data_DYM # _chem_comp.id DYM _chem_comp.name "(2R)-2,3-dihydroxypropyl 2-acetamido-2,4-dideoxy-alpha-L-threo-hex-4-enopyranosiduronic acid" _chem_comp.type L-saccharide _chem_comp.pdbx_type ATOMS _chem_comp.formula "C11 H17 N O8" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ;6-(2,3-DIHYDROXYPROPOXY)-5-ACETAMIDO-5,6-DIHYDRO-4-HYDROXY-4H-PYRAN-2-CARBOXYLIC ACID; 2,3-DIHYDROXYPROPYL ETHER MIMETIC; (2R)-2,3-dihydroxypropyl 2-acetamido-2,4-dideoxy-alpha-L-threo-hex-4-enosiduronic acid; (2R)-2,3-dihydroxypropyl 2-acetamido-2,4-dideoxy-L-threo-hex-4-enosiduronic acid; (2R)-2,3-dihydroxypropyl 2-acetamido-2,4-dideoxy-threo-hex-4-enosiduronic acid ; _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2005-11-28 _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 291.255 _chem_comp.one_letter_code ? _chem_comp.three_letter_code DYM _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 2F13 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # # 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 DYM "6-(2,3-DIHYDROXYPROPOXY)-5-ACETAMIDO-5,6-DIHYDRO-4-HYDROXY-4H-PYRAN-2-CARBOXYLIC ACID" PDB ? 2 DYM "2,3-DIHYDROXYPROPYL ETHER MIMETIC" PDB ? 3 DYM "(2R)-2,3-dihydroxypropyl 2-acetamido-2,4-dideoxy-alpha-L-threo-hex-4-enosiduronic acid" PDB ? 4 DYM "(2R)-2,3-dihydroxypropyl 2-acetamido-2,4-dideoxy-L-threo-hex-4-enosiduronic acid" PDB ? 5 DYM "(2R)-2,3-dihydroxypropyl 2-acetamido-2,4-dideoxy-threo-hex-4-enosiduronic acid" 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 DYM C1 C1 C 0 1 N N N 77.991 30.365 24.640 1.807 3.286 -0.111 C1 DYM 1 DYM C2 C2 C 0 1 N N N 77.516 30.208 25.973 1.587 1.842 0.079 C2 DYM 2 DYM C3 C3 C 0 1 N N N 76.680 31.309 26.690 2.631 1.075 0.358 C3 DYM 3 DYM C4 C4 C 0 1 N N S 76.274 30.879 28.168 2.504 -0.408 0.577 C4 DYM 4 DYM C5 C5 C 0 1 N N R 77.318 29.943 28.807 1.166 -0.894 0.010 C5 DYM 5 DYM C6 C6 C 0 1 N N R 77.429 28.672 27.911 0.064 0.058 0.495 C6 DYM 6 DYM C7 C7 C 0 1 N N N 78.638 26.398 27.603 -2.314 0.354 0.530 C7 DYM 7 DYM C8 C8 C 0 1 N N R 79.711 25.471 28.185 -3.617 -0.226 -0.024 C8 DYM 8 DYM C9 C9 C 0 1 N N N 81.047 25.908 28.038 -4.807 0.504 0.602 C9 DYM 9 DYM C10 C10 C 0 1 N N N 77.454 29.804 31.356 1.403 -3.313 -0.168 C10 DYM 10 DYM C11 C11 C 0 1 N N N 76.732 29.336 32.597 1.121 -4.709 0.323 C11 DYM 11 DYM N5 N5 N 0 1 N N N 76.859 29.598 30.177 0.891 -2.252 0.487 N5 DYM 12 DYM O1A O1A O 0 1 N N N 78.715 29.382 24.031 2.926 3.749 -0.012 O1A DYM 13 DYM O1B O1B O 0 1 N N N 77.749 31.429 23.968 0.767 4.094 -0.401 O1B DYM 14 DYM O4 O4 O 0 1 N N N 76.137 32.092 28.952 3.575 -1.081 -0.087 O4 DYM 15 DYM O6 O6 O 0 1 N N N 77.843 29.040 26.543 0.326 1.359 -0.033 O6 DYM 16 DYM O7 O7 O 0 1 N N N 78.471 27.683 28.439 -1.208 -0.404 0.036 O7 DYM 17 DYM O8 O8 O 0 1 N N N 79.655 25.321 29.539 -3.648 -0.058 -1.443 O8 DYM 18 DYM O9 O9 O 0 1 N N N 82.115 25.186 28.504 -6.023 -0.113 0.175 O9 DYM 19 DYM O10 O10 O 0 1 N N N 78.687 30.419 31.510 2.092 -3.143 -1.152 O10 DYM 20 DYM H3 H3 H 0 1 N N N 76.408 32.252 26.238 3.608 1.531 0.430 H3 DYM 21 DYM H4 H4 H 0 1 N N N 75.310 30.352 28.119 2.546 -0.623 1.644 H4 DYM 22 DYM H5 H5 H 0 1 N N N 78.294 30.449 28.846 1.204 -0.887 -1.079 H5 DYM 23 DYM H6 H6 H 0 1 N N N 76.448 28.176 27.881 0.068 0.099 1.585 H6 DYM 24 DYM H71 H71 H 0 1 N N N 78.926 26.676 26.578 -2.215 1.392 0.213 H71 DYM 25 DYM H72 H72 H 0 1 N N N 77.678 25.861 27.581 -2.329 0.306 1.619 H72 DYM 26 DYM H8 H8 H 0 1 N N N 79.600 24.491 27.698 -3.675 -1.287 0.218 H8 DYM 27 DYM H91 H91 H 0 1 N N N 81.210 26.032 26.957 -4.735 0.451 1.688 H91 DYM 28 DYM H92 H92 H 0 1 N N N 81.103 26.889 28.532 -4.799 1.548 0.288 H92 DYM 29 DYM H111 H111 H 0 0 N N N 77.337 29.572 33.485 0.046 -4.888 0.313 H111 DYM 30 DYM H112 H112 H 0 0 N N N 75.760 29.846 32.670 1.615 -5.430 -0.329 H112 DYM 31 DYM H113 H113 H 0 0 N N N 76.573 28.249 32.540 1.498 -4.820 1.340 H113 DYM 32 DYM HN5 HN5 H 0 1 N N N 75.970 29.143 30.224 0.341 -2.387 1.274 HN5 DYM 33 DYM HO4 HO4 H 0 1 N N N 75.894 31.868 29.843 4.454 -0.822 0.221 HO4 DYM 34 DYM HO8 HO8 H 0 1 N N N 80.348 24.736 29.822 -3.601 0.864 -1.731 HO8 DYM 35 DYM HO9 HO9 H 0 1 N N N 82.921 25.649 28.307 -6.821 0.300 0.534 HO9 DYM 36 DYM HO1B HO1B H 0 0 N N N 78.137 31.354 23.104 0.960 5.034 -0.517 HO1B DYM 37 # # 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 DYM C1 C2 SING N N 1 DYM C1 O1A DOUB N N 2 DYM C1 O1B SING N N 3 DYM C2 C3 DOUB N N 4 DYM C2 O6 SING N N 5 DYM C3 C4 SING N N 6 DYM C3 H3 SING N N 7 DYM C4 C5 SING N N 8 DYM C4 O4 SING N N 9 DYM C4 H4 SING N N 10 DYM C5 C6 SING N N 11 DYM C5 N5 SING N N 12 DYM C5 H5 SING N N 13 DYM C6 O6 SING N N 14 DYM C6 O7 SING N N 15 DYM C6 H6 SING N N 16 DYM C7 C8 SING N N 17 DYM C7 O7 SING N N 18 DYM C7 H71 SING N N 19 DYM C7 H72 SING N N 20 DYM C8 C9 SING N N 21 DYM C8 O8 SING N N 22 DYM C8 H8 SING N N 23 DYM C9 O9 SING N N 24 DYM C9 H91 SING N N 25 DYM C9 H92 SING N N 26 DYM C10 C11 SING N N 27 DYM C10 N5 SING N N 28 DYM C10 O10 DOUB N N 29 DYM C11 H111 SING N N 30 DYM C11 H112 SING N N 31 DYM C11 H113 SING N N 32 DYM N5 HN5 SING N N 33 DYM O4 HO4 SING N N 34 DYM O8 HO8 SING N N 35 DYM O9 HO9 SING N N 36 DYM O1B HO1B SING N N 37 # # 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 DYM SMILES ACDLabs 12.01 "C(C1=CC(C(C(O1)OCC(CO)O)NC(C)=O)O)(=O)O" DYM InChI InChI 1.03 "InChI=1S/C11H17NO8/c1-5(14)12-9-7(16)2-8(10(17)18)20-11(9)19-4-6(15)3-13/h2,6-7,9,11,13,15-16H,3-4H2,1H3,(H,12,14)(H,17,18)/t6-,7+,9-,11-/m1/s1" DYM InChIKey InChI 1.03 HEEZEJCEFZJVGN-YRCORFKGSA-N DYM SMILES_CANONICAL CACTVS 3.385 "CC(=O)N[C@@H]1[C@@H](O)C=C(O[C@H]1OC[C@H](O)CO)C(O)=O" DYM SMILES CACTVS 3.385 "CC(=O)N[CH]1[CH](O)C=C(O[CH]1OC[CH](O)CO)C(O)=O" DYM SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(=O)N[C@@H]1[C@H](C=C(O[C@H]1OC[C@@H](CO)O)C(=O)O)O" DYM SMILES "OpenEye OEToolkits" 2.0.7 "CC(=O)NC1C(C=C(OC1OCC(CO)O)C(=O)O)O" # # 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 DYM "SYSTEMATIC NAME" ACDLabs 12.01 "(2R)-2,3-dihydroxypropyl 2-(acetylamino)-2,4-dideoxy-alpha-L-threo-hex-4-enopyranosiduronic acid" DYM "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 ;(2~{R},3~{R},4~{S})-3-acetamido-2-[(2~{R})-2,3-bis(oxidanyl)propoxy]-4-oxidanyl-3,4-dihydro-2~{H}-pyran-6-carboxylic acid ; # # 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 DYM "CARBOHYDRATE ISOMER" L PDB ? DYM "CARBOHYDRATE RING" dihydropyran PDB ? DYM "CARBOHYDRATE ANOMER" alpha PDB ? DYM "CARBOHYDRATE PRIMARY CARBONYL GROUP" ketose 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 DYM "Create component" 2005-11-28 RCSB DYM "Modify descriptor" 2011-06-04 RCSB DYM "Other modification" 2020-04-11 RCSB DYM "Other modification" 2020-07-03 RCSB DYM "Modify name" 2020-07-17 RCSB DYM "Modify synonyms" 2020-07-17 RCSB DYM "Modify component atom id" 2020-07-17 RCSB ##