data_RZM
#

_chem_comp.id                                   RZM
_chem_comp.name                                 "(2R,3R,4R,5R)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-3-yl alpha-D-glucopyranoside"
_chem_comp.type                                 D-saccharide
_chem_comp.pdbx_type                            ATOMS
_chem_comp.formula                              "C12 H23 N O9"
_chem_comp.mon_nstd_parent_comp_id              GLC
_chem_comp.pdbx_synonyms                        
;(2R,3R,4R,5R)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-3-yl alpha-D-glucoside;
(2R,3R,4R,5R)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-3-yl D-glucoside;
(2R,3R,4R,5R)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-3-yl glucoside
;

_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2014-07-24
_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                       325.312
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    RZM
_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       4U2Y
_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  RZM  "(2R,3R,4R,5R)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-3-yl alpha-D-glucoside"  PDB  ?  
2  RZM  "(2R,3R,4R,5R)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-3-yl D-glucoside"        PDB  ?  
3  RZM  "(2R,3R,4R,5R)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-3-yl glucoside"          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
RZM  "O6'"  "O6'"  O  0  1  N  N  N  27.377  -29.467  278.987  -1.835   3.145   1.620  "O6'"  RZM   1  
RZM  "C6'"  "C6'"  C  0  1  N  N  N  27.245  -30.745  279.614  -1.352   2.313   0.563  "C6'"  RZM   2  
RZM  "C5'"  "C5'"  C  0  1  N  N  R  25.817  -31.076  280.038  -1.720   0.856   0.851  "C5'"  RZM   3  
RZM  "C2'"  "C2'"  C  0  1  N  N  R  23.807  -30.122  280.421  -3.505  -0.271  -0.285  "C2'"  RZM   4  
RZM  "C1'"  "C1'"  C  0  1  N  N  N  23.001  -30.388  281.516  -4.683  -1.157   0.124  "C1'"  RZM   5  
RZM  "O1'"  "O1'"  O  0  1  N  N  N  22.476  -29.096  281.922  -5.864  -0.360   0.232  "O1'"  RZM   6  
RZM  "C3'"  "C3'"  C  0  1  N  N  R  23.671  -31.228  279.271  -2.222  -1.122  -0.453  "C3'"  RZM   7  
RZM  "O3'"  "O3'"  O  0  1  N  N  N  22.529  -30.815  278.373  -2.144  -1.677  -1.768  "O3'"  RZM   8  
RZM  "C4'"  "C4'"  C  0  1  N  N  R  24.793  -31.139  278.719  -1.111  -0.063  -0.229  "C4'"  RZM   9  
RZM  O1     "O4'"  O  0  1  N  N  N  25.143  -32.278  277.850   0.086  -0.679   0.248  O1     RZM  10  
RZM  C1     C1     C  0  1  N  N  S  24.700  -32.030  276.542   0.993  -1.066  -0.786  C1     RZM  11  
RZM  C2     C2     C  0  1  N  N  R  24.367  -33.357  275.937   2.109  -1.928  -0.191  C2     RZM  12  
RZM  O2     O2     O  0  1  N  N  N  23.340  -33.969  276.754   1.539  -3.067   0.456  O2     RZM  13  
RZM  C3     C3     C  0  1  N  N  S  25.591  -34.192  275.830   2.895  -1.099   0.831  C3     RZM  14  
RZM  O3     O3     O  0  1  N  N  N  25.316  -35.529  275.325   3.983  -1.873   1.339  O3     RZM  15  
RZM  C4     C4     C  0  1  N  N  S  26.574  -33.507  274.959   3.435   0.159   0.144  C4     RZM  16  
RZM  O4     O4     O  0  1  N  N  N  27.751  -34.348  274.772   4.108   0.975   1.104  O4     RZM  17  
RZM  C5     C5     C  0  1  N  N  R  26.935  -32.214  275.636   2.268   0.940  -0.465  C5     RZM  18  
RZM  C6     C6     C  0  1  N  N  N  28.029  -31.448  274.963   2.806   2.167  -1.205  C6     RZM  19  
RZM  O6     O6     O  0  1  N  N  N  27.506  -30.774  273.831   1.712   2.958  -1.673  O6     RZM  20  
RZM  O5     O5     O  0  1  N  N  N  25.754  -31.328  275.786   1.562   0.102  -1.382  O5     RZM  21  
RZM  "N5'"  "N5'"  N  0  1  N  N  N  25.297  -30.139  280.783  -3.184   0.688   0.793  "N5'"  RZM  22  
RZM  H1A    H1     H  0  1  N  N  N  28.285  -29.323  278.749  -1.637   4.084   1.503  H1A    RZM  23  
RZM  H2A    H2     H  0  1  N  N  N  27.585  -31.516  278.906  -1.804   2.623  -0.379  H2A    RZM  24  
RZM  H3A    H3     H  0  1  N  N  N  27.885  -30.761  280.508  -0.268   2.407   0.494  H3A    RZM  25  
RZM  H4A    H4     H  0  1  N  N  N  25.799  -32.064  280.521  -1.352   0.569   1.836  H4A    RZM  26  
RZM  H5A    H5     H  0  1  N  N  N  23.561  -29.144  279.982  -3.734   0.260  -1.209  H5A    RZM  27  
RZM  H6     H6     H  0  1  N  N  N  22.182  -31.067  281.237  -4.834  -1.931  -0.629  H6     RZM  28  
RZM  H7     H7     H  0  1  N  N  N  23.590  -30.838  282.329  -4.470  -1.623   1.086  H7     RZM  29  
RZM  H8     H8     H  0  1  N  N  N  21.909  -29.207  282.676  -6.653  -0.858   0.489  H8     RZM  30  
RZM  H9     H9     H  0  1  N  N  N  23.461  -32.204  279.732  -2.172  -1.906   0.303  H9     RZM  31  
RZM  H10    H10    H  0  1  N  N  N  21.708  -30.903  278.843  -2.874  -2.272  -1.987  H10    RZM  32  
RZM  H11    H11    H  0  1  N  N  N  24.925  -30.200  278.162  -0.920   0.495  -1.146  H11    RZM  33  
RZM  H1     H12    H  0  1  N  N  N  23.793  -31.408  276.559   0.458  -1.637  -1.544  H1     RZM  34  
RZM  H2     H13    H  0  1  N  N  N  23.969  -33.188  274.926   2.779  -2.257  -0.986  H2     RZM  35  
RZM  HO2    H14    H  0  1  N  Y  N  22.582  -33.398  276.791   1.023  -3.636  -0.132  HO2    RZM  36  
RZM  H3     H15    H  0  1  N  N  N  26.030  -34.283  276.834   2.236  -0.812   1.651  H3     RZM  37  
RZM  HO3    H16    H  0  1  N  Y  N  24.685  -35.958  275.891   3.711  -2.689   1.783  HO3    RZM  38  
RZM  H4     H17    H  0  1  N  N  N  26.112  -33.289  273.985   4.132  -0.128  -0.644  H4     RZM  39  
RZM  HO4    H18    H  0  1  N  Y  N  27.498  -35.157  274.343   4.861   0.543   1.530  HO4    RZM  40  
RZM  H5     H19    H  0  1  N  N  N  27.288  -32.465  276.647   1.593   1.261   0.328  H5     RZM  41  
RZM  H61    H20    H  0  1  N  N  N  28.820  -32.142  274.643   3.420   2.760  -0.527  H61    RZM  42  
RZM  H62    H21    H  0  1  N  N  N  28.448  -30.713  275.666   3.410   1.844  -2.053  H62    RZM  43  
RZM  HO6    H22    H  0  1  N  Y  N  28.200  -30.287  273.403   1.979   3.754  -2.152  HO6    RZM  44  
RZM  H23    H23    H  0  1  N  N  N  25.420  -30.352  281.752  -3.546   0.370   1.680  H23    RZM  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
RZM  O6     C6     SING  N  N   1  
RZM  O4     C4     SING  N  N   2  
RZM  C4     C5     SING  N  N   3  
RZM  C4     C3     SING  N  N   4  
RZM  C6     C5     SING  N  N   5  
RZM  O3     C3     SING  N  N   6  
RZM  C5     O5     SING  N  N   7  
RZM  O5     C1     SING  N  N   8  
RZM  C3     C2     SING  N  N   9  
RZM  C2     C1     SING  N  N  10  
RZM  C2     O2     SING  N  N  11  
RZM  C1     O1     SING  N  N  12  
RZM  O1     "C4'"  SING  N  N  13  
RZM  "O3'"  "C3'"  SING  N  N  14  
RZM  "C4'"  "C3'"  SING  N  N  15  
RZM  "C4'"  "C5'"  SING  N  N  16  
RZM  "O6'"  "C6'"  SING  N  N  17  
RZM  "C3'"  "C2'"  SING  N  N  18  
RZM  "C6'"  "C5'"  SING  N  N  19  
RZM  "C5'"  "N5'"  SING  N  N  20  
RZM  "C2'"  "N5'"  SING  N  N  21  
RZM  "C2'"  "C1'"  SING  N  N  22  
RZM  "C1'"  "O1'"  SING  N  N  23  
RZM  "O6'"  H1A    SING  N  N  24  
RZM  "C6'"  H2A    SING  N  N  25  
RZM  "C6'"  H3A    SING  N  N  26  
RZM  "C5'"  H4A    SING  N  N  27  
RZM  "C2'"  H5A    SING  N  N  28  
RZM  "C1'"  H6     SING  N  N  29  
RZM  "C1'"  H7     SING  N  N  30  
RZM  "O1'"  H8     SING  N  N  31  
RZM  "C3'"  H9     SING  N  N  32  
RZM  "O3'"  H10    SING  N  N  33  
RZM  "C4'"  H11    SING  N  N  34  
RZM  C1     H1     SING  N  N  35  
RZM  C2     H2     SING  N  N  36  
RZM  O2     HO2    SING  N  N  37  
RZM  C3     H3     SING  N  N  38  
RZM  O3     HO3    SING  N  N  39  
RZM  C4     H4     SING  N  N  40  
RZM  O4     HO4    SING  N  N  41  
RZM  C5     H5     SING  N  N  42  
RZM  C6     H61    SING  N  N  43  
RZM  C6     H62    SING  N  N  44  
RZM  O6     HO6    SING  N  N  45  
RZM  "N5'"  H23    SING  N  N  46  
#   #
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
RZM  SMILES            ACDLabs               12.01  "O(C1C(O)C(NC1CO)CO)C2OC(C(O)C(O)C2O)CO"  
RZM  InChI             InChI                 1.03   "InChI=1S/C12H23NO9/c14-1-4-7(17)11(5(2-15)13-4)22-12-10(20)9(19)8(18)6(3-16)21-12/h4-20H,1-3H2/t4-,5-,6-,7-,8-,9+,10-,11-,12-/m1/s1"  
RZM  InChIKey          InChI                 1.03   AZDBETUGBOOBRU-BBFNFCGLSA-N  
RZM  SMILES_CANONICAL  CACTVS                3.385  "OC[C@H]1N[C@H](CO)[C@@H](O[C@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)[C@@H]1O"  
RZM  SMILES            CACTVS                3.385  "OC[CH]1N[CH](CO)[CH](O[CH]2O[CH](CO)[CH](O)[CH](O)[CH]2O)[CH]1O"  
RZM  SMILES_CANONICAL  "OpenEye OEToolkits"  1.9.2  "C([C@@H]1[C@H]([C@@H]([C@H](N1)CO)O[C@@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O)O)O"  
RZM  SMILES            "OpenEye OEToolkits"  1.9.2  "C(C1C(C(C(N1)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
RZM  "SYSTEMATIC NAME"  ACDLabs               12.01  "(2R,3R,4R,5R)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-3-yl alpha-D-glucopyranoside"  
RZM  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.9.2  
;(2S,3R,4S,5S,6R)-2-[(2R,3R,4R,5R)-2,5-bis(hydroxymethyl)-4-oxidanyl-pyrrolidin-3-yl]oxy-6-(hydroxymethyl)oxane-3,4,5-tr
iol
;
  
#
_pdbx_chem_comp_related.comp_id            RZM
_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  RZM  C1   GLC  C1   "Carbohydrate core"  
 2  RZM  C2   GLC  C2   "Carbohydrate core"  
 3  RZM  C3   GLC  C3   "Carbohydrate core"  
 4  RZM  C4   GLC  C4   "Carbohydrate core"  
 5  RZM  C5   GLC  C5   "Carbohydrate core"  
 6  RZM  C6   GLC  C6   "Carbohydrate core"  
 7  RZM  O2   GLC  O2   "Carbohydrate core"  
 8  RZM  O3   GLC  O3   "Carbohydrate core"  
 9  RZM  O4   GLC  O4   "Carbohydrate core"  
10  RZM  O1   GLC  O1   "Carbohydrate core"  
11  RZM  O5   GLC  O5   "Carbohydrate core"  
12  RZM  O6   GLC  O6   "Carbohydrate core"  
13  RZM  H1   GLC  H1   "Carbohydrate core"  
14  RZM  H2   GLC  H2   "Carbohydrate core"  
15  RZM  HO2  GLC  HO2  "Carbohydrate core"  
16  RZM  H3   GLC  H3   "Carbohydrate core"  
17  RZM  HO3  GLC  HO3  "Carbohydrate core"  
18  RZM  H4   GLC  H4   "Carbohydrate core"  
19  RZM  HO4  GLC  HO4  "Carbohydrate core"  
20  RZM  H5   GLC  H5   "Carbohydrate core"  
21  RZM  H61  GLC  H61  "Carbohydrate core"  
22  RZM  H62  GLC  H62  "Carbohydrate core"  
23  RZM  HO6  GLC  HO6  "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
RZM  "CARBOHYDRATE ISOMER"                  D         PDB  ?  
RZM  "CARBOHYDRATE RING"                    pyranose  PDB  ?  
RZM  "CARBOHYDRATE ANOMER"                  alpha     PDB  ?  
RZM  "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
RZM  "Create component"          2014-07-24  RCSB  
RZM  "Other modification"        2014-08-05  RCSB  
RZM  "Modify descriptor"         2014-09-05  RCSB  
RZM  "Initial release"           2015-08-12  RCSB  
RZM  "Other modification"        2020-07-03  RCSB  
RZM  "Modify parent residue"     2020-07-17  RCSB  
RZM  "Modify synonyms"           2020-07-17  RCSB  
RZM  "Modify linking type"       2020-07-17  RCSB  
RZM  "Modify atom id"            2020-07-17  RCSB  
RZM  "Modify component atom id"  2020-07-17  RCSB  
RZM  "Modify leaving atom flag"  2020-07-17  RCSB  
##
