDB
_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       2R1W
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 RCSB
#   #
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  KDB  "3,4-dehydro-3,4,5-trideoxy-alpha-D-manno-oct-2-ulosonic acid"  PDB  ?  
2  KDB  "3,4,5-trideoxy-alpha-D-erythro-oct-3-en-2-ulosonic acid"       PDB  ?  
3  KDB  "3,4,5-trideoxy-D-erythro-oct-3-en-2-ulosonic acid"             PDB  ?  
4  KDB  "3,4,5-trideoxy-erythro-oct-3-en-2-ulosonic 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
KDB  O2    O2    O  0  1  N  Y  N   -6.095  4.166  69.810   1.379   0.177  -1.737  O2    KDB   1  
KDB  C2    C2    C  0  1  N  N  R   -5.976  4.617  71.275   1.401  -0.025  -0.322  C2    KDB   2  
KDB  C1    C1    C  0  1  N  N  N   -5.540  6.103  71.282   2.450   0.866   0.292  C1    KDB   3  
KDB  O1B   O1B   O  0  1  N  N  N   -4.599  6.402  70.541   3.747   0.676   0.001  O1B   KDB   4  
KDB  O1A   O1A   O  0  1  N  N  N   -6.140  6.906  72.054   2.124   1.751   1.048  O1A   KDB   5  
KDB  C3    C3    C  0  1  N  N  N   -4.977  3.848  71.931   1.733  -1.460  -0.029  C3    KDB   6  
KDB  C4    C4    C  0  1  N  N  N   -5.261  3.009  73.032   0.844  -2.325   0.361  C4    KDB   7  
KDB  C5    C5    C  0  1  N  N  N   -6.585  2.744  73.461  -0.601  -1.962   0.562  C5    KDB   8  
KDB  C6    C6    C  0  1  N  N  S   -7.663  3.180  72.422  -0.899  -0.631  -0.135  C6    KDB   9  
KDB  O6    O6    O  0  1  N  N  N   -7.270  4.489  71.940   0.122   0.303   0.224  O6    KDB  10  
KDB  C7    C7    C  0  1  N  N  R   -9.112  3.257  72.926  -2.263  -0.106   0.318  C7    KDB  11  
KDB  O7    O7    O  0  1  N  N  N   -9.201  4.243  73.961  -3.276  -1.055  -0.020  O7    KDB  12  
KDB  C8    C8    C  0  1  N  N  N   -9.644  1.926  73.484  -2.555   1.223  -0.381  C8    KDB  13  
KDB  O8    O8    O  0  1  N  N  N   -9.365  0.831  72.602  -3.773   1.771   0.128  O8    KDB  14  
KDB  HO2   HO2   H  0  1  N  Y  N   -6.362  3.255  69.779   2.217  -0.023  -2.176  HO2   KDB  15  
KDB  H3    H3    H  0  1  N  N  N   -3.960  3.907  71.574   2.756  -1.788  -0.147  H3    KDB  16  
KDB  H4    H4    H  0  1  N  N  N   -4.440  2.554  73.565   1.155  -3.342   0.546  H4    KDB  17  
KDB  H51   H51   H  0  1  N  N  N   -6.686  1.663  73.638  -1.234  -2.743   0.140  H51   KDB  18  
KDB  H52   H52   H  0  1  N  N  N   -6.764  3.287  74.400  -0.806  -1.866   1.629  H52   KDB  19  
KDB  H6    H6    H  0  1  N  N  N   -7.631  2.465  71.587  -0.902  -0.776  -1.215  H6    KDB  20  
KDB  H7    H7    H  0  1  N  N  N   -9.752  3.553  72.082  -2.253   0.046   1.398  H7    KDB  21  
KDB  HO7   HO7   H  0  1  N  N  N  -10.096  4.293  74.275  -3.342  -1.240  -0.967  HO7   KDB  22  
KDB  H8    H8    H  0  1  N  N  N   -9.167  1.731  74.456  -1.738   1.919  -0.195  H8    KDB  23  
KDB  H8A   H8A   H  0  1  N  N  N  -10.733  2.006  73.619  -2.653   1.055  -1.454  H8A   KDB  24  
KDB  HO8   HO8   H  0  1  N  N  N   -9.706  0.027  72.976  -4.021   2.616  -0.271  HO8   KDB  25  
KDB  HO1B  HO1B  H  0  0  N  N  N   -4.397  7.325  70.641   4.383   1.273   0.420  HO1B  KDB  26  
#   #
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
KDB  O2   C2    SING  N  N   1  
KDB  O2   HO2   SING  N  N   2  
KDB  C2   C1    SING  N  N   3  
KDB  C2   C3    SING  N  N   4  
KDB  C2   O6    SING  N  N   5  
KDB  O1B  C1    SING  N  N   6  
KDB  C1   O1A   DOUB  N  N   7  
KDB  C3   C4    DOUB  N  N   8  
KDB  C3   H3    SING  N  N   9  
KDB  C4   C5    SING  N  N  10  
KDB  C4   H4    SING  N  N  11  
KDB  C6   C5    SING  N  N  12  
KDB  C5   H51   SING  N  N  13  
KDB  C5   H52   SING  N  N  14  
KDB  O6   C6    SING  N  N  15  
KDB  C6   C7    SING  N  N  16  
KDB  C6   H6    SING  N  N  17  
KDB  C7   C8    SING  N  N  18  
KDB  C7   O7    SING  N  N  19  
KDB  C7   H7    SING  N  N  20  
KDB  O7   HO7   SING  N  N  21  
KDB  O8   C8    SING  N  N  22  
KDB  C8   H8    SING  N  N  23  
KDB  C8   H8A   SING  N  N  24  
KDB  O8   HO8   SING  N  N  25  
KDB  O1B  HO1B  SING  N  N  26  
#   #
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
KDB  SMILES            ACDLabs               12.01  "OC1(C(=O)O)C=CCC(C(CO)O)O1"  
KDB  InChI             InChI                 1.03   "InChI=1S/C8H12O6/c9-4-5(10)6-2-1-3-8(13,14-6)7(11)12/h1,3,5-6,9-10,13H,2,4H2,(H,11,12)/t5-,6+,8-/m1/s1"  
KDB  InChIKey          InChI                 1.03   ITFIFEKDEVIBCW-GKROBHDKSA-N  
KDB  SMILES_CANONICAL  CACTVS                3.385  "OC[C@@H](O)[C@@H]1CC=C[C@@](O)(O1)C(O)=O"  
KDB  SMILES            CACTVS                3.385  "OC[CH](O)[CH]1CC=C[C](O)(O1)C(O)=O"  
KDB  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "C1C=C[C@@](O[C@@H]1[C@@H](CO)O)(C(=O)O)O"  
KDB  SMILES            "OpenEye OEToolkits"  2.0.7  "C1C=CC(OC1C(CO)O)(C(=O)O)O"  
#   #
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
KDB  "SYSTEMATIC NAME"  ACDLabs               12.01  "3,4,5-trideoxy-alpha-D-erythro-oct-3-en-2-ulopyranosonic acid"  
KDB  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  "(2~{S},6~{R})-2-[(1~{R})-1,2-bis(oxidanyl)ethyl]-6-oxidanyl-2,3-dihydropyran-6-carboxylic acid"  
#   #
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
KDB  "CARBOHYDRATE ISOMER"                  D             PDB  ?  
KDB  "CARBOHYDRATE RING"                    dihydropyran  PDB  ?  
KDB  "CARBOHYDRATE ANOMER"                  alpha         PDB  ?  
KDB  "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
KDB  "Create component"          2008-01-04  RCSB  
KDB  "Modify descriptor"         2011-06-04  RCSB  
KDB  "Other modification"        2020-04-11  RCSB  
KDB  "Other modification"        2020-07-03  RCSB  
KDB  "Modify synonyms"           2020-07-17  RCSB  
KDB  "Modify linking type"       2020-07-17  RCSB  
KDB  "Modify component atom id"  2020-07-17  RCSB  
##
