data_7K2
#

_chem_comp.id                                   7K2
_chem_comp.name                                 "[(3S,4R,5R)-4,5-dihydroxypiperidin-3-yl]methyl 1-thio-alpha-D-mannopyranoside"
_chem_comp.type                                 D-saccharide
_chem_comp.pdbx_type                            ATOMS
_chem_comp.formula                              "C12 H23 N O7 S"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        
;(2~{R},3~{S},4~{S},5~{S},6~{R})-2-[[(3~{S},4~{R},5~{R})-4,5-bis(oxidanyl)piperidin-3-yl]methylsulfanyl]-6-(hydroxymethy
 l)oxane-3,4,5-triol; isofagomine-thiol-alpha-D-mannopyranoside; [(3S,4R,5R)-4,5-dihydroxypiperidin-3-yl]methyl
1-thio-alpha-D-mannoside; [(3S,4R,5R)-4,5-dihydroxypiperidin-3-yl]methyl 1-thio-D-mannoside;
[(3S,4R,5R)-4,5-dihydroxypiperidin-3-yl]methyl 1-thio-mannoside
;

_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2016-11-03
_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                       325.379
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    7K2
_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       5M77
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 EBI
#   #
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  7K2  
;(2~{R},3~{S},4~{S},5~{S},6~{R})-2-[[(3~{S},4~{R},5~{R})-4,5-bis(oxidanyl)piperidin-3-yl]methylsulfanyl]-6-(hydroxymethy
 l)oxane-3,4,5-triol
;
  PDB  ?  
2  7K2  isofagomine-thiol-alpha-D-mannopyranoside  PDB  ?  
3  7K2  "[(3S,4R,5R)-4,5-dihydroxypiperidin-3-yl]methyl 1-thio-alpha-D-mannoside"  PDB  ?  
4  7K2  "[(3S,4R,5R)-4,5-dihydroxypiperidin-3-yl]methyl 1-thio-D-mannoside"  PDB  ?  
5  7K2  "[(3S,4R,5R)-4,5-dihydroxypiperidin-3-yl]methyl 1-thio-mannoside"  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
7K2  O2   O17  O  0  1  N  N  N  4.105  -32.809   -4.992   2.555  -1.693  -2.020  O2   7K2   1  
7K2  C2   C12  C  0  1  N  N  S  3.153  -32.104   -5.839   2.735  -1.253  -0.672  C2   7K2   2  
7K2  C3   C11  C  0  1  N  N  S  2.373  -31.110   -4.940   4.083  -0.536  -0.543  C3   7K2   3  
7K2  O3   O16  O  0  1  N  N  N  1.635  -31.779   -3.955   4.136   0.551  -1.469  O3   7K2   4  
7K2  C4   C10  C  0  1  N  N  S  3.361  -30.191   -4.277   4.229  -0.001   0.885  C4   7K2   5  
7K2  O4   O15  O  0  1  N  N  N  2.636  -29.059   -3.670   4.241  -1.094   1.805  O4   7K2   6  
7K2  C5   C9   C  0  1  N  N  R  4.327  -29.519   -5.291   3.049   0.920   1.200  C5   7K2   7  
7K2  C6   C13  C  0  1  N  N  N  5.535  -28.751   -4.675   3.069   2.120   0.251  C6   7K2   8  
7K2  O5   O8   O  0  1  N  N  N  4.907  -30.433   -6.241   1.826   0.200   1.031  O5   7K2   9  
7K2  C1   C7   C  0  1  N  N  R  3.972  -31.318   -6.873   1.612  -0.283  -0.296  C1   7K2  10  
7K2  S1   S1   S  0  1  N  N  N  2.807  -30.537   -8.015   0.017  -1.144  -0.377  S1   7K2  11  
7K2  C6A  C6   C  0  1  N  N  N  3.914  -29.973   -9.301  -1.184   0.205  -0.208  C6A  7K2  12  
7K2  C5A  C5   C  0  1  N  N  S  4.030  -30.860  -10.510  -2.602  -0.366  -0.257  C5A  7K2  13  
7K2  C1A  C1   C  0  1  N  N  N  2.704  -30.772  -11.328  -2.834  -1.266   0.959  C1A  7K2  14  
7K2  N    N    N  0  1  N  N  N  2.755  -31.606  -12.567  -4.202  -1.797   0.923  N    7K2  15  
7K2  C2A  C2   C  0  1  N  N  N  3.931  -31.268  -13.421  -5.194  -0.716   0.989  C2A  7K2  16  
7K2  C3A  C3   C  0  1  N  N  R  5.224  -31.321  -12.660  -5.033   0.200  -0.226  C3A  7K2  17  
7K2  O3A  O3   O  0  1  N  N  N  6.269  -30.873  -13.574  -5.984   1.264  -0.150  O3A  7K2  18  
7K2  C4A  C4   C  0  1  N  N  R  5.189  -30.449  -11.433  -3.616   0.782  -0.238  C4A  7K2  19  
7K2  O4A  O4   O  0  1  N  N  N  6.400  -30.517  -10.732  -3.443   1.593  -1.401  O4A  7K2  20  
7K2  HO2  H1   H  0  1  N  Y  N  3.635  -33.310   -4.336   1.721  -2.157  -2.174  HO2  7K2  21  
7K2  H2   H2   H  0  1  N  N  N  2.459  -32.796   -6.339   2.714  -2.113  -0.002  H2   7K2  22  
7K2  H3   H3   H  0  1  N  N  N  1.706  -30.515   -5.580   4.890  -1.237  -0.755  H3   7K2  23  
7K2  HO3  H4   H  0  1  N  Y  N  1.170  -31.145   -3.422   4.042   0.285  -2.394  HO3  7K2  24  
7K2  H4   H5   H  0  1  N  N  N  3.941  -30.736   -3.517   5.162   0.557   0.970  H4   7K2  25  
7K2  HO4  H6   H  0  1  N  Y  N  2.016  -29.387   -3.029   4.962  -1.722   1.661  HO4  7K2  26  
7K2  H5   H7   H  0  1  N  N  N  3.735  -28.779   -5.849   3.125   1.270   2.230  H5   7K2  27  
7K2  H61  H8   H  0  1  N  N  N  6.111  -28.247   -5.465   4.047   2.600   0.293  H61  7K2  28  
7K2  H62  H9   H  0  1  N  N  N  5.183  -28.006   -3.946   2.875   1.781  -0.767  H62  7K2  29  
7K2  H1   H11  H  0  1  N  N  N  4.525  -32.046   -7.485   1.608   0.556  -0.992  H1   7K2  30  
7K2  H12  H12  H  0  1  N  N  N  4.917  -29.872   -8.861  -1.029   0.712   0.745  H12  7K2  31  
7K2  H13  H13  H  0  1  N  N  N  3.561  -28.988   -9.640  -1.049   0.916  -1.023  H13  7K2  32  
7K2  H14  H14  H  0  1  N  N  N  4.179  -31.901  -10.188  -2.729  -0.948  -1.170  H14  7K2  33  
7K2  H15  H15  H  0  1  N  N  N  2.531  -29.724  -11.612  -2.123  -2.092   0.940  H15  7K2  34  
7K2  H16  H16  H  0  1  N  N  N  1.874  -31.123  -10.698  -2.693  -0.687   1.871  H16  7K2  35  
7K2  H17  H17  H  0  1  N  N  N  1.919  -31.453  -13.094  -4.349  -2.468   1.662  H17  7K2  36  
7K2  H19  H19  H  0  1  N  N  N  3.797  -30.252  -13.820  -6.197  -1.142   0.992  H19  7K2  37  
7K2  H20  H20  H  0  1  N  N  N  3.981  -31.985  -14.253  -5.041  -0.140   1.901  H20  7K2  38  
7K2  H21  H21  H  0  1  N  N  N  5.419  -32.360  -12.356  -5.198  -0.372  -1.138  H21  7K2  39  
7K2  H22  H22  H  0  1  N  N  N  7.108  -30.892  -13.130  -6.905   0.968  -0.137  H22  7K2  40  
7K2  H23  H23  H  0  1  N  N  N  5.009  -29.413  -11.755  -3.464   1.388   0.655  H23  7K2  41  
7K2  H24  H24  H  0  1  N  N  N  6.354  -29.960   -9.964  -4.057   2.338  -1.456  H24  7K2  42  
7K2  O6   O1   O  0  1  N  N  N  6.541  -29.987   -3.865   2.062   3.055   0.642  O6   7K2  43  
7K2  HO6  H10  H  0  1  N  Y  N  7.297  -29.570   -3.469   2.018   3.842   0.083  HO6  7K2  44  
#   #
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
7K2  O3A  C3A  SING  N  N   1  
7K2  C2A  C3A  SING  N  N   2  
7K2  C2A  N    SING  N  N   3  
7K2  C3A  C4A  SING  N  N   4  
7K2  N    C1A  SING  N  N   5  
7K2  C4A  O4A  SING  N  N   6  
7K2  C4A  C5A  SING  N  N   7  
7K2  C1A  C5A  SING  N  N   8  
7K2  C5A  C6A  SING  N  N   9  
7K2  C6A  S1   SING  N  N  10  
7K2  S1   C1   SING  N  N  11  
7K2  C1   O5   SING  N  N  12  
7K2  C1   C2   SING  N  N  13  
7K2  O5   C5   SING  N  N  14  
7K2  C2   O2   SING  N  N  15  
7K2  C2   C3   SING  N  N  16  
7K2  C5   C6   SING  N  N  17  
7K2  C5   C4   SING  N  N  18  
7K2  C3   C4   SING  N  N  19  
7K2  C3   O3   SING  N  N  20  
7K2  C4   O4   SING  N  N  21  
7K2  O2   HO2  SING  N  N  22  
7K2  C2   H2   SING  N  N  23  
7K2  C3   H3   SING  N  N  24  
7K2  O3   HO3  SING  N  N  25  
7K2  C4   H4   SING  N  N  26  
7K2  O4   HO4  SING  N  N  27  
7K2  C5   H5   SING  N  N  28  
7K2  C6   H61  SING  N  N  29  
7K2  C6   H62  SING  N  N  30  
7K2  C1   H1   SING  N  N  31  
7K2  C6A  H12  SING  N  N  32  
7K2  C6A  H13  SING  N  N  33  
7K2  C5A  H14  SING  N  N  34  
7K2  C1A  H15  SING  N  N  35  
7K2  C1A  H16  SING  N  N  36  
7K2  N    H17  SING  N  N  37  
7K2  C2A  H19  SING  N  N  38  
7K2  C2A  H20  SING  N  N  39  
7K2  C3A  H21  SING  N  N  40  
7K2  O3A  H22  SING  N  N  41  
7K2  C4A  H23  SING  N  N  42  
7K2  O4A  H24  SING  N  N  43  
7K2  C6   O6   SING  N  N  44  
7K2  O6   HO6  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
7K2  InChI             InChI                 1.03   "InChI=1S/C12H23NO7S/c14-3-7-9(17)10(18)11(19)12(20-7)21-4-5-1-13-2-6(15)8(5)16/h5-19H,1-4H2/t5-,6-,7-,8-,9-,10+,11+,12-/m1/s1"  
7K2  InChIKey          InChI                 1.03   KDPQETHZRPVZAI-TYMLGRTHSA-N  
7K2  SMILES_CANONICAL  CACTVS                3.385  "OC[C@H]1O[C@H](SC[C@H]2CNC[C@@H](O)[C@@H]2O)[C@@H](O)[C@@H](O)[C@@H]1O"  
7K2  SMILES            CACTVS                3.385  "OC[CH]1O[CH](SC[CH]2CNC[CH](O)[CH]2O)[CH](O)[CH](O)[CH]1O"  
7K2  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.6  "C1[C@@H]([C@H]([C@@H](CN1)O)O)CS[C@@H]2[C@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O"  
7K2  SMILES            "OpenEye OEToolkits"  2.0.6  "C1C(C(C(CN1)O)O)CSC2C(C(C(C(O2)CO)O)O)O"  
#
_pdbx_chem_comp_identifier.comp_id          7K2
_pdbx_chem_comp_identifier.type             "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program          "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version  2.0.6
_pdbx_chem_comp_identifier.identifier       
;(2~{R},3~{S},4~{S},5~{S},6~{R})-2-[[(3~{S},4~{R},5~{R})-4,5-bis(oxidanyl)piperidin-3-yl]methylsulfanyl]-6-(hydroxymethy
l)oxane-3,4,5-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
7K2  "CARBOHYDRATE ISOMER"                  D         PDB  ?  
7K2  "CARBOHYDRATE RING"                    pyranose  PDB  ?  
7K2  "CARBOHYDRATE ANOMER"                  alpha     PDB  ?  
7K2  "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
7K2  "Create component"          2016-11-03  EBI   
7K2  "Initial release"           2017-08-09  RCSB  
7K2  "Other modification"        2020-07-03  RCSB  
7K2  "Modify name"               2020-07-17  RCSB  
7K2  "Modify synonyms"           2020-07-17  RCSB  
7K2  "Modify internal type"      2020-07-17  RCSB  
7K2  "Modify linking type"       2020-07-17  RCSB  
7K2  "Modify atom id"            2020-07-17  RCSB  
7K2  "Modify component atom id"  2020-07-17  RCSB  
7K2  "Modify leaving atom flag"  2020-07-17  RCSB  
##
