data_Z3D
#

_chem_comp.id                                   Z3D
_chem_comp.name                                 "(1R,2R,3S,4S,6R)-4-amino-2,3-dihydroxy-6-(hydroxymethyl)cyclohexyl alpha-D-glucopyranoside"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C13 H25 N O9"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2021-04-07
_chem_comp.pdbx_modified_date                   2021-07-09
_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                       339.339
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    Z3D
_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       7MEL
_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
Z3D  C02  C1   C  0  1  N  N  R  25.420  -26.112  345.875   2.228   1.099  -0.274  C02  Z3D   1  
Z3D  C03  C2   C  0  1  N  N  R  25.336  -24.711  346.521   1.164   0.006  -0.161  C03  Z3D   2  
Z3D  C05  C3   C  0  1  N  N  S  24.469  -24.939  348.706  -0.889   1.133  -0.671  C05  Z3D   3  
Z3D  C06  C4   C  0  1  N  N  R  23.173  -25.308  349.431  -1.987   1.972  -0.014  C06  Z3D   4  
Z3D  C08  C5   C  0  1  N  N  S  22.300  -24.097  349.613  -2.857   1.066   0.863  C08  Z3D   5  
Z3D  C10  C6   C  0  1  N  N  S  23.005  -22.987  350.299  -3.427  -0.065   0.001  C10  Z3D   6  
Z3D  C12  C7   C  0  1  N  N  R  24.259  -22.640  349.503  -2.273  -0.826  -0.657  C12  Z3D   7  
Z3D  C13  C8   C  0  1  N  N  N  25.103  -21.543  350.099  -2.836  -1.920  -1.567  C13  Z3D   8  
Z3D  C16  C9   C  0  1  N  N  R  25.209  -23.673  345.391   1.652  -1.084   0.796  C16  Z3D   9  
Z3D  C17  C10  C  0  1  N  N  N  25.120  -22.253  345.977   0.587  -2.177   0.909  C17  Z3D  10  
Z3D  C19  C11  C  0  1  N  N  N  26.418  -23.742  344.445   2.950  -1.690   0.260  C19  Z3D  11  
Z3D  C20  C12  C  0  1  N  N  S  26.598  -25.150  343.837   4.015  -0.596   0.147  C20  Z3D  12  
Z3D  C22  C13  C  0  1  N  N  S  26.650  -26.210  344.962   3.527   0.493  -0.811  C22  Z3D  13  
Z3D  N21  N1   N  0  1  N  N  N  25.493  -25.444  342.922   4.258  -0.011   1.472  N21  Z3D  14  
Z3D  O01  O1   O  0  1  N  N  N  25.464  -27.111  346.888   1.773   2.117  -1.168  O01  Z3D  15  
Z3D  O04  O2   O  0  1  N  N  N  24.196  -24.615  347.362  -0.049   0.572   0.339  O04  Z3D  16  
Z3D  O07  O3   O  0  1  N  N  N  22.490  -26.308  348.648  -1.392   2.989   0.794  O07  Z3D  17  
Z3D  O09  O4   O  0  1  N  N  N  21.095  -24.459  350.371  -3.929   1.827   1.422  O09  Z3D  18  
Z3D  O11  O5   O  0  1  N  N  N  22.143  -21.871  350.439  -4.181  -0.959   0.823  O11  Z3D  19  
Z3D  O14  O6   O  0  1  N  N  N  25.598  -21.873  351.382  -1.762  -2.704  -2.090  O14  Z3D  20  
Z3D  O15  O7   O  0  1  N  N  N  25.133  -23.832  349.366  -1.486   0.081  -1.433  O15  Z3D  21  
Z3D  O18  O8   O  0  1  N  N  N  26.178  -22.075  346.868   1.013  -3.160   1.854  O18  Z3D  22  
Z3D  O23  O9   O  0  1  N  N  N  26.710  -27.495  344.391   4.521   1.514  -0.916  O23  Z3D  23  
Z3D  H1   H1   H  0  1  N  N  N  24.522  -26.255  345.255   2.409   1.533   0.709  H1   Z3D  24  
Z3D  H2   H2   H  0  1  N  N  N  26.259  -24.519  347.087   0.984  -0.429  -1.145  H2   Z3D  25  
Z3D  H3   H3   H  0  1  N  N  N  25.131  -25.817  348.739  -0.293   1.765  -1.330  H3   Z3D  26  
Z3D  H4   H4   H  0  1  N  N  N  23.427  -25.718  350.420  -2.604   2.433  -0.785  H4   Z3D  27  
Z3D  H5   H5   H  0  1  N  N  N  21.992  -23.747  348.617  -2.251   0.643   1.664  H5   Z3D  28  
Z3D  H6   H6   H  0  1  N  N  N  23.319  -23.334  351.294  -4.074   0.354  -0.770  H6   Z3D  29  
Z3D  H7   H7   H  0  1  N  N  N  23.945  -22.322  348.498  -1.650  -1.280   0.114  H7   Z3D  30  
Z3D  H8   H8   H  0  1  N  N  N  25.956  -21.352  349.431  -3.507  -2.559  -0.994  H8   Z3D  31  
Z3D  H9   H9   H  0  1  N  N  N  24.491  -20.633  350.181  -3.385  -1.461  -2.390  H9   Z3D  32  
Z3D  H10  H10  H  0  1  N  N  N  24.294  -23.880  344.817   1.832  -0.649   1.779  H10  Z3D  33  
Z3D  H11  H11  H  0  1  N  N  N  25.189  -21.512  345.167  -0.352  -1.736   1.241  H11  Z3D  34  
Z3D  H12  H12  H  0  1  N  N  N  24.164  -22.129  346.507   0.444  -2.647  -0.064  H12  Z3D  35  
Z3D  H13  H13  H  0  1  N  N  N  27.325  -23.480  345.009   3.298  -2.466   0.942  H13  Z3D  36  
Z3D  H14  H14  H  0  1  N  N  N  26.272  -23.019  343.629   2.770  -2.124  -0.724  H14  Z3D  37  
Z3D  H15  H15  H  0  1  N  N  N  27.550  -25.176  343.287   4.940  -1.028  -0.235  H15  Z3D  38  
Z3D  H16  H16  H  0  1  N  N  N  27.548  -26.024  345.569   3.346   0.059  -1.794  H16  Z3D  39  
Z3D  H17  H17  H  0  1  N  N  N  25.616  -26.357  342.532   4.958   0.715   1.424  H17  Z3D  40  
Z3D  H18  H18  H  0  1  N  N  N  24.628  -25.409  343.422   3.402   0.339   1.875  H18  Z3D  41  
Z3D  H20  H20  H  0  1  N  N  N  24.696  -27.035  347.442   2.399   2.844  -1.288  H20  Z3D  42  
Z3D  H21  H21  H  0  1  N  N  N  21.681  -26.552  349.081  -0.823   3.598   0.304  H21  Z3D  43  
Z3D  H22  H22  H  0  1  N  N  N  20.548  -23.690  350.483  -3.640   2.565   1.975  H22  Z3D  44  
Z3D  H23  H23  H  0  1  N  N  N  21.375  -22.124  350.938  -4.927  -0.542   1.275  H23  Z3D  45  
Z3D  H24  H24  H  0  1  N  N  N  26.122  -21.154  351.715  -2.046  -3.418  -2.677  H24  Z3D  46  
Z3D  H25  H25  H  0  1  N  N  N  26.137  -21.201  347.239   0.386  -3.886   1.977  H25  Z3D  47  
Z3D  H26  H26  H  0  1  N  N  N  26.742  -28.147  345.081   4.279   2.239  -1.508  H26  Z3D  48  
#   #
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
Z3D  N21  C20  SING  N  N   1  
Z3D  C20  C19  SING  N  N   2  
Z3D  C20  C22  SING  N  N   3  
Z3D  O23  C22  SING  N  N   4  
Z3D  C19  C16  SING  N  N   5  
Z3D  C22  C02  SING  N  N   6  
Z3D  C16  C17  SING  N  N   7  
Z3D  C16  C03  SING  N  N   8  
Z3D  C02  C03  SING  N  N   9  
Z3D  C02  O01  SING  N  N  10  
Z3D  C17  O18  SING  N  N  11  
Z3D  C03  O04  SING  N  N  12  
Z3D  O04  C05  SING  N  N  13  
Z3D  O07  C06  SING  N  N  14  
Z3D  C05  O15  SING  N  N  15  
Z3D  C05  C06  SING  N  N  16  
Z3D  O15  C12  SING  N  N  17  
Z3D  C06  C08  SING  N  N  18  
Z3D  C12  C13  SING  N  N  19  
Z3D  C12  C10  SING  N  N  20  
Z3D  C08  C10  SING  N  N  21  
Z3D  C08  O09  SING  N  N  22  
Z3D  C13  O14  SING  N  N  23  
Z3D  C10  O11  SING  N  N  24  
Z3D  C02  H1   SING  N  N  25  
Z3D  C03  H2   SING  N  N  26  
Z3D  C05  H3   SING  N  N  27  
Z3D  C06  H4   SING  N  N  28  
Z3D  C08  H5   SING  N  N  29  
Z3D  C10  H6   SING  N  N  30  
Z3D  C12  H7   SING  N  N  31  
Z3D  C13  H8   SING  N  N  32  
Z3D  C13  H9   SING  N  N  33  
Z3D  C16  H10  SING  N  N  34  
Z3D  C17  H11  SING  N  N  35  
Z3D  C17  H12  SING  N  N  36  
Z3D  C19  H13  SING  N  N  37  
Z3D  C19  H14  SING  N  N  38  
Z3D  C20  H15  SING  N  N  39  
Z3D  C22  H16  SING  N  N  40  
Z3D  N21  H17  SING  N  N  41  
Z3D  N21  H18  SING  N  N  42  
Z3D  O01  H20  SING  N  N  43  
Z3D  O07  H21  SING  N  N  44  
Z3D  O09  H22  SING  N  N  45  
Z3D  O11  H23  SING  N  N  46  
Z3D  O14  H24  SING  N  N  47  
Z3D  O18  H25  SING  N  N  48  
Z3D  O23  H26  SING  N  N  49  
#   #
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
Z3D  SMILES            ACDLabs               12.01  "OCC1CC(N)C(O)C(O)C1OC1OC(CO)C(O)C(O)C1O"  
Z3D  InChI             InChI                 1.03   "InChI=1S/C13H25NO9/c14-5-1-4(2-15)12(10(20)7(5)17)23-13-11(21)9(19)8(18)6(3-16)22-13/h4-13,15-21H,1-3,14H2/t4-,5+,6-,7+,8-,9+,10-,11-,12-,13-/m1/s1"  
Z3D  InChIKey          InChI                 1.03   IURYEWAUXBUYIM-BTADNHFESA-N  
Z3D  SMILES_CANONICAL  CACTVS                3.385  "N[C@H]1C[C@H](CO)[C@@H](O[C@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)[C@H](O)[C@H]1O"  
Z3D  SMILES            CACTVS                3.385  "N[CH]1C[CH](CO)[CH](O[CH]2O[CH](CO)[CH](O)[CH](O)[CH]2O)[CH](O)[CH]1O"  
Z3D  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "C1[C@@H]([C@H]([C@@H]([C@H]([C@H]1N)O)O)O[C@@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O)CO"  
Z3D  SMILES            "OpenEye OEToolkits"  2.0.7  "C1C(C(C(C(C1N)O)O)OC2C(C(C(C(O2)CO)O)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
Z3D  "SYSTEMATIC NAME"  ACDLabs               12.01  "(1R,2R,3S,4S,6R)-4-amino-2,3-dihydroxy-6-(hydroxymethyl)cyclohexyl alpha-D-glucopyranoside"  
Z3D  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  "(2~{S},3~{R},4~{S},5~{S},6~{R})-2-[(1~{R},2~{R},3~{S},4~{S},6~{R})-4-azanyl-6-(hydroxymethyl)-2,3-bis(oxidanyl)cyclohexyl]oxy-6-(hydroxymethyl)oxane-3,4,5-triol"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
Z3D  "Create component"  2021-04-07  RCSB  
Z3D  "Initial release"   2021-07-14  RCSB  
##
