data_5N6
#

_chem_comp.id                                   5N6
_chem_comp.name                                 "9-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                        
;(2~{R},4~{S},5~{R},6~{R})-5-acetamido-6-[(1~{R},2~{R})-3-acetyloxy-1,2-bis(oxidanyl)propyl]-2,4-bis(oxidanyl)oxane-2-ca
 rboxylic acid; 9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulosonic acid;
9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-D-galacto-non-2-ulosonic acid;
9-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                    2015-10-27
_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                    5N6
_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       5E65
_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  5N6  
;(2~{R},4~{S},5~{R},6~{R})-5-acetamido-6-[(1~{R},2~{R})-3-acetyloxy-1,2-bis(oxidanyl)propyl]-2,4-bis(oxidanyl)oxane-2-ca
 rboxylic acid
;
  PDB  ?  
2  5N6  "9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-alpha-D-galacto-non-2-ulosonic acid"  PDB  ?  
3  5N6  "9-O-acetyl-5-acetamido-3,5-dideoxy-D-glycero-D-galacto-non-2-ulosonic acid"  PDB  ?  
4  5N6  "9-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
5N6  CAF   CAF  C  0  1  N  N  N  -27.397  -38.640  -62.635  -6.842   0.535  -0.004  CAF   5N6   1  
5N6  CAG   CAG  C  0  1  N  N  N  -28.570  -38.481  -63.542  -5.600  -0.313  -0.098  CAG   5N6   2  
5N6  C11   CAH  C  0  1  N  N  N  -24.362  -43.751  -64.093   2.514  -4.216   1.219  C11   5N6   3  
5N6  C10   CAI  C  0  1  N  N  N  -25.150  -43.198  -65.249   2.444  -3.040   0.278  C10   5N6   4  
5N6  C9    CAX  C  0  1  N  N  N  -28.444  -39.511  -65.451  -3.238  -0.629  -0.054  C9    5N6   5  
5N6  C8    CAY  C  0  1  N  N  R  -27.439  -39.532  -66.541  -1.957   0.185   0.136  C8    5N6   6  
5N6  C7    CAZ  C  0  1  N  N  R  -26.525  -40.681  -66.264  -0.741  -0.715  -0.094  C7    5N6   7  
5N6  N5    NAB  N  0  1  N  N  N  -24.433  -42.752  -66.268   1.820  -1.908   0.659  N5    5N6   8  
5N6  C5    CBA  C  0  1  N  N  R  -24.963  -42.200  -67.497   1.752  -0.766  -0.255  C5    5N6   9  
5N6  C4    CBB  C  0  1  N  N  S  -23.770  -42.067  -68.414   3.026   0.074  -0.119  C4    5N6  10  
5N6  C6    CBC  C  0  1  N  N  R  -25.435  -40.819  -67.296   0.540   0.100   0.097  C6    5N6  11  
5N6  C3    CBD  C  0  1  N  N  N  -24.087  -41.461  -69.716   2.910   1.307  -1.022  C3    5N6  12  
5N6  C2    CBE  C  0  1  N  N  R  -24.764  -40.179  -69.492   1.653   2.092  -0.641  C2    5N6  13  
5N6  C1    CBF  C  0  1  N  N  N  -23.771  -39.163  -68.979   1.775   2.577   0.781  C1    5N6  14  
5N6  OBJ   OBJ  O  0  1  N  N  N  -29.694  -38.460  -63.093  -5.694  -1.500  -0.303  OBJ   5N6  15  
5N6  O9    OBK  O  0  1  N  N  N  -28.258  -38.310  -64.814  -4.390   0.249   0.047  O9    5N6  16  
5N6  O10   OBL  O  0  1  N  N  N  -26.359  -43.153  -65.186   2.950  -3.113  -0.821  O10   5N6  17  
5N6  O7    OBW  O  0  1  N  N  N  -27.293  -41.844  -66.178  -0.780  -1.236  -1.424  O7    5N6  18  
5N6  O8    OBX  O  0  1  N  N  N  -26.754  -38.354  -66.378  -1.918   0.707   1.466  O8    5N6  19  
5N6  O4    OBY  O  0  1  N  N  N  -23.242  -43.304  -68.650   4.157  -0.705  -0.515  O4    5N6  20  
5N6  O6    OBZ  O  0  1  N  N  N  -25.799  -40.287  -68.555   0.509   1.244  -0.759  O6    5N6  21  
5N6  O1B   OCA  O  0  1  N  N  N  -24.217  -38.312  -68.223   2.021   1.702   1.769  O1B   5N6  22  
5N6  O1A   OCB  O  0  1  N  N  N  -22.618  -39.212  -69.406   1.651   3.752   1.032  O1A   5N6  23  
5N6  H1    H1   H  0  1  N  N  N  -27.746  -38.723  -61.595  -7.722  -0.091  -0.147  H1    5N6  24  
5N6  H2    H2   H  0  1  N  N  N  -26.842  -39.549  -62.909  -6.886   1.007   0.977  H2    5N6  25  
5N6  H3    H3   H  0  1  N  N  N  -26.738  -37.765  -62.732  -6.814   1.305  -0.776  H3    5N6  26  
5N6  H111  H4   H  0  0  N  N  N  -25.051  -44.060  -63.293   3.053  -5.033   0.740  H111  5N6  27  
5N6  H113  H5   H  0  0  N  N  N  -23.778  -44.621  -64.430   3.034  -3.921   2.130  H113  5N6  28  
5N6  H112  H6   H  0  0  N  N  N  -23.680  -42.977  -63.711   1.504  -4.543   1.467  H112  5N6  29  
5N6  H92   H7   H  0  1  N  N  N  -29.462  -39.576  -65.863  -3.226  -1.100  -1.037  H92   5N6  30  
5N6  H91   H8   H  0  1  N  N  N  -28.276  -40.347  -64.756  -3.298  -1.398   0.716  H91   5N6  31  
5N6  H8    H9   H  0  1  N  N  N  -27.915  -39.627  -67.528  -1.940   1.009  -0.578  H8    5N6  32  
5N6  H7    H10  H  0  1  N  N  N  -26.042  -40.498  -65.293  -0.758  -1.538   0.620  H7    5N6  33  
5N6  HN5   H11  H  0  1  N  N  N  -23.438  -42.801  -66.182   1.415  -1.850   1.539  HN5   5N6  34  
5N6  H5    H12  H  0  1  N  N  N  -25.740  -42.839  -67.941   1.659  -1.124  -1.280  H5    5N6  35  
5N6  H4    H13  H  0  1  N  N  N  -23.026  -41.434  -67.909   3.145   0.391   0.917  H4    5N6  36  
5N6  H6    H14  H  0  1  N  N  N  -24.577  -40.239  -66.924   0.613   0.424   1.135  H6    5N6  37  
5N6  H32   H15  H  0  1  N  N  N  -24.747  -42.132  -70.285   3.789   1.939  -0.890  H32   5N6  38  
5N6  H31   H16  H  0  1  N  N  N  -23.158  -41.294  -70.281   2.841   0.991  -2.063  H31   5N6  39  
5N6  HO7   H18  H  0  1  N  Y  N  -26.821  -42.500  -65.679  -0.768  -0.558  -2.113  HO7   5N6  40  
5N6  HO8   H19  H  0  1  N  Y  N  -27.334  -37.623  -66.554  -1.930   0.029   2.155  HO8   5N6  41  
5N6  HO4   H20  H  0  1  N  Y  N  -23.027  -43.720  -67.823   4.999  -0.234  -0.454  HO4   5N6  42  
5N6  HO1B  H21  H  0  0  N  N  N  -23.534  -37.687  -68.011   2.090   2.060   2.665  HO1B  5N6  43  
5N6  O2    O1   O  0  1  N  Y  N  -25.315  -39.787  -70.713   1.508   3.213  -1.515  O2    5N6  44  
5N6  HO2   H17  H  0  1  N  Y  N  -25.764  -38.957  -70.606   0.730   3.757  -1.331  HO2   5N6  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
5N6  C3   C2    SING  N  N   1  
5N6  C3   C4    SING  N  N   2  
5N6  C2   C1    SING  N  N   3  
5N6  C2   O6    SING  N  N   4  
5N6  O1A  C1    DOUB  N  N   5  
5N6  C1   O1B   SING  N  N   6  
5N6  O4   C4    SING  N  N   7  
5N6  O6   C6    SING  N  N   8  
5N6  C4   C5    SING  N  N   9  
5N6  C5   C6    SING  N  N  10  
5N6  C5   N5    SING  N  N  11  
5N6  C6   C7    SING  N  N  12  
5N6  C8   O8    SING  N  N  13  
5N6  C8   C7    SING  N  N  14  
5N6  C8   C9    SING  N  N  15  
5N6  N5   C10   SING  N  N  16  
5N6  C7   O7    SING  N  N  17  
5N6  C9   O9    SING  N  N  18  
5N6  C10  O10   DOUB  N  N  19  
5N6  C10  C11   SING  N  N  20  
5N6  O9   CAG   SING  N  N  21  
5N6  CAG  OBJ   DOUB  N  N  22  
5N6  CAG  CAF   SING  N  N  23  
5N6  CAF  H1    SING  N  N  24  
5N6  CAF  H2    SING  N  N  25  
5N6  CAF  H3    SING  N  N  26  
5N6  C11  H111  SING  N  N  27  
5N6  C11  H113  SING  N  N  28  
5N6  C11  H112  SING  N  N  29  
5N6  C9   H92   SING  N  N  30  
5N6  C9   H91   SING  N  N  31  
5N6  C8   H8    SING  N  N  32  
5N6  C7   H7    SING  N  N  33  
5N6  N5   HN5   SING  N  N  34  
5N6  C5   H5    SING  N  N  35  
5N6  C4   H4    SING  N  N  36  
5N6  C6   H6    SING  N  N  37  
5N6  C3   H32   SING  N  N  38  
5N6  C3   H31   SING  N  N  39  
5N6  O7   HO7   SING  N  N  40  
5N6  O8   HO8   SING  N  N  41  
5N6  O4   HO4   SING  N  N  42  
5N6  O1B  HO1B  SING  N  N  43  
5N6  C2   O2    SING  N  N  44  
5N6  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
5N6  InChI             InChI                 1.03   "InChI=1S/C13H21NO10/c1-5(15)14-9-7(17)3-13(22,12(20)21)24-11(9)10(19)8(18)4-23-6(2)16/h7-11,17-19,22H,3-4H2,1-2H3,(H,14,15)(H,20,21)/t7-,8+,9+,10+,11+,13+/m0/s1"  
5N6  InChIKey          InChI                 1.03   NYWZBRWKDRMPAS-CTAKWSDESA-N  
5N6  SMILES_CANONICAL  CACTVS                3.385  "CC(=O)N[C@@H]1[C@@H](O)C[C@@](O)(O[C@H]1[C@H](O)[C@H](O)COC(C)=O)C(O)=O"  
5N6  SMILES            CACTVS                3.385  "CC(=O)N[CH]1[CH](O)C[C](O)(O[CH]1[CH](O)[CH](O)COC(C)=O)C(O)=O"  
5N6  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.4  "CC(=O)N[C@@H]1[C@H](C[C@@](O[C@H]1[C@@H]([C@@H](COC(=O)C)O)O)(C(=O)O)O)O"  
5N6  SMILES            "OpenEye OEToolkits"  2.0.4  "CC(=O)NC1C(CC(OC1C(C(COC(=O)C)O)O)(C(=O)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
5N6  "SYSTEMATIC NAME"            "OpenEye OEToolkits"  2.0.4  
;(2~{R},4~{S},5~{R},6~{R})-5-acetamido-6-[(1~{R},2~{R})-3-acetyloxy-1,2-bis(oxidanyl)propyl]-2,4-bis(oxidanyl)oxane-2-ca
rboxylic acid
;
  
5N6  "IUPAC CARBOHYDRATE SYMBOL"  PDB-CARE              1.0    a-D-Neup5Ac9Ac  
#
_pdbx_chem_comp_related.comp_id            5N6
_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  5N6  C11   SIA  C11   "Carbohydrate core"  
 2  5N6  C10   SIA  C10   "Carbohydrate core"  
 3  5N6  C9    SIA  C9    "Carbohydrate core"  
 4  5N6  C8    SIA  C8    "Carbohydrate core"  
 5  5N6  C7    SIA  C7    "Carbohydrate core"  
 6  5N6  C5    SIA  C5    "Carbohydrate core"  
 7  5N6  C4    SIA  C4    "Carbohydrate core"  
 8  5N6  C6    SIA  C6    "Carbohydrate core"  
 9  5N6  C3    SIA  C3    "Carbohydrate core"  
10  5N6  C2    SIA  C2    "Carbohydrate core"  
11  5N6  C1    SIA  C1    "Carbohydrate core"  
12  5N6  N5    SIA  N5    "Carbohydrate core"  
13  5N6  O2    SIA  O2    "Carbohydrate core"  
14  5N6  O9    SIA  O9    "Carbohydrate core"  
15  5N6  O10   SIA  O10   "Carbohydrate core"  
16  5N6  O7    SIA  O7    "Carbohydrate core"  
17  5N6  O8    SIA  O8    "Carbohydrate core"  
18  5N6  O4    SIA  O4    "Carbohydrate core"  
19  5N6  O6    SIA  O6    "Carbohydrate core"  
20  5N6  O1B   SIA  O1B   "Carbohydrate core"  
21  5N6  O1A   SIA  O1A   "Carbohydrate core"  
22  5N6  H7    SIA  H7    "Carbohydrate core"  
23  5N6  HN5   SIA  HN5   "Carbohydrate core"  
24  5N6  H5    SIA  H5    "Carbohydrate core"  
25  5N6  H4    SIA  H4    "Carbohydrate core"  
26  5N6  H6    SIA  H6    "Carbohydrate core"  
27  5N6  H32   SIA  H32   "Carbohydrate core"  
28  5N6  H31   SIA  H31   "Carbohydrate core"  
29  5N6  HO2   SIA  HO2   "Carbohydrate core"  
30  5N6  HO7   SIA  HO7   "Carbohydrate core"  
31  5N6  HO8   SIA  HO8   "Carbohydrate core"  
32  5N6  HO4   SIA  HO4   "Carbohydrate core"  
33  5N6  HO1B  SIA  HO1B  "Carbohydrate core"  
34  5N6  H111  SIA  H111  "Carbohydrate core"  
35  5N6  H113  SIA  H113  "Carbohydrate core"  
36  5N6  H112  SIA  H112  "Carbohydrate core"  
37  5N6  H92   SIA  H92   "Carbohydrate core"  
38  5N6  H91   SIA  H91   "Carbohydrate core"  
39  5N6  H8    SIA  H8    "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
5N6  "CARBOHYDRATE ISOMER"                  D         PDB  ?  
5N6  "CARBOHYDRATE RING"                    pyranose  PDB  ?  
5N6  "CARBOHYDRATE ANOMER"                  alpha     PDB  ?  
5N6  "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
5N6  "Create component"          2015-10-27  RCSB  
5N6  "Initial release"           2016-03-23  RCSB  
5N6  "Other modification"        2020-07-03  RCSB  
5N6  "Modify parent residue"     2020-07-17  RCSB  
5N6  "Modify name"               2020-07-17  RCSB  
5N6  "Modify synonyms"           2020-07-17  RCSB  
5N6  "Modify internal type"      2020-07-17  RCSB  
5N6  "Modify linking type"       2020-07-17  RCSB  
5N6  "Modify atom id"            2020-07-17  RCSB  
5N6  "Modify component atom id"  2020-07-17  RCSB  
5N6  "Modify leaving atom flag"  2020-07-17  RCSB  
##
