data_9KJ
#

_chem_comp.id                                   9KJ
_chem_comp.name                                 "{[(2R,3R,4R,5R)-3-(alpha-D-glucopyranosyloxy)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-1-yl]methyl}phosphonic acid"
_chem_comp.type                                 D-saccharide
_chem_comp.pdbx_type                            ATOMS
_chem_comp.formula                              "C13 H26 N O12 P"
_chem_comp.mon_nstd_parent_comp_id              GLC
_chem_comp.pdbx_synonyms                        
;{[(2R,3R,4R,5R)-3-(alpha-D-glucosyloxy)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-1-yl]methyl}phosphonic acid;
{[(2R,3R,4R,5R)-3-(D-glucosyloxy)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-1-yl]methyl}phosphonic acid;
{[(2R,3R,4R,5R)-3-(glucosyloxy)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-1-yl]methyl}phosphonic acid
;

_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2017-05-17
_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                       419.319
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    9KJ
_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       5VT4
_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  9KJ  "{[(2R,3R,4R,5R)-3-(alpha-D-glucosyloxy)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-1-yl]methyl}phosphonic acid"  PDB  ?  
2  9KJ  "{[(2R,3R,4R,5R)-3-(D-glucosyloxy)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-1-yl]methyl}phosphonic acid"        PDB  ?  
3  9KJ  "{[(2R,3R,4R,5R)-3-(glucosyloxy)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-1-yl]methyl}phosphonic 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
9KJ  C20  C20  C  0  1  N  N  N  140.158  145.642  -342.805   0.508   1.741  -0.219  C20  9KJ   1  
9KJ  C2   C22  C  0  1  N  N  R  136.887  148.539  -346.317  -3.746  -1.533  -0.083  C2   9KJ   2  
9KJ  C3   C24  C  0  1  N  N  S  135.876  147.410  -346.589  -4.139  -0.472  -1.115  C3   9KJ   3  
9KJ  C4   C26  C  0  1  N  N  S  136.579  146.156  -347.133  -4.467   0.835  -0.387  C4   9KJ   4  
9KJ  O4   O27  O  0  1  N  N  N  135.650  145.051  -347.198  -4.765   1.853  -1.345  O4   9KJ   5  
9KJ  O6   O01  O  0  1  N  N  N  139.797  145.016  -347.184  -2.438   2.994   1.921  O6   9KJ   6  
9KJ  C6   C02  C  0  1  N  N  N  138.492  144.560  -346.838  -3.600   2.533   1.229  C6   9KJ   7  
9KJ  C5   C03  C  0  1  N  N  R  137.780  145.783  -346.246  -3.259   1.260   0.452  C5   9KJ   8  
9KJ  O5   O04  O  0  1  N  N  N  138.727  146.854  -346.098  -2.928   0.216   1.369  O5   9KJ   9  
9KJ  C1   C05  C  0  1  N  N  S  138.164  148.076  -345.608  -2.566  -1.017   0.744  C1   9KJ  10  
9KJ  O1   O06  O  0  1  N  N  N  137.858  147.931  -344.225  -1.441  -0.806  -0.111  O1   9KJ  11  
9KJ  C07  C07  C  0  1  N  N  R  139.095  147.805  -343.525  -0.222  -0.541   0.587  C07  9KJ  12  
9KJ  C08  C08  C  0  1  N  N  R  139.399  149.028  -342.627   0.560  -1.853   0.859  C08  9KJ  13  
9KJ  O09  O09  O  0  1  N  N  N  140.244  149.972  -343.272   0.141  -2.445   2.090  O09  9KJ  14  
9KJ  C10  C10  C  0  1  N  N  R  140.162  148.294  -341.528   2.023  -1.373   0.954  C10  9KJ  15  
9KJ  C11  C11  C  0  1  N  N  N  140.514  149.238  -340.373   2.951  -2.395   0.295  C11  9KJ  16  
9KJ  O12  O12  O  0  1  N  N  N  141.814  148.862  -339.915   2.471  -2.697  -1.017  O12  9KJ  17  
9KJ  N13  N13  N  0  1  N  N  N  139.189  147.250  -341.197   2.107  -0.085   0.240  N13  9KJ  18  
9KJ  C14  C14  C  0  1  N  N  N  137.882  147.840  -340.855   3.117  -0.140  -0.826  C14  9KJ  19  
9KJ  P15  P15  P  0  1  N  N  N  137.670  147.996  -338.985   4.604   0.775  -0.302  P15  9KJ  20  
9KJ  O16  O16  O  0  1  N  N  N  137.410  149.440  -338.561   5.300   0.007   0.930  O16  9KJ  21  
9KJ  O17  O17  O  0  1  N  N  N  138.928  147.506  -338.365   5.639   0.866  -1.532  O17  9KJ  22  
9KJ  O18  O18  O  0  1  N  N  N  136.524  147.127  -338.567   4.220   2.140   0.122  O18  9KJ  23  
9KJ  C19  C19  C  0  1  N  N  R  139.024  146.634  -342.520   0.773   0.236  -0.310  C19  9KJ  24  
9KJ  O21  O21  O  0  1  N  N  N  140.275  144.821  -341.656   1.357   2.430  -1.140  O21  9KJ  25  
9KJ  O2   O23  O  0  1  N  N  N  136.272  149.484  -345.427  -3.368  -2.736  -0.756  O2   9KJ  26  
9KJ  O3   O25  O  0  1  N  N  N  134.934  147.858  -347.568  -5.285  -0.915  -1.845  O3   9KJ  27  
9KJ  H1A  H1   H  0  1  N  N  N  139.914  145.030  -343.686  -0.534   1.942  -0.466  H1A  9KJ  28  
9KJ  H2A  H2   H  0  1  N  N  N  141.099  146.182  -342.983   0.715   2.086   0.794  H2A  9KJ  29  
9KJ  H2   H3   H  0  1  N  N  N  137.155  149.021  -347.269  -4.592  -1.734   0.574  H2   9KJ  30  
9KJ  H3   H4   H  0  1  N  N  N  135.363  147.155  -345.650  -3.310  -0.308  -1.804  H3   9KJ  31  
9KJ  H4   H5   H  0  1  N  N  N  136.953  146.381  -348.143  -5.328   0.684   0.264  H4   9KJ  32  
9KJ  HO4  H6   H  0  1  N  Y  N  136.095  144.282  -347.535  -5.518   1.648  -1.916  HO4  9KJ  33  
9KJ  HO6  H7   H  0  1  N  Y  N  140.294  144.299  -347.560  -2.581   3.800   2.436  HO6  9KJ  34  
9KJ  H61  H8   H  0  1  N  N  N  137.960  144.199  -347.731  -4.390   2.319   1.949  H61  9KJ  35  
9KJ  H62  H9   H  0  1  N  N  N  138.551  143.751  -346.095  -3.939   3.302   0.535  H62  9KJ  36  
9KJ  H5   H10  H  0  1  N  N  N  137.393  145.503  -345.255  -2.410   1.451  -0.204  H5   9KJ  37  
9KJ  H1   H11  H  0  1  N  N  N  138.910  148.876  -345.722  -2.310  -1.751   1.508  H1   9KJ  38  
9KJ  H12  H12  H  0  1  N  N  N  139.932  147.643  -344.220  -0.415  -0.003   1.515  H12  9KJ  39  
9KJ  H13  H13  H  0  1  N  N  N  138.471  149.475  -342.241   0.437  -2.553   0.032  H13  9KJ  40  
9KJ  H14  H14  H  0  1  N  N  N  140.405  150.704  -342.688   0.600  -3.269   2.306  H14  9KJ  41  
9KJ  H15  H15  H  0  1  N  N  N  141.081  147.853  -341.941   2.301  -1.236   1.999  H15  9KJ  42  
9KJ  H16  H16  H  0  1  N  N  N  140.523  150.280  -340.725   3.957  -1.983   0.228  H16  9KJ  43  
9KJ  H17  H17  H  0  1  N  N  N  139.781  149.132  -339.560   2.970  -3.306   0.893  H17  9KJ  44  
9KJ  H18  H18  H  0  1  N  N  N  142.072  149.426  -339.195   3.012  -3.340  -1.495  H18  9KJ  45  
9KJ  H20  H20  H  0  1  N  N  N  137.810  148.839  -341.309   3.380  -1.179  -1.024  H20  9KJ  46  
9KJ  H21  H21  H  0  1  N  N  N  137.083  147.198  -341.254   2.713   0.312  -1.732  H21  9KJ  47  
9KJ  H22  H22  H  0  1  N  N  N  136.572  149.494  -338.117   5.513  -0.919   0.747  H22  9KJ  48  
9KJ  H23  H23  H  0  1  N  N  N  138.742  146.742  -337.832   6.456   1.341  -1.324  H23  9KJ  49  
9KJ  H24  H24  H  0  1  N  N  N  138.050  146.129  -342.601   0.695  -0.100  -1.343  H24  9KJ  50  
9KJ  H25  H25  H  0  1  N  N  N  140.970  144.187  -341.789   1.243   3.390  -1.136  H25  9KJ  51  
9KJ  HO2  H26  H  0  1  N  Y  N  136.880  150.191  -345.245  -3.102  -3.452  -0.162  HO2  9KJ  52  
9KJ  HO3  H27  H  0  1  N  Y  N  134.489  148.634  -347.248  -5.149  -1.743  -2.326  HO3  9KJ  53  
#   #
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
9KJ  O3   C3   SING  N  N   1  
9KJ  O4   C4   SING  N  N   2  
9KJ  O6   C6   SING  N  N   3  
9KJ  C4   C3   SING  N  N   4  
9KJ  C4   C5   SING  N  N   5  
9KJ  C6   C5   SING  N  N   6  
9KJ  C3   C2   SING  N  N   7  
9KJ  C2   C1   SING  N  N   8  
9KJ  C2   O2   SING  N  N   9  
9KJ  C5   O5   SING  N  N  10  
9KJ  O5   C1   SING  N  N  11  
9KJ  C1   O1   SING  N  N  12  
9KJ  O1   C07  SING  N  N  13  
9KJ  C07  C08  SING  N  N  14  
9KJ  C07  C19  SING  N  N  15  
9KJ  O09  C08  SING  N  N  16  
9KJ  C20  C19  SING  N  N  17  
9KJ  C20  O21  SING  N  N  18  
9KJ  C08  C10  SING  N  N  19  
9KJ  C19  N13  SING  N  N  20  
9KJ  C10  N13  SING  N  N  21  
9KJ  C10  C11  SING  N  N  22  
9KJ  N13  C14  SING  N  N  23  
9KJ  C14  P15  SING  N  N  24  
9KJ  C11  O12  SING  N  N  25  
9KJ  P15  O18  DOUB  N  N  26  
9KJ  P15  O16  SING  N  N  27  
9KJ  P15  O17  SING  N  N  28  
9KJ  C20  H1A  SING  N  N  29  
9KJ  C20  H2A  SING  N  N  30  
9KJ  C2   H2   SING  N  N  31  
9KJ  C3   H3   SING  N  N  32  
9KJ  C4   H4   SING  N  N  33  
9KJ  O4   HO4  SING  N  N  34  
9KJ  O6   HO6  SING  N  N  35  
9KJ  C6   H61  SING  N  N  36  
9KJ  C6   H62  SING  N  N  37  
9KJ  C5   H5   SING  N  N  38  
9KJ  C1   H1   SING  N  N  39  
9KJ  C07  H12  SING  N  N  40  
9KJ  C08  H13  SING  N  N  41  
9KJ  O09  H14  SING  N  N  42  
9KJ  C10  H15  SING  N  N  43  
9KJ  C11  H16  SING  N  N  44  
9KJ  C11  H17  SING  N  N  45  
9KJ  O12  H18  SING  N  N  46  
9KJ  C14  H20  SING  N  N  47  
9KJ  C14  H21  SING  N  N  48  
9KJ  O16  H22  SING  N  N  49  
9KJ  O17  H23  SING  N  N  50  
9KJ  C19  H24  SING  N  N  51  
9KJ  O21  H25  SING  N  N  52  
9KJ  O2   HO2  SING  N  N  53  
9KJ  O3   HO3  SING  N  N  54  
#   #
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
9KJ  SMILES            ACDLabs               12.01  "C(C2C(OC1C(O)C(C(C(CO)O1)O)O)C(C(N2CP(=O)(O)O)CO)O)O"  
9KJ  InChI             InChI                 1.03   "InChI=1S/C13H26NO12P/c15-1-5-8(18)12(6(2-16)14(5)4-27(22,23)24)26-13-11(21)10(20)9(19)7(3-17)25-13/h5-13,15-21H,1-4H2,(H2,22,23,24)/t5-,6-,7-,8-,9-,10+,11-,12-,13-/m1/s1"  
9KJ  InChIKey          InChI                 1.03   QVTCDBMCRXGRKE-DFIZWEOJSA-N  
9KJ  SMILES_CANONICAL  CACTVS                3.385  "OC[C@H]1O[C@H](O[C@H]2[C@H](O)[C@@H](CO)N(C[P](O)(O)=O)[C@@H]2CO)[C@H](O)[C@@H](O)[C@@H]1O"  
9KJ  SMILES            CACTVS                3.385  "OC[CH]1O[CH](O[CH]2[CH](O)[CH](CO)N(C[P](O)(O)=O)[CH]2CO)[CH](O)[CH](O)[CH]1O"  
9KJ  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.6  "C([C@@H]1[C@H]([C@@H]([C@H](N1CP(=O)(O)O)CO)O[C@@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O)O)O"  
9KJ  SMILES            "OpenEye OEToolkits"  2.0.6  "C(C1C(C(C(N1CP(=O)(O)O)CO)OC2C(C(C(C(O2)CO)O)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
9KJ  "SYSTEMATIC NAME"  ACDLabs               12.01  "{[(2R,3R,4R,5R)-3-(alpha-D-glucopyranosyloxy)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-1-yl]methyl}phosphonic acid"  
9KJ  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.6  
;[(2~{R},3~{R},4~{R},5~{R})-2,5-bis(hydroxymethyl)-3-[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxida
nyl)oxan-2-yl]oxy-4-oxidanyl-pyrrolidin-1-yl]methylphosphonic acid
;
  
#
_pdbx_chem_comp_related.comp_id            9KJ
_pdbx_chem_comp_related.related_comp_id    GLC
_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  9KJ  C6   GLC  C6   "Carbohydrate core"  
 2  9KJ  C5   GLC  C5   "Carbohydrate core"  
 3  9KJ  C1   GLC  C1   "Carbohydrate core"  
 4  9KJ  C2   GLC  C2   "Carbohydrate core"  
 5  9KJ  C3   GLC  C3   "Carbohydrate core"  
 6  9KJ  C4   GLC  C4   "Carbohydrate core"  
 7  9KJ  O6   GLC  O6   "Carbohydrate core"  
 8  9KJ  O5   GLC  O5   "Carbohydrate core"  
 9  9KJ  O1   GLC  O1   "Carbohydrate core"  
10  9KJ  O2   GLC  O2   "Carbohydrate core"  
11  9KJ  O3   GLC  O3   "Carbohydrate core"  
12  9KJ  O4   GLC  O4   "Carbohydrate core"  
13  9KJ  H5   GLC  H5   "Carbohydrate core"  
14  9KJ  H1   GLC  H1   "Carbohydrate core"  
15  9KJ  HO2  GLC  HO2  "Carbohydrate core"  
16  9KJ  HO3  GLC  HO3  "Carbohydrate core"  
17  9KJ  H2   GLC  H2   "Carbohydrate core"  
18  9KJ  H3   GLC  H3   "Carbohydrate core"  
19  9KJ  H4   GLC  H4   "Carbohydrate core"  
20  9KJ  HO4  GLC  HO4  "Carbohydrate core"  
21  9KJ  HO6  GLC  HO6  "Carbohydrate core"  
22  9KJ  H61  GLC  H61  "Carbohydrate core"  
23  9KJ  H62  GLC  H62  "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
9KJ  "CARBOHYDRATE ISOMER"                  D         PDB  ?  
9KJ  "CARBOHYDRATE RING"                    pyranose  PDB  ?  
9KJ  "CARBOHYDRATE ANOMER"                  alpha     PDB  ?  
9KJ  "CARBOHYDRATE PRIMARY CARBONYL GROUP"  aldose    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
9KJ  "Create component"          2017-05-17  RCSB  
9KJ  "Initial release"           2017-06-07  RCSB  
9KJ  "Other modification"        2020-07-03  RCSB  
9KJ  "Modify parent residue"     2020-07-17  RCSB  
9KJ  "Modify synonyms"           2020-07-17  RCSB  
9KJ  "Modify internal type"      2020-07-17  RCSB  
9KJ  "Modify linking type"       2020-07-17  RCSB  
9KJ  "Modify atom id"            2020-07-17  RCSB  
9KJ  "Modify component atom id"  2020-07-17  RCSB  
9KJ  "Modify leaving atom flag"  2020-07-17  RCSB  
##
