data_RY7
#

_chem_comp.id                                   RY7
_chem_comp.name                                 "4,6-dideoxy-4-{[(1S,2S,3S,4R,5R)-2,3,4-trihydroxy-5-(hydroxymethyl)cyclohexyl]amino}-alpha-D-glucopyranose"
_chem_comp.type                                 "D-saccharide, alpha linking"
_chem_comp.pdbx_type                            ATOMS
_chem_comp.formula                              "C13 H25 N O8"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2020-03-02
_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                       323.340
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    RY7
_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       1GAI
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 RCSB
#   #
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
RY7  C1A   C1A   C  0  1  N  N  S  33.170  20.622   8.181   0.855  -0.516   1.181  C1A   RY7   1  
RY7  C2A   C2A   C  0  1  N  N  S  34.370  20.482   9.121   1.391   0.892   1.445  C2A   RY7   2  
RY7  C3A   C3A   C  0  1  N  N  S  33.998  19.616  10.323   2.185   1.371   0.228  C3A   RY7   3  
RY7  C4A   C4A   C  0  1  N  N  R  32.901  20.289  11.143   3.355   0.419  -0.025  C4A   RY7   4  
RY7  C5A   C5A   C  0  1  N  N  R  31.630  20.514  10.300   2.819  -0.989  -0.289  C5A   RY7   5  
RY7  C6A   C6A   C  0  1  N  N  N  30.612  21.349  11.082   3.989  -1.942  -0.541  C6A   RY7   6  
RY7  C7A   C7A   C  0  1  N  N  N  31.948  21.184   8.934   2.025  -1.469   0.928  C7A   RY7   7  
RY7  O2A   O2A   O  0  1  N  N  N  35.453  19.879   8.431   0.298   1.781   1.681  O2A   RY7   8  
RY7  O3A   O3A   O  0  1  N  N  N  35.144  19.427  11.142   2.685   2.687   0.474  O3A   RY7   9  
RY7  O4A   O4A   O  0  1  N  N  N  32.594  19.474  12.273   4.096   0.867  -1.162  O4A   RY7  10  
RY7  O6A   O6A   O  0  1  N  N  N  31.127  22.642  11.401   4.661  -1.562  -1.744  O6A   RY7  11  
RY7  C1    C1    C  0  1  N  N  S  31.706  18.270   3.522  -4.229  -0.463  -0.224  C1    RY7  12  
RY7  C2    C2    C  0  1  N  N  R  33.179  18.615   3.786  -3.539   0.903  -0.241  C2    RY7  13  
RY7  C3    C3    C  0  1  N  N  S  33.494  18.445   5.286  -2.064   0.716  -0.609  C3    RY7  14  
RY7  C4    C4    C  0  1  N  N  S  32.573  19.381   6.087  -1.418  -0.249   0.389  C4    RY7  15  
RY7  C5    C5    C  0  1  N  N  R  31.127  18.938   5.790  -2.190  -1.571   0.382  C5    RY7  16  
RY7  C6    C6    C  0  1  N  N  N  30.066  19.772   6.483  -1.588  -2.519   1.421  C6    RY7  17  
RY7  N4    N4    N  0  1  N  N  N  32.876  19.318   7.536  -0.022  -0.494   0.003  N4    RY7  18  
RY7  O2    O2    O  0  1  N  N  N  34.002  17.737   3.025  -4.169   1.745  -1.209  O2    RY7  19  
RY7  O3    O3    O  0  1  N  N  N  34.864  18.740   5.542  -1.394   1.977  -0.557  O3    RY7  20  
RY7  O5    O5    O  0  1  N  N  N  30.863  19.049   4.371  -3.561  -1.322   0.702  O5    RY7  21  
RY7  O1    O1    O  0  1  N  Y  N  31.575  16.907   3.824  -4.178  -1.040  -1.530  O1    RY7  22  
RY7  H1A   H1A   H  0  1  N  N  N  33.440  21.344   7.396   0.289  -0.858   2.048  H1A   RY7  23  
RY7  H2A   H2A   H  0  1  N  N  N  34.656  21.482   9.480   2.041   0.876   2.319  H2A   RY7  24  
RY7  H3A   H3A   H  0  1  N  N  N  33.625  18.647   9.960   1.534   1.388  -0.647  H3A   RY7  25  
RY7  H4A   H4A   H  0  1  N  N  N  33.269  21.269  11.480   4.006   0.403   0.849  H4A   RY7  26  
RY7  H5A   H5A   H  0  1  N  N  N  31.180  19.531  10.096   2.168  -0.973  -1.163  H5A   RY7  27  
RY7  H6A1  H6A1  H  0  0  N  N  N  29.704  21.467  10.473   4.686  -1.891   0.295  H6A1  RY7  28  
RY7  H6A2  H6A2  H  0  0  N  N  N  30.362  20.824  12.016   3.614  -2.960  -0.641  H6A2  RY7  29  
RY7  H7A1  H7A1  H  0  0  N  N  N  32.126  22.254   9.116   2.676  -1.485   1.803  H7A1  RY7  30  
RY7  H7A2  H7A2  H  0  0  N  N  N  31.067  21.064   8.286   1.643  -2.472   0.741  H7A2  RY7  31  
RY7  HOA2  HOA2  H  0  0  N  N  N  36.195  19.794   9.018   0.564   2.694   1.855  HOA2  RY7  32  
RY7  HOA3  HOA3  H  0  0  N  N  N  34.914  18.888  11.890   3.200   3.055  -0.258  HOA3  RY7  33  
RY7  HOA4  HOA4  H  0  0  N  N  N  33.380  19.338  12.789   4.467   1.755  -1.065  HOA4  RY7  34  
RY7  HOA6  HOA6  H  0  0  N  N  N  30.473  23.133  11.884   5.416  -2.124  -1.967  HOA6  RY7  35  
RY7  H1    H1    H  0  1  N  N  N  31.475  18.463   2.464  -5.269  -0.341   0.079  H1    RY7  36  
RY7  H2    H2    H  0  1  N  N  N  33.360  19.661   3.499  -3.613   1.361   0.745  H2    RY7  37  
RY7  H3    H3    H  0  1  N  N  N  33.272  17.407   5.573  -1.988   0.305  -1.616  H3    RY7  38  
RY7  H4    H4    H  0  1  N  N  N  32.710  20.411   5.725  -1.448   0.186   1.388  H4    RY7  39  
RY7  H5    H5    H  0  1  N  N  N  31.014  17.890   6.106  -2.124  -2.025  -0.606  H5    RY7  40  
RY7  H62   H62   H  0  1  N  N  N  30.216  19.726   7.572  -1.551  -2.021   2.390  H62   RY7  41  
RY7  H63   H63   H  0  1  N  N  N  30.143  20.816   6.146  -2.205  -3.415   1.496  H63   RY7  42  
RY7  H61   H61   H  0  1  N  N  N  29.070  19.379   6.233  -0.579  -2.797   1.117  H61   RY7  43  
RY7  HN41  HN41  H  0  0  N  N  N  32.086  18.915   7.999   0.062  -1.349  -0.526  HN41  RY7  44  
RY7  HO2   HO2   H  0  1  N  Y  N  34.916  17.943   3.182  -5.109   1.902  -1.040  HO2   RY7  45  
RY7  HO3   HO3   H  0  1  N  Y  N  35.044  18.631   6.468  -1.756   2.641  -1.160  HO3   RY7  46  
RY7  HO1   HO1   H  0  1  N  Y  N  30.677  16.635   3.678  -4.598  -1.909  -1.594  HO1   RY7  47  
#   #
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
RY7  O2   C2    SING  N  N   1  
RY7  C1   C2    SING  N  N   2  
RY7  C1   O1    SING  N  N   3  
RY7  C1   O5    SING  N  N   4  
RY7  C2   C3    SING  N  N   5  
RY7  O5   C5    SING  N  N   6  
RY7  C3   O3    SING  N  N   7  
RY7  C3   C4    SING  N  N   8  
RY7  C5   C4    SING  N  N   9  
RY7  C5   C6    SING  N  N  10  
RY7  C4   N4    SING  N  N  11  
RY7  N4   C1A   SING  N  N  12  
RY7  C1A  C7A   SING  N  N  13  
RY7  C1A  C2A   SING  N  N  14  
RY7  O2A  C2A   SING  N  N  15  
RY7  C7A  C5A   SING  N  N  16  
RY7  C2A  C3A   SING  N  N  17  
RY7  C5A  C6A   SING  N  N  18  
RY7  C5A  C4A   SING  N  N  19  
RY7  C3A  O3A   SING  N  N  20  
RY7  C3A  C4A   SING  N  N  21  
RY7  C6A  O6A   SING  N  N  22  
RY7  C4A  O4A   SING  N  N  23  
RY7  C1A  H1A   SING  N  N  24  
RY7  C2A  H2A   SING  N  N  25  
RY7  C3A  H3A   SING  N  N  26  
RY7  C4A  H4A   SING  N  N  27  
RY7  C5A  H5A   SING  N  N  28  
RY7  C6A  H6A1  SING  N  N  29  
RY7  C6A  H6A2  SING  N  N  30  
RY7  C7A  H7A1  SING  N  N  31  
RY7  C7A  H7A2  SING  N  N  32  
RY7  O2A  HOA2  SING  N  N  33  
RY7  O3A  HOA3  SING  N  N  34  
RY7  O4A  HOA4  SING  N  N  35  
RY7  O6A  HOA6  SING  N  N  36  
RY7  C1   H1    SING  N  N  37  
RY7  C2   H2    SING  N  N  38  
RY7  C3   H3    SING  N  N  39  
RY7  C4   H4    SING  N  N  40  
RY7  C5   H5    SING  N  N  41  
RY7  C6   H62   SING  N  N  42  
RY7  C6   H63   SING  N  N  43  
RY7  C6   H61   SING  N  N  44  
RY7  N4   HN41  SING  N  N  45  
RY7  O2   HO2   SING  N  N  46  
RY7  O3   HO3   SING  N  N  47  
RY7  O1   HO1   SING  N  N  48  
#   #
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
RY7  SMILES            ACDLabs               12.01  "C1(CC(C(C(C1O)O)O)CO)NC2C(C(C(O)OC2C)O)O"  
RY7  InChI             InChI                 1.03   "InChI=1S/C13H25NO8/c1-4-7(10(18)12(20)13(21)22-4)14-6-2-5(3-15)8(16)11(19)9(6)17/h4-21H,2-3H2,1H3/t4-,5-,6+,7-,8-,9+,10+,11+,12-,13+/m1/s1"  
RY7  InChIKey          InChI                 1.03   PFUNPXBPUXETIR-KJEWDVBSSA-N  
RY7  SMILES_CANONICAL  CACTVS                3.385  "C[C@H]1O[C@H](O)[C@H](O)[C@@H](O)[C@@H]1N[C@H]2C[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O"  
RY7  SMILES            CACTVS                3.385  "C[CH]1O[CH](O)[CH](O)[CH](O)[CH]1N[CH]2C[CH](CO)[CH](O)[CH](O)[CH]2O"  
RY7  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "C[C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O)O)O)N[C@H]2C[C@@H]([C@H]([C@@H]([C@H]2O)O)O)CO"  
RY7  SMILES            "OpenEye OEToolkits"  2.0.7  "CC1C(C(C(C(O1)O)O)O)NC2CC(C(C(C2O)O)O)CO"  
#   #
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
RY7  "SYSTEMATIC NAME"  ACDLabs               12.01  "4,6-dideoxy-4-{[(1S,2S,3S,4R,5R)-2,3,4-trihydroxy-5-(hydroxymethyl)cyclohexyl]amino}-alpha-D-glucopyranose"  
RY7  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  "(2~{S},3~{R},4~{S},5~{S},6~{R})-5-[[(1~{S},2~{S},3~{S},4~{R},5~{R})-5-(hydroxymethyl)-2,3,4-tris(oxidanyl)cyclohexyl]amino]-6-methyl-oxane-2,3,4-triol"  
#   #
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
RY7  "CARBOHYDRATE ISOMER"                  D         PDB  ?  
RY7  "CARBOHYDRATE RING"                    pyranose  PDB  ?  
RY7  "CARBOHYDRATE ANOMER"                  alpha     PDB  ?  
RY7  "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
RY7  "Create component"  2020-03-02  RCSB  
RY7  "Modify name"       2020-06-01  RCSB  
RY7  "Initial release"   2020-07-29  RCSB  
##
