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 ##