data_M55 # _chem_comp.id M55 _chem_comp.name "benzyl alpha-D-glucopyranuronate" _chem_comp.type "D-saccharide, alpha linking" _chem_comp.pdbx_type ATOMS _chem_comp.formula "C13 H16 O7" _chem_comp.mon_nstd_parent_comp_id GCU _chem_comp.pdbx_synonyms "Benzyl D-glucuronoate" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2019-10-03 _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 284.262 _chem_comp.one_letter_code ? _chem_comp.three_letter_code M55 _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 6T0E _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id M55 _pdbx_chem_comp_synonyms.name "Benzyl D-glucuronoate" _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 M55 C3 C3 C 0 1 N N S -13.417 -1.119 -15.739 -2.842 -1.275 0.167 C3 M55 1 M55 C4 C4 C 0 1 N N S -14.405 -1.843 -14.820 -1.498 -0.784 -0.378 C4 M55 2 M55 C1 C1 C 0 1 N N S -13.698 -3.005 -17.350 -3.606 1.101 0.194 C1 M55 3 M55 C01 C01 C 0 1 N N N -16.129 -4.919 -12.166 2.410 1.133 -0.730 C01 M55 4 M55 C02 C02 C 0 1 Y N N -15.325 -4.405 -9.846 4.271 0.796 0.910 C02 M55 5 M55 C03 C03 C 0 1 Y N N -14.651 -4.741 -8.690 5.371 0.098 1.371 C03 M55 6 M55 C04 C04 C 0 1 Y N N -14.055 -5.975 -8.574 5.812 -1.024 0.694 C04 M55 7 M55 C05 C05 C 0 1 Y N N -14.133 -6.875 -9.623 5.153 -1.446 -0.446 C05 M55 8 M55 C06 C06 C 0 1 Y N N -14.805 -6.543 -10.776 4.053 -0.748 -0.907 C06 M55 9 M55 C07 C07 C 0 1 Y N N -15.414 -5.309 -10.881 3.609 0.371 -0.227 C07 M55 10 M55 C2 C2 C 0 1 N N R -13.687 -1.478 -17.210 -3.946 -0.313 -0.284 C2 M55 11 M55 C5 C5 C 0 1 N N S -14.387 -3.340 -15.161 -1.253 0.649 0.103 C5 M55 12 M55 C6 C6 C 0 1 N N N -15.456 -3.961 -14.266 0.040 1.160 -0.478 C6 M55 13 M55 O6B O01 O 0 1 N N N -15.143 -4.286 -12.942 1.204 0.588 -0.131 O6B M55 14 M55 O1 O1 O 0 1 N Y N -12.445 -3.556 -17.046 -3.567 1.125 1.622 O1 M55 15 M55 O2 O2 O 0 1 N N N -12.712 -0.881 -18.043 -5.194 -0.720 0.279 O2 M55 16 M55 O3 O3 O 0 1 N N N -13.596 0.261 -15.587 -3.114 -2.584 -0.337 O3 M55 17 M55 O4 O4 O 0 1 N N N -14.116 -1.661 -13.451 -0.451 -1.633 0.097 O4 M55 18 M55 O5 O5 O 0 1 N N N -14.700 -3.537 -16.507 -2.330 1.484 -0.324 O5 M55 19 M55 O6A O6B O 0 1 N N N -16.543 -4.137 -14.696 0.029 2.084 -1.256 O6A M55 20 M55 H3 H3 H 0 1 N N N -12.391 -1.418 -15.476 -2.805 -1.304 1.256 H3 M55 21 M55 H4 H4 H 0 1 N N N -15.413 -1.459 -15.037 -1.517 -0.804 -1.468 H4 M55 22 M55 H1 H1 H 0 1 N N N -13.950 -3.238 -18.395 -4.366 1.797 -0.161 H1 M55 23 M55 H01 H01 H 0 1 N N N -16.959 -4.229 -11.954 2.508 2.184 -0.459 H01 M55 24 M55 H02 H02 H 0 1 N N N -16.516 -5.811 -12.681 2.351 1.041 -1.814 H02 M55 25 M55 H08 H08 H 0 1 N N N -15.783 -3.432 -9.939 3.927 1.673 1.439 H08 M55 26 M55 H09 H09 H 0 1 N N N -14.591 -4.034 -7.875 5.886 0.428 2.261 H09 M55 27 M55 H10 H10 H 0 1 N N N -13.529 -6.241 -7.669 6.671 -1.570 1.054 H10 M55 28 M55 H11 H11 H 0 1 N N N -13.663 -7.844 -9.535 5.497 -2.322 -0.975 H11 M55 29 M55 H12 H12 H 0 1 N N N -14.856 -7.245 -11.595 3.538 -1.078 -1.798 H12 M55 30 M55 H2 H2 H 0 1 N N N -14.686 -1.101 -17.477 -4.015 -0.323 -1.372 H2 M55 31 M55 H5 H5 H 0 1 N N N -13.403 -3.762 -14.909 -1.192 0.661 1.191 H5 M55 32 M55 HO1 HO1 H 0 1 N Y N -12.482 -4.500 -17.141 -3.357 1.992 1.995 HO1 M55 33 M55 HO2 HO2 H 0 1 N Y N -12.733 0.062 -17.931 -5.938 -0.152 0.038 HO2 M55 34 M55 HO3 HO3 H 0 1 N Y N -13.434 0.504 -14.683 -3.951 -2.957 -0.031 HO3 M55 35 M55 HO4 HO4 H 0 1 N Y N -14.756 -2.129 -12.927 0.430 -1.380 -0.211 HO4 M55 36 # # 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 M55 O2 C2 SING N N 1 M55 C1 C2 SING N N 2 M55 C1 O1 SING N N 3 M55 C1 O5 SING N N 4 M55 C2 C3 SING N N 5 M55 O5 C5 SING N N 6 M55 C3 O3 SING N N 7 M55 C3 C4 SING N N 8 M55 C5 C4 SING N N 9 M55 C5 C6 SING N N 10 M55 C4 O4 SING N N 11 M55 O6A C6 DOUB N N 12 M55 C6 O6B SING N N 13 M55 O6B C01 SING N N 14 M55 C01 C07 SING N N 15 M55 C07 C06 DOUB Y N 16 M55 C07 C02 SING Y N 17 M55 C06 C05 SING Y N 18 M55 C02 C03 DOUB Y N 19 M55 C05 C04 DOUB Y N 20 M55 C03 C04 SING Y N 21 M55 C3 H3 SING N N 22 M55 C4 H4 SING N N 23 M55 C1 H1 SING N N 24 M55 C01 H01 SING N N 25 M55 C01 H02 SING N N 26 M55 C02 H08 SING N N 27 M55 C03 H09 SING N N 28 M55 C04 H10 SING N N 29 M55 C05 H11 SING N N 30 M55 C06 H12 SING N N 31 M55 C2 H2 SING N N 32 M55 C5 H5 SING N N 33 M55 O1 HO1 SING N N 34 M55 O2 HO2 SING N N 35 M55 O3 HO3 SING N N 36 M55 O4 HO4 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 M55 InChI InChI 1.03 "InChI=1S/C13H16O7/c14-8-9(15)11(20-12(17)10(8)16)13(18)19-6-7-4-2-1-3-5-7/h1-5,8-12,14-17H,6H2/t8-,9-,10+,11-,12-/m0/s1" M55 InChIKey InChI 1.03 MYEUFSLWFIOAGY-SVNGYHJRSA-N M55 SMILES_CANONICAL CACTVS 3.385 "O[C@H]1O[C@@H]([C@@H](O)[C@H](O)[C@H]1O)C(=O)OCc2ccccc2" M55 SMILES CACTVS 3.385 "O[CH]1O[CH]([CH](O)[CH](O)[CH]1O)C(=O)OCc2ccccc2" M55 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)COC(=O)[C@@H]2[C@H]([C@@H]([C@H]([C@H](O2)O)O)O)O" M55 SMILES "OpenEye OEToolkits" 2.0.7 "c1ccc(cc1)COC(=O)C2C(C(C(C(O2)O)O)O)O" # _pdbx_chem_comp_identifier.comp_id M55 _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "(phenylmethyl) (2~{S},3~{S},4~{S},5~{R},6~{S})-3,4,5,6-tetrakis(oxidanyl)oxane-2-carboxylate" # _pdbx_chem_comp_related.comp_id M55 _pdbx_chem_comp_related.related_comp_id GCU _pdbx_chem_comp_related.relationship_type "Carbohydrate core" _pdbx_chem_comp_related.details ? # # loop_ _pdbx_chem_comp_atom_related.ordinal _pdbx_chem_comp_atom_related.comp_id _pdbx_chem_comp_atom_related.atom_id _pdbx_chem_comp_atom_related.related_comp_id _pdbx_chem_comp_atom_related.related_atom_id _pdbx_chem_comp_atom_related.related_type 1 M55 C1 GCU C1 "Carbohydrate core" 2 M55 C2 GCU C2 "Carbohydrate core" 3 M55 C3 GCU C3 "Carbohydrate core" 4 M55 C4 GCU C4 "Carbohydrate core" 5 M55 C5 GCU C5 "Carbohydrate core" 6 M55 C6 GCU C6 "Carbohydrate core" 7 M55 O6B GCU O6B "Carbohydrate core" 8 M55 O1 GCU O1 "Carbohydrate core" 9 M55 O2 GCU O2 "Carbohydrate core" 10 M55 O3 GCU O3 "Carbohydrate core" 11 M55 O4 GCU O4 "Carbohydrate core" 12 M55 O5 GCU O5 "Carbohydrate core" 13 M55 O6A GCU O6A "Carbohydrate core" 14 M55 H1 GCU H1 "Carbohydrate core" 15 M55 H2 GCU H2 "Carbohydrate core" 16 M55 H3 GCU H3 "Carbohydrate core" 17 M55 H4 GCU H4 "Carbohydrate core" 18 M55 H5 GCU H5 "Carbohydrate core" 19 M55 HO1 GCU HO1 "Carbohydrate core" 20 M55 HO2 GCU HO2 "Carbohydrate core" 21 M55 HO3 GCU HO3 "Carbohydrate core" 22 M55 HO4 GCU HO4 "Carbohydrate core" # # 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 M55 "CARBOHYDRATE ISOMER" D PDB ? M55 "CARBOHYDRATE RING" pyranose PDB ? M55 "CARBOHYDRATE ANOMER" alpha PDB ? M55 "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 M55 "Create component" 2019-10-03 EBI M55 "Initial release" 2019-11-27 RCSB M55 "Other modification" 2020-07-03 RCSB M55 "Modify parent residue" 2020-07-17 RCSB M55 "Modify name" 2020-07-17 RCSB M55 "Modify synonyms" 2020-07-17 RCSB M55 "Modify internal type" 2020-07-17 RCSB M55 "Modify linking type" 2020-07-17 RCSB M55 "Modify atom id" 2020-07-17 RCSB M55 "Modify component atom id" 2020-07-17 RCSB M55 "Modify leaving atom flag" 2020-07-17 RCSB ##