data_PKM
#

_chem_comp.id                                   PKM
_chem_comp.name                                 "4-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid"
_chem_comp.type                                 "D-saccharide, alpha linking"
_chem_comp.pdbx_type                            ATOMS
_chem_comp.formula                              "C13 H21 N O10"
_chem_comp.mon_nstd_parent_comp_id              SIA
_chem_comp.pdbx_synonyms                        
;4-O-acetyl-5-(acetylamino)-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid;
4-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulosonic acid;
4-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-D-galacto-non-2-ulosonic acid;
4-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-galacto-non-2-ulosonic acid
;

_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2019-08-14
_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                       351.307
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    PKM
_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       6TYO
_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  PKM  "4-O-acetyl-5-(acetylamino)-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid"  PDB  ?  
2  PKM  "4-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulosonic acid"            PDB  ?  
3  PKM  "4-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-D-galacto-non-2-ulosonic acid"                  PDB  ?  
4  PKM  "4-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-galacto-non-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
PKM  C1    C1    C  0  1  N  N  N  52.202  24.462  23.233  -0.105  -2.593  -0.726  C1    PKM   1  
PKM  C10   C10   C  0  1  N  N  N  54.139  24.939  17.355   1.521   2.825  -0.245  C10   PKM   2  
PKM  C11   C11   C  0  1  N  N  N  55.479  25.211  16.634   1.788   3.969  -1.190  C11   PKM   3  
PKM  O1A   O1B   O  0  1  N  N  N  52.947  23.506  23.564  -0.429  -3.730  -0.973  O1A   PKM   4  
PKM  C2    C2    C  0  1  N  N  R  51.318  24.314  22.027  -0.139  -2.091   0.694  C2    PKM   5  
PKM  C3    C3    C  0  1  N  N  N  51.311  25.639  21.276   1.236  -1.531   1.070  C3    PKM   6  
PKM  C4    C4    C  0  1  N  N  S  52.527  25.839  20.406   1.558  -0.339   0.163  C4    PKM   7  
PKM  O4    O4    O  0  1  N  N  N  52.205  26.975  19.569   2.827   0.244   0.560  O4    PKM   8  
PKM  C5    C5    C  0  1  N  N  R  52.877  24.686  19.552   0.447   0.707   0.299  C5    PKM   9  
PKM  C6    C6    C  0  1  N  N  R  53.121  23.520  20.481  -0.897   0.060  -0.047  C6    PKM  10  
PKM  C7    C7    C  0  1  N  N  R  53.554  22.267  19.829  -2.019   1.083   0.144  C7    PKM  11  
PKM  C8    C8    C  0  1  N  N  R  53.503  21.128  20.906  -3.371   0.403  -0.081  C8    PKM  12  
PKM  C9    C9    C  0  1  N  N  N  54.180  19.910  20.311  -4.494   1.426   0.111  C9    PKM  13  
PKM  O10   O10   O  0  1  N  N  N  53.136  24.756  16.744   2.040   2.810   0.851  O10   PKM  14  
PKM  N5    N5    N  0  1  N  N  N  54.145  24.937  18.822   0.706   1.819  -0.619  N5    PKM  15  
PKM  C     C     C  0  1  N  N  N  53.100  28.064  19.650   3.931  -0.241  -0.029  C     PKM  16  
PKM  O     O     O  0  1  N  N  N  54.173  27.922  20.156   3.840  -1.123  -0.850  O     PKM  17  
PKM  CH3   CH3   C  0  1  N  N  N  52.644  29.420  19.064   5.285   0.315   0.332  CH3   PKM  18  
PKM  O1B   O1    O  0  1  N  N  N  52.204  25.541  23.899   0.289  -1.777  -1.717  O1B   PKM  19  
PKM  O6    O6    O  0  1  N  N  N  51.830  23.204  21.202  -1.121  -1.059   0.812  O6    PKM  20  
PKM  O7    O7    O  0  1  N  N  N  52.674  21.967  18.796  -1.964   1.607   1.472  O7    PKM  21  
PKM  O8    O8    O  0  1  N  N  N  54.138  21.507  22.096  -3.426  -0.121  -1.409  O8    PKM  22  
PKM  O9    O9    O  0  1  N  N  N  54.256  18.917  21.301  -5.759   0.767   0.016  O9    PKM  23  
PKM  H111  H113  H  0  0  N  N  N  55.319  25.200  15.546   1.048   4.752  -1.030  H111  PKM  24  
PKM  H113  H112  H  0  0  N  N  N  55.865  26.195  16.937   2.785   4.368  -1.005  H113  PKM  25  
PKM  H112  H111  H  0  0  N  N  N  56.206  24.432  16.906   1.725   3.613  -2.218  H112  PKM  26  
PKM  H32   H32   H  0  1  N  N  N  51.269  26.456  22.011   1.224  -1.205   2.110  H32   PKM  27  
PKM  H31   H31   H  0  1  N  N  N  50.416  25.674  20.638   1.992  -2.304   0.939  H31   PKM  28  
PKM  H4    H4    H  0  1  N  N  N  53.385  26.086  21.049   1.619  -0.674  -0.872  H4    PKM  29  
PKM  H5    H5    H  0  1  N  N  N  52.062  24.454  18.851   0.420   1.078   1.324  H5    PKM  30  
PKM  H6    H6    H  0  1  N  N  N  53.875  23.816  21.225  -0.883  -0.274  -1.084  H6    PKM  31  
PKM  H7    H7    H  0  1  N  N  N  54.587  22.367  19.463  -1.897   1.895  -0.572  H7    PKM  32  
PKM  H8    H8    H  0  1  N  N  N  52.447  20.887  21.097  -3.494  -0.409   0.636  H8    PKM  33  
PKM  H92   H92   H  0  1  N  N  N  53.594  19.539  19.457  -4.398   1.890   1.092  H92   PKM  34  
PKM  H91   H91   H  0  1  N  N  N  55.192  20.176  19.973  -4.423   2.191  -0.662  H91   PKM  35  
PKM  HN5   HN5   H  0  1  N  N  N  54.994  25.103  19.324   0.292   1.831  -1.496  HN5   PKM  36  
PKM  H14   H14   H  0  1  N  N  N  53.443  30.165  19.197   5.701  -0.253   1.164  H14   PKM  37  
PKM  H16   H16   H  0  1  N  N  N  52.428  29.302  17.992   5.950   0.239  -0.528  H16   PKM  38  
PKM  H15   H15   H  0  1  N  N  N  51.737  29.758  19.586   5.182   1.361   0.621  H15   PKM  39  
PKM  HO1B  HOB1  H  0  0  N  N  N  52.822  25.469  24.617   0.298  -2.145  -2.611  HO1B  PKM  40  
PKM  HO7   HO7   H  0  1  N  Y  N  52.946  21.162  18.371  -2.066   0.939   2.164  HO7   PKM  41  
PKM  HO8   HO8   H  0  1  N  Y  N  53.640  22.200  22.514  -3.324   0.547  -2.100  HO8   PKM  42  
PKM  HO9   HO9   H  0  1  N  Y  N  54.679  18.145  20.944  -6.517   1.356   0.127  HO9   PKM  43  
PKM  O2    O2    O  0  1  N  Y  N  49.972  23.995  22.450  -0.471  -3.168   1.572  O2    PKM  44  
PKM  HO2   H1    H  0  1  N  Y  N  49.631  24.704  22.983  -1.331  -3.572   1.392  HO2   PKM  45  
#   #
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
PKM  C11  C10   SING  N  N   1  
PKM  O10  C10   DOUB  N  N   2  
PKM  C10  N5    SING  N  N   3  
PKM  O7   C7    SING  N  N   4  
PKM  N5   C5    SING  N  N   5  
PKM  CH3  C     SING  N  N   6  
PKM  C5   C4    SING  N  N   7  
PKM  C5   C6    SING  N  N   8  
PKM  O4   C     SING  N  N   9  
PKM  O4   C4    SING  N  N  10  
PKM  C    O     DOUB  N  N  11  
PKM  C7   C6    SING  N  N  12  
PKM  C7   C8    SING  N  N  13  
PKM  C9   C8    SING  N  N  14  
PKM  C9   O9    SING  N  N  15  
PKM  C4   C3    SING  N  N  16  
PKM  C6   O6    SING  N  N  17  
PKM  C8   O8    SING  N  N  18  
PKM  O6   C2    SING  N  N  19  
PKM  C3   C2    SING  N  N  20  
PKM  C2   C1    SING  N  N  21  
PKM  C1   O1A   DOUB  N  N  22  
PKM  C1   O1B   SING  N  N  23  
PKM  C11  H111  SING  N  N  24  
PKM  C11  H113  SING  N  N  25  
PKM  C11  H112  SING  N  N  26  
PKM  C3   H32   SING  N  N  27  
PKM  C3   H31   SING  N  N  28  
PKM  C4   H4    SING  N  N  29  
PKM  C5   H5    SING  N  N  30  
PKM  C6   H6    SING  N  N  31  
PKM  C7   H7    SING  N  N  32  
PKM  C8   H8    SING  N  N  33  
PKM  C9   H92   SING  N  N  34  
PKM  C9   H91   SING  N  N  35  
PKM  N5   HN5   SING  N  N  36  
PKM  CH3  H14   SING  N  N  37  
PKM  CH3  H16   SING  N  N  38  
PKM  CH3  H15   SING  N  N  39  
PKM  O1B  HO1B  SING  N  N  40  
PKM  O7   HO7   SING  N  N  41  
PKM  O8   HO8   SING  N  N  42  
PKM  O9   HO9   SING  N  N  43  
PKM  C2   O2    SING  N  N  44  
PKM  O2   HO2   SING  N  N  45  
#   #
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
PKM  SMILES            ACDLabs               12.01  "C(=O)(O)C1(O)CC(OC(=O)C)C(C(O1)C(C(O)CO)O)NC(C)=O"  
PKM  InChI             InChI                 1.03   "InChI=1S/C13H21NO10/c1-5(16)14-9-8(23-6(2)17)3-13(22,12(20)21)24-11(9)10(19)7(18)4-15/h7-11,15,18-19,22H,3-4H2,1-2H3,(H,14,16)(H,20,21)/t7-,8+,9-,10-,11-,13-/m1/s1"  
PKM  InChIKey          InChI                 1.03   LVBIMVQYUKOENY-CYBLFPARSA-N  
PKM  SMILES_CANONICAL  CACTVS                3.385  "CC(=O)N[C@@H]1[C@H](C[C@@](O)(O[C@H]1[C@H](O)[C@H](O)CO)C(O)=O)OC(C)=O"  
PKM  SMILES            CACTVS                3.385  "CC(=O)N[CH]1[CH](C[C](O)(O[CH]1[CH](O)[CH](O)CO)C(O)=O)OC(C)=O"  
PKM  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "CC(=O)N[C@@H]1[C@H](C[C@@](O[C@H]1[C@@H]([C@@H](CO)O)O)(C(=O)O)O)OC(=O)C"  
PKM  SMILES            "OpenEye OEToolkits"  2.0.7  "CC(=O)NC1C(CC(OC1C(C(CO)O)O)(C(=O)O)O)OC(=O)C"  
#   #
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
PKM  "SYSTEMATIC NAME"  ACDLabs               12.01  "4-O-acetyl-5-(acetylamino)-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulopyranosonic acid"  
PKM  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  
;(2~{R},4~{S},5~{R},6~{R})-5-acetamido-4-acetyloxy-2-oxidanyl-6-[(1~{R},2~{R})-1,2,3-tris(oxidanyl)propyl]oxane-2-carbox
ylic acid
;
  
#
_pdbx_chem_comp_related.comp_id            PKM
_pdbx_chem_comp_related.related_comp_id    SIA
_pdbx_chem_comp_related.relationship_type  "Carbohydrate core"
_pdbx_chem_comp_related.details            ?
#   #
loop_
_pdbx_chem_comp_atom_related.ordinal
_pdbx_chem_comp_atom_related.comp_id
_pdbx_chem_comp_atom_related.atom_id
_pdbx_chem_comp_atom_related.related_comp_id
_pdbx_chem_comp_atom_related.related_atom_id
_pdbx_chem_comp_atom_related.related_type
 1  PKM  C1    SIA  C1    "Carbohydrate core"  
 2  PKM  C10   SIA  C10   "Carbohydrate core"  
 3  PKM  C11   SIA  C11   "Carbohydrate core"  
 4  PKM  C2    SIA  C2    "Carbohydrate core"  
 5  PKM  C3    SIA  C3    "Carbohydrate core"  
 6  PKM  C4    SIA  C4    "Carbohydrate core"  
 7  PKM  C5    SIA  C5    "Carbohydrate core"  
 8  PKM  C6    SIA  C6    "Carbohydrate core"  
 9  PKM  C7    SIA  C7    "Carbohydrate core"  
10  PKM  C8    SIA  C8    "Carbohydrate core"  
11  PKM  C9    SIA  C9    "Carbohydrate core"  
12  PKM  N5    SIA  N5    "Carbohydrate core"  
13  PKM  O1B   SIA  O1B   "Carbohydrate core"  
14  PKM  O10   SIA  O10   "Carbohydrate core"  
15  PKM  O1A   SIA  O1A   "Carbohydrate core"  
16  PKM  O2    SIA  O2    "Carbohydrate core"  
17  PKM  O4    SIA  O4    "Carbohydrate core"  
18  PKM  O6    SIA  O6    "Carbohydrate core"  
19  PKM  O7    SIA  O7    "Carbohydrate core"  
20  PKM  O8    SIA  O8    "Carbohydrate core"  
21  PKM  O9    SIA  O9    "Carbohydrate core"  
22  PKM  HO2   SIA  HO2   "Carbohydrate core"  
23  PKM  H112  SIA  H112  "Carbohydrate core"  
24  PKM  H113  SIA  H113  "Carbohydrate core"  
25  PKM  H111  SIA  H111  "Carbohydrate core"  
26  PKM  H31   SIA  H31   "Carbohydrate core"  
27  PKM  H32   SIA  H32   "Carbohydrate core"  
28  PKM  H4    SIA  H4    "Carbohydrate core"  
29  PKM  H5    SIA  H5    "Carbohydrate core"  
30  PKM  H6    SIA  H6    "Carbohydrate core"  
31  PKM  H7    SIA  H7    "Carbohydrate core"  
32  PKM  H8    SIA  H8    "Carbohydrate core"  
33  PKM  H91   SIA  H91   "Carbohydrate core"  
34  PKM  H92   SIA  H92   "Carbohydrate core"  
35  PKM  HN5   SIA  HN5   "Carbohydrate core"  
36  PKM  HO7   SIA  HO7   "Carbohydrate core"  
37  PKM  HO8   SIA  HO8   "Carbohydrate core"  
38  PKM  HO9   SIA  HO9   "Carbohydrate core"  
39  PKM  HO1B  SIA  HO1B  "Carbohydrate core"  
#   #
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
PKM  "CARBOHYDRATE ISOMER"                  D         PDB  ?  
PKM  "CARBOHYDRATE RING"                    pyranose  PDB  ?  
PKM  "CARBOHYDRATE ANOMER"                  alpha     PDB  ?  
PKM  "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
PKM  "Create component"          2019-08-14  RCSB  
PKM  "Initial release"           2020-02-12  RCSB  
PKM  "Other modification"        2020-07-03  RCSB  
PKM  "Modify name"               2020-07-17  RCSB  
PKM  "Modify synonyms"           2020-07-17  RCSB  
PKM  "Modify linking type"       2020-07-17  RCSB  
PKM  "Modify atom id"            2020-07-17  RCSB  
PKM  "Modify component atom id"  2020-07-17  RCSB  
PKM  "Modify leaving atom flag"  2020-07-17  RCSB  
##
