data_GDL # _chem_comp.id GDL _chem_comp.name "2-(acetylamido)-2-deoxy-D-glucono-1,5-lactone" _chem_comp.type D-saccharide _chem_comp.pdbx_type ATOMS _chem_comp.formula "C8 H13 N O6" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "2-ACETAMIDO-2-DEOXY-D-GLUCONO-1,5-LACTONE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2002-10-29 _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 219.192 _chem_comp.one_letter_code ? _chem_comp.three_letter_code GDL _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 1O7A _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id GDL _pdbx_chem_comp_synonyms.name "2-ACETAMIDO-2-DEOXY-D-GLUCONO-1,5-LACTONE" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? # # 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 GDL C1 C1 C 0 1 N N N 71.823 81.429 26.794 1.148 -0.144 0.140 C1 GDL 1 GDL C2 C2 C 0 1 N N R 71.207 80.369 27.893 -0.163 0.190 0.815 C2 GDL 2 GDL C3 C3 C 0 1 N N R 71.287 78.803 27.382 -1.307 -0.317 -0.070 C3 GDL 3 GDL C4 C4 C 0 1 N N S 71.332 78.733 25.818 -1.136 0.248 -1.483 C4 GDL 4 GDL C5 C5 C 0 1 N N R 72.461 79.615 25.332 0.194 -0.236 -2.067 C5 GDL 5 GDL C6 C6 C 0 1 N N N 72.592 79.524 23.783 0.410 0.397 -3.443 C6 GDL 6 GDL C7 C7 C 0 1 N N N 73.278 80.507 29.348 0.227 0.175 3.220 C7 GDL 7 GDL C8 C8 C 0 1 N N N 73.810 80.749 30.780 0.162 -0.498 4.567 C8 GDL 8 GDL N2 N1 N 0 1 N N N 71.913 80.484 29.202 -0.226 -0.464 2.125 N2 GDL 9 GDL O1 O1 O 0 1 N N N 71.752 82.624 27.152 2.052 -0.663 0.752 O1 GDL 10 GDL O3 O3 O 0 1 N N N 70.148 78.121 27.886 -2.558 0.114 0.470 O3 GDL 11 GDL O4 O4 O 0 1 N N N 71.562 77.400 25.434 -2.212 -0.199 -2.309 O4 GDL 12 GDL O5 O5 O 0 1 N N N 72.323 81.038 25.681 1.273 0.156 -1.171 O5 GDL 13 GDL O6 O6 O 0 1 N N N 73.808 80.188 23.404 1.652 -0.055 -3.986 O6 GDL 14 GDL O7 O7 O 0 1 N N N 74.058 80.541 28.388 0.687 1.293 3.123 O7 GDL 15 GDL H2 H2 H 0 1 N N N 70.147 80.640 28.011 -0.247 1.269 0.941 H2 GDL 16 GDL H3 H3 H 0 1 N N N 72.206 78.328 27.755 -1.283 -1.406 -0.108 H3 GDL 17 GDL H4 H4 H 0 1 N N N 70.383 79.078 25.382 -1.139 1.337 -1.441 H4 GDL 18 GDL H5 H5 H 0 1 N N N 73.354 79.231 25.847 0.176 -1.321 -2.164 H5 GDL 19 GDL H61 H6C1 H 0 1 N N N 72.629 78.469 23.472 -0.403 0.109 -4.108 H61 GDL 20 GDL H62 H6C2 H 0 1 N N N 71.728 79.999 23.296 0.432 1.483 -3.343 H62 GDL 21 GDL H81 H8C1 H 0 1 N N N 73.993 79.782 31.272 0.572 0.168 5.326 H81 GDL 22 GDL H82 H8C2 H 0 1 N N N 74.750 81.319 30.730 -0.874 -0.729 4.808 H82 GDL 23 GDL H83 H8C3 H 0 1 N N N 73.066 81.318 31.356 0.744 -1.419 4.541 H83 GDL 24 GDL HN2 HB H 0 1 N N N 71.357 80.548 30.025 -0.594 -1.358 2.203 HN2 GDL 25 GDL HO3 HC H 0 1 N Y N 70.293 77.144 27.822 -2.622 -0.259 1.359 HO3 GDL 26 GDL HO4 HD H 0 1 N N N 70.695 76.940 25.302 -2.066 0.178 -3.188 HO4 GDL 27 GDL HO6 H6 H 0 1 N N N 74.500 79.513 23.188 1.749 0.366 -4.850 HO6 GDL 28 # # 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 GDL C1 C2 SING N N 1 GDL C1 O1 DOUB N N 2 GDL C1 O5 SING N N 3 GDL C2 C3 SING N N 4 GDL C2 N2 SING N N 5 GDL C2 H2 SING N N 6 GDL C3 C4 SING N N 7 GDL C3 O3 SING N N 8 GDL C3 H3 SING N N 9 GDL C4 C5 SING N N 10 GDL C4 O4 SING N N 11 GDL C4 H4 SING N N 12 GDL C5 C6 SING N N 13 GDL C5 O5 SING N N 14 GDL C5 H5 SING N N 15 GDL C6 O6 SING N N 16 GDL C6 H61 SING N N 17 GDL C6 H62 SING N N 18 GDL C7 C8 SING N N 19 GDL C7 N2 SING N N 20 GDL C7 O7 DOUB N N 21 GDL C8 H81 SING N N 22 GDL C8 H82 SING N N 23 GDL C8 H83 SING N N 24 GDL N2 HN2 SING N N 25 GDL O3 HO3 SING N N 26 GDL O4 HO4 SING N N 27 GDL O6 HO6 SING N N 28 # # 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 GDL SMILES ACDLabs 10.04 "O=C1OC(CO)C(O)C(O)C1NC(=O)C" GDL SMILES_CANONICAL CACTVS 3.341 "CC(=O)N[C@@H]1[C@@H](O)[C@H](O)[C@@H](CO)OC1=O" GDL SMILES CACTVS 3.341 "CC(=O)N[CH]1[CH](O)[CH](O)[CH](CO)OC1=O" GDL SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC(=O)N[C@@H]1[C@H]([C@@H]([C@H](OC1=O)CO)O)O" GDL SMILES "OpenEye OEToolkits" 1.5.0 "CC(=O)NC1C(C(C(OC1=O)CO)O)O" GDL InChI InChI 1.03 "InChI=1S/C8H13NO6/c1-3(11)9-5-7(13)6(12)4(2-10)15-8(5)14/h4-7,10,12-13H,2H2,1H3,(H,9,11)/t4-,5-,6-,7-/m1/s1" GDL InChIKey InChI 1.03 NELQYZRSPDCGRQ-DBRKOABJSA-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 GDL "SYSTEMATIC NAME" ACDLabs 10.04 "N-[(3R,4R,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-oxotetrahydro-2H-pyran-3-yl]acetamide (non-preferred name)" GDL "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "N-[(3R,4R,5S,6R)-4,5-dihydroxy-6-(hydroxymethyl)-2-oxo-oxan-3-yl]ethanamide" # # 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 GDL "CARBOHYDRATE ISOMER" D PDB ? GDL "CARBOHYDRATE RING" pyranose PDB ? GDL "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 GDL "Create component" 2002-10-29 EBI GDL "Modify descriptor" 2011-06-04 RCSB GDL "Other modification" 2020-07-03 RCSB GDL "Modify name" 2020-07-17 RCSB GDL "Modify synonyms" 2020-07-17 RCSB GDL "Modify internal type" 2020-07-17 RCSB GDL "Modify linking type" 2020-07-17 RCSB GDL "Modify atom id" 2020-07-17 RCSB GDL "Modify component atom id" 2020-07-17 RCSB GDL "Modify leaving atom flag" 2020-07-17 RCSB ##