data_XIL # _chem_comp.id XIL _chem_comp.name "(3S,4R)-3-hydroxy-2-oxopiperidin-4-yl beta-D-xylopyranoside" _chem_comp.type D-saccharide _chem_comp.pdbx_type ATOMS _chem_comp.formula "C10 H17 N O7" _chem_comp.mon_nstd_parent_comp_id XYP _chem_comp.pdbx_synonyms ;3-HYDROXY-4-(3,4,5-TRIHYDROXY-TETRAHYDRO-PYRAN-2-YLOXY)-PIPERIDIN-2-ONE; (3S,4R)-3-hydroxy-2-oxopiperidin-4-yl beta-D-xyloside; (3S,4R)-3-hydroxy-2-oxopiperidin-4-yl D-xyloside; (3S,4R)-3-hydroxy-2-oxopiperidin-4-yl xyloside ; _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2002-10-28 _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 263.244 _chem_comp.one_letter_code ? _chem_comp.three_letter_code XIL _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 1J01 _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 XIL "3-HYDROXY-4-(3,4,5-TRIHYDROXY-TETRAHYDRO-PYRAN-2-YLOXY)-PIPERIDIN-2-ONE" PDB ? 2 XIL "(3S,4R)-3-hydroxy-2-oxopiperidin-4-yl beta-D-xyloside" PDB ? 3 XIL "(3S,4R)-3-hydroxy-2-oxopiperidin-4-yl D-xyloside" PDB ? 4 XIL "(3S,4R)-3-hydroxy-2-oxopiperidin-4-yl 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 XIL C1 C1 C 0 1 N N S 16.939 65.278 38.689 -0.205 -0.045 0.834 C1 XIL 1 XIL C2 C2 C 0 1 N N R 16.736 64.264 39.823 -0.895 -0.645 2.062 C2 XIL 2 XIL O2 O2 O 0 1 N N N 17.611 63.163 39.627 -2.312 -0.540 1.913 O2 XIL 3 XIL C3 C3 C 0 1 N N S 15.286 63.764 39.853 -0.450 0.121 3.312 C3 XIL 4 XIL O3 O3 O 0 1 N N N 15.075 62.968 41.013 -0.969 -0.520 4.479 O3 XIL 5 XIL C4 C4 C 0 1 N N R 14.307 64.934 39.857 1.082 0.131 3.361 C4 XIL 6 XIL O4 O4 O 0 1 N N N 12.986 64.439 39.710 1.520 0.968 4.434 O4 XIL 7 XIL C5 C5 C 0 1 N N N 14.626 65.900 38.709 1.622 0.672 2.036 C5 XIL 8 XIL O5 O5 O 0 1 N N N 15.995 66.354 38.807 1.209 -0.173 0.964 O5 XIL 9 XIL "N1'" "N1'" N 0 1 N N N 20.301 67.776 35.697 -0.130 1.205 -4.005 "N1'" XIL 10 XIL "C2'" "C2'" C 0 1 N N N 20.340 68.338 37.000 0.231 -0.074 -3.901 "C2'" XIL 11 XIL "C3'" "C3'" C 0 1 N N S 19.648 67.693 38.053 0.040 -0.891 -2.655 "C3'" XIL 12 XIL "O2'" "O2'" O 0 1 N N N 21.192 69.177 37.263 0.743 -0.606 -4.863 "O2'" XIL 13 XIL "O3'" "O3'" O 0 1 N N N 19.226 68.461 39.162 1.208 -1.681 -2.422 "O3'" XIL 14 XIL "C4'" "C4'" C 0 1 N N R 18.550 66.655 37.644 -0.197 0.031 -1.458 "C4'" XIL 15 XIL O1 "O4'" O 0 1 N N N 18.277 65.824 38.768 -0.639 -0.737 -0.337 O1 XIL 16 XIL "C5'" "C5'" C 0 1 N N N 19.028 65.850 36.431 -1.275 1.053 -1.839 "C5'" XIL 17 XIL "C6'" "C6'" C 0 1 N N N 19.271 66.834 35.322 -0.712 1.981 -2.916 "C6'" XIL 18 XIL H1 H1 H 0 1 N N N 16.788 64.759 37.713 -0.468 1.008 0.751 H1 XIL 19 XIL H2 H2 H 0 1 N N N 16.958 64.763 40.794 -0.615 -1.694 2.161 H2 XIL 20 XIL HO2 HO2 H 0 1 N Y N 17.485 62.535 40.329 -2.547 -1.031 1.114 HO2 XIL 21 XIL H3 H3 H 0 1 N N N 15.108 63.152 38.937 -0.819 1.146 3.263 H3 XIL 22 XIL HO3 HO3 H 0 1 N Y N 14.177 62.658 41.031 -0.665 -0.005 5.239 HO3 XIL 23 XIL H4 H4 H 0 1 N N N 14.399 65.483 40.822 1.448 -0.883 3.517 H4 XIL 24 XIL HO4 HO4 H 0 1 N Y N 12.376 65.167 39.712 2.487 0.948 4.426 HO4 XIL 25 XIL H51 H51 H 0 1 N N N 14.405 65.450 37.712 1.237 1.679 1.872 H51 XIL 26 XIL H52 H52 H 0 1 N N N 13.906 66.750 38.667 2.710 0.704 2.074 H52 XIL 27 XIL "HN'" "HN'" H 0 1 N N N 21.018 68.050 35.025 0.001 1.646 -4.858 "HN'" XIL 28 XIL "H3'" "H3'" H 0 1 N N N 20.524 67.117 38.431 -0.821 -1.547 -2.782 "H3'" XIL 29 XIL "HO'" "HO'" H 0 1 N N N 18.761 68.028 39.868 1.318 -2.252 -3.194 "HO'" XIL 30 XIL "H4'" "H4'" H 0 1 N N N 17.605 67.167 37.346 0.726 0.550 -1.205 "H4'" XIL 31 XIL "H5'1" "H5'1" H 0 0 N N N 19.913 65.209 36.651 -2.151 0.533 -2.227 "H5'1" XIL 32 XIL "H5'2" "H5'2" H 0 0 N N N 18.328 65.030 36.144 -1.552 1.637 -0.962 "H5'2" XIL 33 XIL "H6'1" "H6'1" H 0 0 N N N 18.331 67.348 35.011 -1.513 2.606 -3.309 "H6'1" XIL 34 XIL "H6'2" "H6'2" H 0 0 N N N 19.507 66.323 34.359 0.056 2.617 -2.477 "H6'2" XIL 35 # # 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 XIL C1 C2 SING N N 1 XIL C1 O5 SING N N 2 XIL C1 O1 SING N N 3 XIL C1 H1 SING N N 4 XIL C2 O2 SING N N 5 XIL C2 C3 SING N N 6 XIL C2 H2 SING N N 7 XIL O2 HO2 SING N N 8 XIL C3 O3 SING N N 9 XIL C3 C4 SING N N 10 XIL C3 H3 SING N N 11 XIL O3 HO3 SING N N 12 XIL C4 O4 SING N N 13 XIL C4 C5 SING N N 14 XIL C4 H4 SING N N 15 XIL O4 HO4 SING N N 16 XIL C5 O5 SING N N 17 XIL C5 H51 SING N N 18 XIL C5 H52 SING N N 19 XIL "N1'" "C2'" SING N N 20 XIL "N1'" "C6'" SING N N 21 XIL "N1'" "HN'" SING N N 22 XIL "C2'" "C3'" SING N N 23 XIL "C2'" "O2'" DOUB N N 24 XIL "C3'" "O3'" SING N N 25 XIL "C3'" "C4'" SING N N 26 XIL "C3'" "H3'" SING N N 27 XIL "O3'" "HO'" SING N N 28 XIL "C4'" O1 SING N N 29 XIL "C4'" "C5'" SING N N 30 XIL "C4'" "H4'" SING N N 31 XIL "C5'" "C6'" SING N N 32 XIL "C5'" "H5'1" SING N N 33 XIL "C5'" "H5'2" SING N N 34 XIL "C6'" "H6'1" SING N N 35 XIL "C6'" "H6'2" SING N N 36 # # 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 XIL SMILES ACDLabs 10.04 "O=C2NCCC(OC1OCC(O)C(O)C1O)C2O" XIL SMILES_CANONICAL CACTVS 3.341 "O[C@@H]1CO[C@@H](O[C@@H]2CCNC(=O)[C@H]2O)[C@H](O)[C@H]1O" XIL SMILES CACTVS 3.341 "O[CH]1CO[CH](O[CH]2CCNC(=O)[CH]2O)[CH](O)[CH]1O" XIL SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1CNC(=O)[C@H]([C@@H]1O[C@H]2[C@@H]([C@H]([C@@H](CO2)O)O)O)O" XIL SMILES "OpenEye OEToolkits" 1.5.0 "C1CNC(=O)C(C1OC2C(C(C(CO2)O)O)O)O" XIL InChI InChI 1.03 "InChI=1S/C10H17NO7/c12-4-3-17-10(8(15)6(4)13)18-5-1-2-11-9(16)7(5)14/h4-8,10,12-15H,1-3H2,(H,11,16)/t4-,5-,6+,7+,8-,10+/m1/s1" XIL InChIKey InChI 1.03 BHZMHPRIYUPDCT-BQWZOORQSA-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 XIL "SYSTEMATIC NAME" ACDLabs 10.04 "(3S,4R)-3-hydroxy-2-oxopiperidin-4-yl beta-D-xylopyranoside" XIL "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(3S,4R)-3-hydroxy-4-[(2S,3R,4S,5R)-3,4,5-trihydroxyoxan-2-yl]oxy-piperidin-2-one" # _pdbx_chem_comp_related.comp_id XIL _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 XIL C1 XYP C1 "Carbohydrate core" 2 XIL C2 XYP C2 "Carbohydrate core" 3 XIL C3 XYP C3 "Carbohydrate core" 4 XIL C4 XYP C4 "Carbohydrate core" 5 XIL C5 XYP C5 "Carbohydrate core" 6 XIL O2 XYP O2 "Carbohydrate core" 7 XIL O3 XYP O3 "Carbohydrate core" 8 XIL O4 XYP O4 "Carbohydrate core" 9 XIL O1 XYP O1 "Carbohydrate core" 10 XIL O5 XYP O5 "Carbohydrate core" 11 XIL H1 XYP H1 "Carbohydrate core" 12 XIL H2 XYP H2 "Carbohydrate core" 13 XIL H3 XYP H3 "Carbohydrate core" 14 XIL H4 XYP H4 "Carbohydrate core" 15 XIL H51 XYP H51 "Carbohydrate core" 16 XIL H52 XYP H52 "Carbohydrate core" 17 XIL HO2 XYP HO2 "Carbohydrate core" 18 XIL HO3 XYP HO3 "Carbohydrate core" 19 XIL 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 XIL "CARBOHYDRATE ISOMER" D PDB ? XIL "CARBOHYDRATE RING" pyranose PDB ? XIL "CARBOHYDRATE ANOMER" beta PDB ? XIL "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 XIL "Create component" 2002-10-28 RCSB XIL "Modify descriptor" 2011-06-04 RCSB XIL "Other modification" 2020-07-03 RCSB XIL "Modify parent residue" 2020-07-17 RCSB XIL "Modify name" 2020-07-17 RCSB XIL "Modify synonyms" 2020-07-17 RCSB XIL "Modify internal type" 2020-07-17 RCSB XIL "Modify linking type" 2020-07-17 RCSB XIL "Modify atom id" 2020-07-17 RCSB XIL "Modify component atom id" 2020-07-17 RCSB XIL "Modify leaving atom flag" 2020-07-17 RCSB ##