data_SMD # _chem_comp.id SMD _chem_comp.name "METHYL-2-S-(ALPHA-D-MANNOPYRANOSYL)-2-THIO-ALPHA-D-MANNOPYRANOSIDE" _chem_comp.type saccharide _chem_comp.pdbx_type ATOMS _chem_comp.formula "C13 H24 O10 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2004-09-03 _chem_comp.pdbx_modified_date 2020-07-17 _chem_comp.pdbx_ambiguous_flag N _chem_comp.pdbx_release_status OBS _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 372.389 _chem_comp.one_letter_code ? _chem_comp.three_letter_code SMD _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 1X9D _chem_comp.pdbx_subcomponent_list "Z5L MAN" _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 _chem_comp_atom.pdbx_residue_numbering _chem_comp_atom.pdbx_polymer_type _chem_comp_atom.pdbx_component_id SMD S22 S22 S 0 1 N N N 2.759 -5.803 -0.496 0.027 -1.476 0.271 S2 Z5L 1 1 polymer 1 SMD C22 C22 C 0 1 N N S 2.918 -7.077 0.784 -0.993 -0.692 -1.008 C2 Z5L 2 1 polymer 1 SMD C21 C21 C 0 1 N N S 3.993 -8.069 0.411 -1.207 0.783 -0.662 C1 Z5L 3 1 polymer 1 SMD O21 O21 O 0 1 N N N 4.209 -8.893 1.557 -2.035 1.389 -1.656 O1 Z5L 4 1 polymer 1 SMD C27 C27 C 0 1 N N N 5.377 -9.728 1.466 -2.003 2.798 -1.418 C1M Z5L 5 1 polymer 1 SMD O25 O25 O 0 1 N N N 3.592 -8.831 -0.720 -1.838 0.893 0.612 O5 Z5L 6 1 polymer 1 SMD C23 C23 C 0 1 N N S 1.611 -7.844 1.050 -2.353 -1.392 -1.079 C3 Z5L 7 1 polymer 1 SMD O23 O23 O 0 1 N N N 0.589 -6.898 1.339 -2.165 -2.798 -1.253 O3 Z5L 8 1 polymer 1 SMD C24 C24 C 0 1 N N S 1.225 -8.756 -0.126 -3.106 -1.132 0.231 C4 Z5L 9 1 polymer 1 SMD O24 O24 O 0 1 N N N 0.158 -9.646 0.278 -4.435 -1.649 0.131 O4 Z5L 10 1 polymer 1 SMD C25 C25 C 0 1 N N R 2.393 -9.621 -0.554 -3.161 0.376 0.484 C5 Z5L 11 1 polymer 1 SMD C26 C26 C 0 1 N N N 2.071 -10.262 -1.885 -3.940 0.646 1.773 C6 Z5L 12 1 polymer 1 SMD O26 O26 O 0 1 N N N 3.033 -11.285 -2.161 -4.099 2.055 1.947 O6 Z5L 13 1 polymer 1 SMD C11 C11 C 0 1 N N R 1.967 -4.366 0.314 1.583 -0.576 0.029 C1 MAN 14 2 polymer 1 SMD C12 C12 C 0 1 N N S 1.425 -3.472 -0.762 2.691 -1.246 0.844 C2 MAN 15 2 polymer 1 SMD C13 C13 C 0 1 N N S 1.915 -2.055 -0.693 4.008 -0.500 0.605 C3 MAN 16 2 polymer 1 SMD C14 C14 C 0 1 N N S 3.407 -1.986 -0.468 3.789 0.988 0.905 C4 MAN 17 2 polymer 1 SMD C15 C15 C 0 1 N N R 3.757 -2.686 0.838 2.597 1.490 0.086 C5 MAN 18 2 polymer 1 SMD C16 C16 C 0 1 N N N 3.843 -1.644 1.953 2.876 1.273 -1.402 C6 MAN 19 2 polymer 1 SMD O12 O12 O 0 1 N N N -0.004 -3.449 -0.670 2.831 -2.607 0.431 O2 MAN 20 2 polymer 1 SMD O13 O13 O 0 1 N N N 1.267 -1.342 0.398 4.416 -0.660 -0.755 O3 MAN 21 2 polymer 1 SMD O14 O14 O 0 1 N N N 4.093 -2.518 -1.627 3.520 1.162 2.297 O4 MAN 22 2 polymer 1 SMD O15 O15 O 0 1 N N N 2.779 -3.650 1.277 1.420 0.775 0.457 O5 MAN 23 2 polymer 1 SMD O16 O16 O 0 1 N N N 4.094 -2.242 3.206 1.803 1.818 -2.173 O6 MAN 24 2 polymer 1 SMD H22 H22 H 0 1 N N N 3.188 -6.534 1.720 -0.492 -0.770 -1.973 H2 Z5L 25 1 polymer 1 SMD H21 H21 H 0 1 N N N 4.941 -7.556 0.125 -0.243 1.292 -0.634 H1 Z5L 26 1 polymer 1 SMD H271 1H27 H 0 0 N N N 6.282 -9.113 1.250 -0.977 3.157 -1.498 H31 Z5L 27 1 polymer 1 SMD H272 2H27 H 0 0 N N N 5.546 -10.371 2.361 -2.624 3.305 -2.156 H32 Z5L 28 1 polymer 1 SMD H273 3H27 H 0 0 N N N 5.344 -10.347 0.539 -2.384 3.006 -0.418 H33 Z5L 29 1 polymer 1 SMD H23 H23 H 0 1 N N N 1.754 -8.522 1.923 -2.927 -0.993 -1.916 H3 Z5L 30 1 polymer 1 SMD H2 H2 H 0 1 N N N -0.218 -7.372 1.503 -3.046 -3.197 -1.280 HO3 Z5L 31 1 polymer 1 SMD H24 H24 H 0 1 N N N 0.910 -8.099 -0.970 -2.585 -1.622 1.054 H4 Z5L 32 1 polymer 1 SMD H1 H1 H 0 1 N N N -0.080 -10.209 -0.449 -4.873 -1.459 0.972 HO4 Z5L 33 1 polymer 1 SMD H25 H25 H 0 1 N N N 2.564 -10.389 0.236 -3.662 0.865 -0.351 H5 Z5L 34 1 polymer 1 SMD H261 1H26 H 0 0 N N N 2.001 -9.514 -2.709 -4.921 0.174 1.711 H61 Z5L 35 1 polymer 1 SMD H262 2H26 H 0 0 N N N 1.024 -10.643 -1.929 -3.393 0.235 2.621 H62 Z5L 36 1 polymer 1 SMD H26 H26 H 0 1 N N N 2.831 -11.688 -2.997 -4.594 2.181 2.768 HO6 Z5L 37 1 polymer 1 SMD H11 H11 H 0 1 N N N 1.147 -4.762 0.957 1.850 -0.591 -1.027 H1 MAN 38 2 polymer 1 SMD H12 H12 H 0 1 N N N 1.787 -3.897 -1.727 2.439 -1.211 1.904 H2 MAN 39 2 polymer 1 SMD H13 H13 H 0 1 N N N 1.667 -1.585 -1.673 4.778 -0.896 1.267 H3 MAN 40 2 polymer 1 SMD H14 H14 H 0 1 N N N 3.751 -0.931 -0.357 4.682 1.550 0.632 H4 MAN 41 2 polymer 1 SMD H15 H15 H 0 1 N N N 4.716 -3.218 0.640 2.450 2.553 0.276 H5 MAN 42 2 polymer 1 SMD H161 1H16 H 0 0 N N N 2.931 -1.004 1.983 3.808 1.770 -1.674 H61 MAN 43 2 polymer 1 SMD H162 2H16 H 0 0 N N N 4.599 -0.858 1.718 2.962 0.205 -1.604 H62 MAN 44 2 polymer 1 SMD H5 H5 H 0 1 N N N -0.314 -4.346 -0.714 1.982 -3.039 0.598 HO2 MAN 45 2 polymer 1 SMD H4 H4 H 0 1 N N N 1.577 -0.445 0.442 4.542 -1.608 -0.899 HO3 MAN 46 2 polymer 1 SMD H3 H3 H 0 1 N N N 5.031 -2.475 -1.485 4.294 0.834 2.775 HO4 MAN 47 2 polymer 1 SMD H16 H16 H 0 1 N N N 4.147 -1.594 3.899 2.018 1.660 -3.102 HO6 MAN 48 2 polymer 1 # # 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 SMD O12 C12 SING N N 1 SMD O12 H5 SING N N 2 SMD C12 C13 SING N N 3 SMD C12 C11 SING N N 4 SMD C12 H12 SING N N 5 SMD C13 O13 SING N N 6 SMD C13 C14 SING N N 7 SMD C13 H13 SING N N 8 SMD O13 H4 SING N N 9 SMD C14 O14 SING N N 10 SMD C14 C15 SING N N 11 SMD C14 H14 SING N N 12 SMD O14 H3 SING N N 13 SMD C15 C16 SING N N 14 SMD C15 O15 SING N N 15 SMD C15 H15 SING N N 16 SMD C16 O16 SING N N 17 SMD C16 H161 SING N N 18 SMD C16 H162 SING N N 19 SMD O16 H16 SING N N 20 SMD O15 C11 SING N N 21 SMD C11 S22 SING N N 22 SMD C11 H11 SING N N 23 SMD S22 C22 SING N N 24 SMD C22 C21 SING N N 25 SMD C22 C23 SING N N 26 SMD C22 H22 SING N N 27 SMD C21 O21 SING N N 28 SMD C21 O25 SING N N 29 SMD C21 H21 SING N N 30 SMD O21 C27 SING N N 31 SMD C27 H271 SING N N 32 SMD C27 H272 SING N N 33 SMD C27 H273 SING N N 34 SMD O25 C25 SING N N 35 SMD C23 O23 SING N N 36 SMD C23 C24 SING N N 37 SMD C23 H23 SING N N 38 SMD O23 H2 SING N N 39 SMD C24 O24 SING N N 40 SMD C24 C25 SING N N 41 SMD C24 H24 SING N N 42 SMD O24 H1 SING N N 43 SMD C25 C26 SING N N 44 SMD C25 H25 SING N N 45 SMD C26 O26 SING N N 46 SMD C26 H261 SING N N 47 SMD C26 H262 SING N N 48 SMD O26 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 SMD SMILES ACDLabs 10.04 "S(C1C(OC)OC(CO)C(O)C1O)C2OC(C(O)C(O)C2O)CO" SMD SMILES_CANONICAL CACTVS 3.341 "CO[C@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]1S[C@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]2O" SMD SMILES CACTVS 3.341 "CO[CH]1O[CH](CO)[CH](O)[CH](O)[CH]1S[CH]2O[CH](CO)[CH](O)[CH](O)[CH]2O" SMD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CO[C@@H]1[C@H]([C@H]([C@@H]([C@H](O1)CO)O)O)S[C@@H]2[C@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O" SMD SMILES "OpenEye OEToolkits" 1.5.0 "COC1C(C(C(C(O1)CO)O)O)SC2C(C(C(C(O2)CO)O)O)O" SMD InChI InChI 1.03 "InChI=1S/C13H24O10S/c1-21-12-11(9(19)7(17)4(2-14)22-12)24-13-10(20)8(18)6(16)5(3-15)23-13/h4-20H,2-3H2,1H3/t4-,5-,6-,7-,8+,9+,10+,11+,12+,13-/m1/s1" SMD InChIKey InChI 1.03 WAYOKHSZGNFKSX-ZEEOCKJESA-N # # 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 SMD "SYSTEMATIC NAME" ACDLabs 10.04 "methyl 2-S-alpha-D-mannopyranosyl-2-thio-alpha-D-mannopyranoside" SMD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2R,3S,4S,5S,6R)-2-[(2S,3S,4S,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-methoxy-oxan-3-yl]sulfanyl-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 SMD "Create component" 2004-09-03 RCSB SMD "Modify descriptor" 2011-06-04 RCSB SMD "Other modification" 2020-07-03 RCSB SMD "Obsolete component" 2020-07-17 RCSB ##