data_C5X # _chem_comp.id C5X _chem_comp.name "3-[(2R)-oxiran-2-yl]propyl beta-D-xylopyranoside" _chem_comp.type D-saccharide _chem_comp.pdbx_type ATOMS _chem_comp.formula "C10 H18 O6" _chem_comp.mon_nstd_parent_comp_id XYP _chem_comp.pdbx_synonyms ;4,5-EPOXYPENTYL-BETA-D-XYLOSIDE; 3-[(2R)-oxiran-2-yl]propyl beta-D-xyloside; 3-[(2R)-oxiran-2-yl]propyl D-xyloside; 3-[(2R)-oxiran-2-yl]propyl xyloside ; _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-08 _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 234.246 _chem_comp.one_letter_code ? _chem_comp.three_letter_code C5X _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 1RED _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # # 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 C5X "4,5-EPOXYPENTYL-BETA-D-XYLOSIDE" PDB ? 2 C5X "3-[(2R)-oxiran-2-yl]propyl beta-D-xyloside" PDB ? 3 C5X "3-[(2R)-oxiran-2-yl]propyl D-xyloside" PDB ? 4 C5X "3-[(2R)-oxiran-2-yl]propyl xyloside" 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 C5X C1 C1 C 0 1 N N R 82.258 22.825 10.584 -0.150 0.151 0.944 C1 C5X 1 C5X C2 C2 C 0 1 N N R 81.868 23.979 11.515 -1.057 -0.244 2.111 C2 C5X 2 C5X C3 C3 C 0 1 N N S 83.094 24.270 12.384 -0.447 0.274 3.419 C3 C5X 3 C5X C4 C4 C 0 1 N N R 83.521 23.013 13.157 0.999 -0.223 3.516 C4 C5X 4 C5X C5 C5 C 0 1 N N N 83.694 21.816 12.210 1.750 0.170 2.242 C5 C5X 5 C5X O1 O1 O 0 1 N N N 81.238 22.543 9.645 -0.728 -0.303 -0.280 O1 C5X 6 C5X O2 O2 O 0 1 N N N 81.498 25.147 10.806 -2.353 0.328 1.926 O2 C5X 7 C5X O3 O3 O 0 1 N N N 82.835 25.298 13.304 -1.204 -0.214 4.528 O3 C5X 8 C5X O4 O4 O 0 1 N N N 84.759 23.270 13.809 1.634 0.371 4.649 O4 C5X 9 C5X O5 O5 O 0 1 N N N 82.543 21.677 11.373 1.136 -0.441 1.110 O5 C5X 10 C5X "C1'" "C1'" C 0 1 N N N 81.497 21.470 8.706 0.154 0.099 -1.329 "C1'" C5X 11 C5X "C2'" "C2'" C 0 1 N N N 80.572 21.585 7.471 -0.409 -0.359 -2.675 "C2'" C5X 12 C5X "C3'" "C3'" C 0 1 N N N 79.161 21.025 7.723 0.536 0.071 -3.798 "C3'" C5X 13 C5X "C4'" "C4'" C 0 1 N N R 78.474 21.685 8.934 -0.027 -0.387 -5.144 "C4'" C5X 14 C5X "C5'" "C5'" C 0 1 N N N 77.295 20.929 9.485 0.757 -0.025 -6.406 "C5'" C5X 15 C5X "O'" "O'" O 0 1 N N N 78.049 22.983 8.545 -0.471 0.618 -6.057 "O'" C5X 16 C5X H1 H1 H 0 1 N N N 83.162 23.121 10.002 -0.048 1.236 0.916 H1 C5X 17 C5X H2 H2 H 0 1 N N N 80.978 23.685 12.120 -1.141 -1.330 2.156 H2 C5X 18 C5X H3 H3 H 0 1 N N N 83.913 24.589 11.699 -0.457 1.364 3.420 H3 C5X 19 C5X H4 H4 H 0 1 N N N 82.728 22.765 13.901 1.005 -1.308 3.622 H4 C5X 20 C5X H51 H51 H 0 1 N N N 84.634 21.887 11.615 1.725 1.254 2.127 H51 C5X 21 C5X H52 H52 H 0 1 N N N 83.921 20.875 12.764 2.786 -0.160 2.315 H52 C5X 22 C5X HO2 HO2 H 0 1 N Y N 81.256 25.862 11.382 -2.696 -0.020 1.091 HO2 C5X 23 C5X HO3 HO3 H 0 1 N Y N 83.595 25.478 13.843 -0.786 0.135 5.327 HO3 C5X 24 C5X HO4 HO4 H 0 1 N Y N 85.023 22.492 14.287 2.540 0.034 4.671 HO4 C5X 25 C5X "H1'1" "H1'1" H 0 0 N N N 82.572 21.428 8.413 0.250 1.184 -1.326 "H1'1" C5X 26 C5X "H1'2" "H1'2" H 0 0 N N N 81.415 20.469 9.190 1.134 -0.352 -1.172 "H1'2" C5X 27 C5X "H2'1" "H2'1" H 0 0 N N N 80.523 22.637 7.106 -0.505 -1.445 -2.678 "H2'1" C5X 28 C5X "H2'2" "H2'2" H 0 0 N N N 81.037 21.104 6.578 -1.388 0.091 -2.831 "H2'2" C5X 29 C5X "H3'1" "H3'1" H 0 0 N N N 78.527 21.105 6.808 0.632 1.157 -3.795 "H3'1" C5X 30 C5X "H3'2" "H3'2" H 0 0 N N N 79.182 19.915 7.828 1.516 -0.380 -3.641 "H3'2" C5X 31 C5X "H4'" "H4'" H 0 1 N N N 79.227 21.704 9.755 -0.562 -1.336 -5.134 "H4'" C5X 32 C5X "H5'1" "H5'1" H 0 0 N N N 76.613 20.046 9.501 1.680 0.542 -6.285 "H5'1" C5X 33 C5X "H5'2" "H5'2" H 0 0 N N N 76.792 20.341 10.288 0.742 -0.733 -7.234 "H5'2" C5X 34 # # 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 C5X C1 C2 SING N N 1 C5X C1 O1 SING N N 2 C5X C1 O5 SING N N 3 C5X C1 H1 SING N N 4 C5X C2 C3 SING N N 5 C5X C2 O2 SING N N 6 C5X C2 H2 SING N N 7 C5X C3 C4 SING N N 8 C5X C3 O3 SING N N 9 C5X C3 H3 SING N N 10 C5X C4 C5 SING N N 11 C5X C4 O4 SING N N 12 C5X C4 H4 SING N N 13 C5X C5 O5 SING N N 14 C5X C5 H51 SING N N 15 C5X C5 H52 SING N N 16 C5X O1 "C1'" SING N N 17 C5X O2 HO2 SING N N 18 C5X O3 HO3 SING N N 19 C5X O4 HO4 SING N N 20 C5X "C1'" "C2'" SING N N 21 C5X "C1'" "H1'1" SING N N 22 C5X "C1'" "H1'2" SING N N 23 C5X "C2'" "C3'" SING N N 24 C5X "C2'" "H2'1" SING N N 25 C5X "C2'" "H2'2" SING N N 26 C5X "C3'" "C4'" SING N N 27 C5X "C3'" "H3'1" SING N N 28 C5X "C3'" "H3'2" SING N N 29 C5X "C4'" "C5'" SING N N 30 C5X "C4'" "O'" SING N N 31 C5X "C4'" "H4'" SING N N 32 C5X "C5'" "O'" SING N N 33 C5X "C5'" "H5'1" SING N N 34 C5X "C5'" "H5'2" SING N N 35 # # 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 C5X SMILES ACDLabs 10.04 "O(CCCC1OC1)C2OCC(O)C(O)C2O" C5X SMILES_CANONICAL CACTVS 3.341 "O[C@@H]1CO[C@@H](OCCC[C@@H]2CO2)[C@H](O)[C@H]1O" C5X SMILES CACTVS 3.341 "O[CH]1CO[CH](OCCC[CH]2CO2)[CH](O)[CH]1O" C5X SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1[C@H](O1)CCCO[C@H]2[C@@H]([C@H]([C@@H](CO2)O)O)O" C5X SMILES "OpenEye OEToolkits" 1.5.0 "C1C(O1)CCCOC2C(C(C(CO2)O)O)O" C5X InChI InChI 1.03 "InChI=1S/C10H18O6/c11-7-5-16-10(9(13)8(7)12)14-3-1-2-6-4-15-6/h6-13H,1-5H2/t6-,7-,8+,9-,10-/m1/s1" C5X InChIKey InChI 1.03 DMNHSULDBMDHLY-HOTMZDKISA-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 C5X "SYSTEMATIC NAME" ACDLabs 10.04 "3-[(2R)-oxiran-2-yl]propyl beta-D-xylopyranoside" C5X "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2R,3R,4S,5R)-2-[3-[(2R)-oxiran-2-yl]propoxy]oxane-3,4,5-triol" # _pdbx_chem_comp_related.comp_id C5X _pdbx_chem_comp_related.related_comp_id XYP _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 C5X C1 XYP C1 "Carbohydrate core" 2 C5X C2 XYP C2 "Carbohydrate core" 3 C5X C3 XYP C3 "Carbohydrate core" 4 C5X C4 XYP C4 "Carbohydrate core" 5 C5X C5 XYP C5 "Carbohydrate core" 6 C5X O1 XYP O1 "Carbohydrate core" 7 C5X O2 XYP O2 "Carbohydrate core" 8 C5X O3 XYP O3 "Carbohydrate core" 9 C5X O4 XYP O4 "Carbohydrate core" 10 C5X O5 XYP O5 "Carbohydrate core" 11 C5X H1 XYP H1 "Carbohydrate core" 12 C5X H2 XYP H2 "Carbohydrate core" 13 C5X H3 XYP H3 "Carbohydrate core" 14 C5X H4 XYP H4 "Carbohydrate core" 15 C5X H51 XYP H51 "Carbohydrate core" 16 C5X H52 XYP H52 "Carbohydrate core" 17 C5X HO2 XYP HO2 "Carbohydrate core" 18 C5X HO3 XYP HO3 "Carbohydrate core" 19 C5X HO4 XYP 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 C5X "CARBOHYDRATE ISOMER" D PDB ? C5X "CARBOHYDRATE RING" pyranose PDB ? C5X "CARBOHYDRATE ANOMER" beta PDB ? C5X "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 C5X "Create component" 1999-07-08 EBI C5X "Modify descriptor" 2011-06-04 RCSB C5X "Other modification" 2020-07-03 RCSB C5X "Modify parent residue" 2020-07-17 RCSB C5X "Modify name" 2020-07-17 RCSB C5X "Modify synonyms" 2020-07-17 RCSB C5X "Modify internal type" 2020-07-17 RCSB C5X "Modify linking type" 2020-07-17 RCSB C5X "Modify leaving atom flag" 2020-07-17 RCSB ##