data_XDX # _chem_comp.id XDX _chem_comp.name "(2R)-2-(alpha-D-glucopyranosyloxy)-3-(phosphonooxy)propanoic acid" _chem_comp.type D-saccharide _chem_comp.pdbx_type ATOMS _chem_comp.formula "C9 H17 O12 P" _chem_comp.mon_nstd_parent_comp_id GLC _chem_comp.pdbx_synonyms ;(2R)-2-(alpha-D-glucosyloxy)-3-(phosphonooxy)propanoic acid; (2R)-2-(D-glucosyloxy)-3-(phosphonooxy)propanoic acid; (2R)-2-(glucosyloxy)-3-(phosphonooxy)propanoic acid ; _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2016-05-10 _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 348.198 _chem_comp.one_letter_code ? _chem_comp.three_letter_code XDX _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 5JT0 _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 XDX "(2R)-2-(alpha-D-glucosyloxy)-3-(phosphonooxy)propanoic acid" PDB ? 2 XDX "(2R)-2-(D-glucosyloxy)-3-(phosphonooxy)propanoic acid" PDB ? 3 XDX "(2R)-2-(glucosyloxy)-3-(phosphonooxy)propanoic 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 XDX OAN OAN O 0 1 N N N 1.132 -7.778 2.943 -2.911 -2.585 -0.651 OAN XDX 1 XDX PAL PAL P 0 1 N N N 2.096 -7.370 1.912 -3.538 -1.112 -0.478 PAL XDX 2 XDX OAO OAO O 0 1 N N N 3.362 -7.069 2.575 -4.285 -0.684 -1.838 OAO XDX 3 XDX OAP OAP O 0 1 N N N 1.549 -6.004 1.693 -4.511 -1.118 0.638 OAP XDX 4 XDX OAM OAM O 0 1 N N N 2.278 -8.407 0.744 -2.361 -0.062 -0.158 OAM XDX 5 XDX CAQ CAQ C 0 1 N N N 3.417 -8.382 -0.101 -1.580 -0.108 1.038 CAQ XDX 6 XDX CAR CAR C 0 1 N N R 3.193 -8.805 -1.546 -0.556 1.028 1.022 CAR XDX 7 XDX CAS CAS C 0 1 N N N 1.818 -8.257 -1.985 -1.265 2.342 0.818 CAS XDX 8 XDX OAV OAV O 0 1 N N N 1.458 -7.127 -1.450 -2.115 2.798 1.752 OAV XDX 9 XDX OAU OAU O 0 1 N N N 1.072 -8.901 -2.809 -1.070 2.985 -0.186 OAU XDX 10 XDX O1 O1 O 0 1 N N N 3.326 -10.194 -1.789 0.373 0.818 -0.044 O1 XDX 11 XDX C1 C1 C 0 1 N N R 3.048 -10.762 -3.103 1.678 1.341 0.210 C1 XDX 12 XDX O5 O5 O 0 1 N N N 4.150 -10.747 -4.044 2.315 0.559 1.223 O5 XDX 13 XDX C5 C5 C 0 1 N N R 5.309 -11.632 -3.892 2.450 -0.825 0.893 C5 XDX 14 XDX C6 C6 C 0 1 N N N 6.274 -11.497 -5.032 3.116 -1.564 2.055 C6 XDX 15 XDX O6 O6 O 0 1 N N N 5.713 -10.817 -6.215 2.257 -1.530 3.197 O6 XDX 16 XDX C4 C4 C 0 1 N N S 4.787 -13.008 -3.649 3.312 -0.967 -0.364 C4 XDX 17 XDX O4 O4 O 0 1 N N N 5.928 -13.892 -3.376 3.400 -2.346 -0.730 O4 XDX 18 XDX C3 C3 C 0 1 N N S 3.777 -12.995 -2.511 2.670 -0.175 -1.507 C3 XDX 19 XDX O3 O3 O 0 1 N N N 3.468 -14.281 -2.004 3.506 -0.242 -2.664 O3 XDX 20 XDX C2 C2 C 0 1 N N R 2.532 -12.177 -2.959 2.509 1.286 -1.074 C2 XDX 21 XDX O2 O2 O 0 1 N N N 1.373 -12.294 -2.126 1.845 2.019 -2.105 O2 XDX 22 XDX H1A H1 H 0 1 N N N 0.523 -7.067 3.107 -2.264 -2.656 -1.366 H1A XDX 23 XDX H2A H2 H 0 1 N N N 3.457 -6.128 2.666 -5.008 -1.274 -2.093 H2A XDX 24 XDX H3A H3 H 0 1 N N N 4.171 -9.055 0.333 -2.234 0.004 1.903 H3A XDX 25 XDX H4A H4 H 0 1 N N N 3.806 -7.353 -0.109 -1.061 -1.064 1.096 H4A XDX 26 XDX H5A H5 H 0 1 N N N 3.947 -8.279 -2.151 -0.020 1.048 1.971 H5A XDX 27 XDX H6 H6 H 0 1 N N N 0.595 -6.887 -1.766 -2.546 3.645 1.577 H6 XDX 28 XDX H1 H7 H 0 1 N N N 2.231 -10.174 -3.546 1.597 2.374 0.547 H1 XDX 29 XDX H5 H8 H 0 1 N N N 5.842 -11.323 -2.981 1.464 -1.252 0.707 H5 XDX 30 XDX H61 H9 H 0 1 N N N 6.597 -12.504 -5.333 3.299 -2.600 1.769 H61 XDX 31 XDX H62 H10 H 0 1 N N N 7.144 -10.922 -4.683 4.063 -1.082 2.297 H62 XDX 32 XDX HO6 H11 H 0 1 N Y N 6.374 -10.766 -6.895 2.617 -1.980 3.973 HO6 XDX 33 XDX H4 H12 H 0 1 N N N 4.276 -13.356 -4.559 4.311 -0.578 -0.167 H4 XDX 34 XDX HO4 H13 H 0 1 N Y N 5.615 -14.775 -3.218 3.933 -2.510 -1.520 HO4 XDX 35 XDX H3 H14 H 0 1 N N N 4.239 -12.419 -1.695 1.692 -0.597 -1.739 H3 XDX 36 XDX HO3 H15 H 0 1 N Y N 2.835 -14.201 -1.300 3.159 0.240 -3.428 HO3 XDX 37 XDX H2 H16 H 0 1 N N N 2.268 -12.530 -3.967 3.492 1.721 -0.891 H2 XDX 38 XDX HO2 H17 H 0 1 N Y N 1.106 -13.204 -2.081 1.705 2.953 -1.896 HO2 XDX 39 # # 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 XDX O6 C6 SING N N 1 XDX C6 C5 SING N N 2 XDX O5 C5 SING N N 3 XDX O5 C1 SING N N 4 XDX C5 C4 SING N N 5 XDX C4 O4 SING N N 6 XDX C4 C3 SING N N 7 XDX C1 C2 SING N N 8 XDX C1 O1 SING N N 9 XDX C2 C3 SING N N 10 XDX C2 O2 SING N N 11 XDX OAU CAS DOUB N N 12 XDX C3 O3 SING N N 13 XDX CAS CAR SING N N 14 XDX CAS OAV SING N N 15 XDX O1 CAR SING N N 16 XDX CAR CAQ SING N N 17 XDX CAQ OAM SING N N 18 XDX OAM PAL SING N N 19 XDX OAP PAL DOUB N N 20 XDX PAL OAO SING N N 21 XDX PAL OAN SING N N 22 XDX OAN H1A SING N N 23 XDX OAO H2A SING N N 24 XDX CAQ H3A SING N N 25 XDX CAQ H4A SING N N 26 XDX CAR H5A SING N N 27 XDX OAV H6 SING N N 28 XDX C1 H1 SING N N 29 XDX C5 H5 SING N N 30 XDX C6 H61 SING N N 31 XDX C6 H62 SING N N 32 XDX O6 HO6 SING N N 33 XDX C4 H4 SING N N 34 XDX O4 HO4 SING N N 35 XDX C3 H3 SING N N 36 XDX O3 HO3 SING N N 37 XDX C2 H2 SING N N 38 XDX O2 HO2 SING N N 39 # # 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 XDX SMILES ACDLabs 12.01 "OP(O)(=O)OCC(C(O)=O)OC1C(C(C(C(O1)CO)O)O)O" XDX InChI InChI 1.03 "InChI=1S/C9H17O12P/c10-1-3-5(11)6(12)7(13)9(20-3)21-4(8(14)15)2-19-22(16,17)18/h3-7,9-13H,1-2H2,(H,14,15)(H2,16,17,18)/t3-,4-,5-,6+,7-,9-/m1/s1" XDX InChIKey InChI 1.03 RJDBNSZFZDWPFL-CECBSOHTSA-N XDX SMILES_CANONICAL CACTVS 3.385 "OC[C@H]1O[C@H](O[C@H](CO[P](O)(O)=O)C(O)=O)[C@H](O)[C@@H](O)[C@@H]1O" XDX SMILES CACTVS 3.385 "OC[CH]1O[CH](O[CH](CO[P](O)(O)=O)C(O)=O)[CH](O)[CH](O)[CH]1O" XDX SMILES_CANONICAL "OpenEye OEToolkits" 2.0.4 "C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O[C@H](COP(=O)(O)O)C(=O)O)O)O)O)O" XDX SMILES "OpenEye OEToolkits" 2.0.4 "C(C1C(C(C(C(O1)OC(COP(=O)(O)O)C(=O)O)O)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 XDX "SYSTEMATIC NAME" ACDLabs 12.01 "(2R)-2-(alpha-D-glucopyranosyloxy)-3-(phosphonooxy)propanoic acid" XDX "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.4 ;(2~{R})-2-[(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-3-phosphonooxy-propanoic acid ; # _pdbx_chem_comp_related.comp_id XDX _pdbx_chem_comp_related.related_comp_id GLC _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 XDX C1 GLC C1 "Carbohydrate core" 2 XDX C2 GLC C2 "Carbohydrate core" 3 XDX C3 GLC C3 "Carbohydrate core" 4 XDX C4 GLC C4 "Carbohydrate core" 5 XDX C5 GLC C5 "Carbohydrate core" 6 XDX C6 GLC C6 "Carbohydrate core" 7 XDX O1 GLC O1 "Carbohydrate core" 8 XDX O2 GLC O2 "Carbohydrate core" 9 XDX O3 GLC O3 "Carbohydrate core" 10 XDX O4 GLC O4 "Carbohydrate core" 11 XDX O5 GLC O5 "Carbohydrate core" 12 XDX O6 GLC O6 "Carbohydrate core" 13 XDX H62 GLC H62 "Carbohydrate core" 14 XDX HO6 GLC HO6 "Carbohydrate core" 15 XDX H4 GLC H4 "Carbohydrate core" 16 XDX HO4 GLC HO4 "Carbohydrate core" 17 XDX H3 GLC H3 "Carbohydrate core" 18 XDX HO3 GLC HO3 "Carbohydrate core" 19 XDX H2 GLC H2 "Carbohydrate core" 20 XDX HO2 GLC HO2 "Carbohydrate core" 21 XDX H1 GLC H1 "Carbohydrate core" 22 XDX H5 GLC H5 "Carbohydrate core" 23 XDX H61 GLC H61 "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 XDX "CARBOHYDRATE ISOMER" D PDB ? XDX "CARBOHYDRATE RING" pyranose PDB ? XDX "CARBOHYDRATE ANOMER" alpha PDB ? XDX "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 XDX "Create component" 2016-05-10 RCSB XDX "Initial release" 2017-05-24 RCSB XDX "Other modification" 2020-07-03 RCSB XDX "Modify parent residue" 2020-07-17 RCSB XDX "Modify synonyms" 2020-07-17 RCSB XDX "Modify internal type" 2020-07-17 RCSB XDX "Modify linking type" 2020-07-17 RCSB XDX "Modify atom id" 2020-07-17 RCSB XDX "Modify component atom id" 2020-07-17 RCSB XDX "Modify leaving atom flag" 2020-07-17 RCSB ##