data_07E # _chem_comp.id 07E _chem_comp.name "(3S)-3-hydroxybutyl beta-D-xylopyranoside" _chem_comp.type D-saccharide _chem_comp.pdbx_type ATOMS _chem_comp.formula "C9 H18 O6" _chem_comp.mon_nstd_parent_comp_id XYP _chem_comp.pdbx_synonyms "(3S)-3-hydroxybutyl beta-D-xyloside; (3S)-3-hydroxybutyl D-xyloside; (3S)-3-hydroxybutyl xyloside" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2011-09-23 _chem_comp.pdbx_modified_date 2024-09-27 _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 222.236 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 07E _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 1REE _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _chem_comp.pdbx_pcm Y # 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 07E "(3S)-3-hydroxybutyl beta-D-xyloside" PDB ? 2 07E "(3S)-3-hydroxybutyl D-xyloside" PDB ? 3 07E "(3S)-3-hydroxybutyl 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.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _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 07E C1 C1 C 0 1 N N R N N N 81.727 22.727 10.669 0.450 0.166 -0.277 C1 07E 1 07E C2 C2 C 0 1 N N R N N N 81.511 23.929 11.629 1.582 1.056 0.240 C2 07E 2 07E C3 C3 C 0 1 N N S N N N 82.839 24.205 12.359 2.926 0.472 -0.207 C3 07E 3 07E C4 C4 C 0 1 N N R N N N 83.290 22.965 13.153 3.039 -0.968 0.303 C4 07E 4 07E C5 C5 C 0 1 N N N N N N 83.348 21.754 12.193 1.850 -1.781 -0.217 C5 07E 5 07E O1 O1 O 0 1 N N N N N N 80.550 22.369 9.904 -0.804 0.673 0.184 O1 07E 6 07E O2 O2 O 0 1 N N N N N N 81.157 25.111 10.936 1.434 2.374 -0.291 O2 07E 7 07E O3 O3 O 0 1 N N N N N N 82.705 25.289 13.235 3.992 1.256 0.333 O3 07E 8 07E O4 O4 O 0 1 N N N N N N 84.565 23.200 13.751 4.257 -1.548 -0.170 O4 07E 9 07E O5 O5 O 0 1 N N N N N N 82.114 21.609 11.462 0.632 -1.166 0.209 O5 07E 10 07E "C1'" "C1'" C 0 1 N N N N N N 80.806 22.016 8.510 -1.939 -0.023 -0.336 "C1'" 07E 11 07E "C2'" "C2'" C 0 1 N N N N N N 79.665 21.226 7.835 -3.220 0.603 0.222 "C2'" 07E 12 07E "C3'" "C3'" C 0 1 N N S N N N 78.447 21.995 7.288 -4.435 -0.142 -0.335 "C3'" 07E 13 07E "C4'" "C4'" C 0 1 N N N N N N 78.759 22.998 6.145 -5.716 0.559 0.122 "C4'" 07E 14 07E "O'" "O'" O 0 1 N N N N N N 77.874 22.690 8.366 -4.430 -1.487 0.147 "O'" 07E 15 07E H1 H1 H 0 1 N N N N N N 82.495 23.019 9.938 0.461 0.159 -1.367 H1 07E 16 07E H2 H2 H 0 1 N N N N N N 80.694 23.667 12.318 1.547 1.095 1.329 H2 07E 17 07E H3 H3 H 0 1 N N N N N N 83.597 24.445 11.599 2.982 0.479 -1.296 H3 07E 18 07E H4 H4 H 0 1 N N N N N N 82.573 22.755 13.960 3.034 -0.970 1.393 H4 07E 19 07E H51 H5 H 0 1 N N N N N N 83.523 20.841 12.781 1.880 -1.812 -1.306 H51 07E 20 07E H52 H6 H 0 1 N N N N N N 84.170 21.905 11.478 1.903 -2.795 0.178 H52 07E 21 07E HO2 H7 H 0 1 N Y N N N N 81.035 25.819 11.558 0.602 2.804 -0.051 HO2 07E 22 07E HO3 H8 H 0 1 N Y N N N N 83.532 25.445 13.676 4.873 0.942 0.089 HO3 07E 23 07E HO4 H9 H 0 1 N Y N N N N 84.508 23.946 14.336 4.394 -2.461 0.116 HO4 07E 24 07E H10 H10 H 0 1 N N N N N N 81.712 21.393 8.480 -1.943 0.050 -1.423 H10 07E 25 07E H11 H11 H 0 1 N N N N N N 80.950 22.949 7.946 -1.889 -1.071 -0.041 H11 07E 26 07E H12 H12 H 0 1 N N N N N N 79.278 20.529 8.593 -3.216 0.531 1.309 H12 07E 27 07E H13 H13 H 0 1 N N N N N N 80.114 20.703 6.977 -3.270 1.651 -0.073 H13 07E 28 07E H14 H14 H 0 1 N N N N N N 77.771 21.251 6.841 -4.391 -0.146 -1.424 H14 07E 29 07E H15 H15 H 0 1 N N N N N N 77.829 23.492 5.826 -5.719 1.585 -0.245 H15 07E 30 07E H16 H16 H 0 1 N N N N N N 79.471 23.755 6.506 -6.581 0.029 -0.274 H16 07E 31 07E H17 H17 H 0 1 N N N N N N 79.197 22.458 5.293 -5.759 0.563 1.211 H17 07E 32 07E H18 H18 H 0 1 N N N N N N 77.681 22.081 9.069 -4.468 -1.560 1.111 H18 07E 33 # 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 07E "C4'" "C3'" SING N N 1 07E "C3'" "C2'" SING N N 2 07E "C3'" "O'" SING N N 3 07E "C2'" "C1'" SING N N 4 07E "C1'" O1 SING N N 5 07E O1 C1 SING N N 6 07E C1 O5 SING N N 7 07E C1 C2 SING N N 8 07E O2 C2 SING N N 9 07E O5 C5 SING N N 10 07E C2 C3 SING N N 11 07E C5 C4 SING N N 12 07E C3 C4 SING N N 13 07E C3 O3 SING N N 14 07E C4 O4 SING N N 15 07E C1 H1 SING N N 16 07E C2 H2 SING N N 17 07E C3 H3 SING N N 18 07E C4 H4 SING N N 19 07E C5 H51 SING N N 20 07E C5 H52 SING N N 21 07E O2 HO2 SING N N 22 07E O3 HO3 SING N N 23 07E O4 HO4 SING N N 24 07E "C1'" H10 SING N N 25 07E "C1'" H11 SING N N 26 07E "C2'" H12 SING N N 27 07E "C2'" H13 SING N N 28 07E "C3'" H14 SING N N 29 07E "C4'" H15 SING N N 30 07E "C4'" H16 SING N N 31 07E "C4'" H17 SING N N 32 07E "O'" H18 SING N N 33 # 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 07E SMILES ACDLabs 12.01 "O(CCC(O)C)C1OCC(O)C(O)C1O" 07E InChI InChI 1.03 "InChI=1S/C9H18O6/c1-5(10)2-3-14-9-8(13)7(12)6(11)4-15-9/h5-13H,2-4H2,1H3/t5-,6+,7-,8+,9+/m0/s1" 07E InChIKey InChI 1.03 KAKVKOIRYXYSBS-KVEIKIFDSA-N 07E SMILES_CANONICAL CACTVS 3.370 "C[C@H](O)CCO[C@@H]1OC[C@@H](O)[C@H](O)[C@H]1O" 07E SMILES CACTVS 3.370 "C[CH](O)CCO[CH]1OC[CH](O)[CH](O)[CH]1O" 07E SMILES_CANONICAL "OpenEye OEToolkits" 1.7.2 "C[C@@H](CCO[C@H]1[C@@H]([C@H]([C@@H](CO1)O)O)O)O" 07E SMILES "OpenEye OEToolkits" 1.7.2 "CC(CCOC1C(C(C(CO1)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 07E "SYSTEMATIC NAME" ACDLabs 12.01 "(3S)-3-hydroxybutyl beta-D-xylopyranoside" 07E "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.2 "(2R,3R,4S,5R)-2-[(3S)-3-oxidanylbutoxy]oxane-3,4,5-triol" # _pdbx_chem_comp_related.comp_id 07E _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 07E C1 XYP C1 "Carbohydrate core" 2 07E C2 XYP C2 "Carbohydrate core" 3 07E C3 XYP C3 "Carbohydrate core" 4 07E C4 XYP C4 "Carbohydrate core" 5 07E C5 XYP C5 "Carbohydrate core" 6 07E O1 XYP O1 "Carbohydrate core" 7 07E O2 XYP O2 "Carbohydrate core" 8 07E O3 XYP O3 "Carbohydrate core" 9 07E O4 XYP O4 "Carbohydrate core" 10 07E O5 XYP O5 "Carbohydrate core" 11 07E H1 XYP H1 "Carbohydrate core" 12 07E H2 XYP H2 "Carbohydrate core" 13 07E H3 XYP H3 "Carbohydrate core" 14 07E H4 XYP H4 "Carbohydrate core" 15 07E H51 XYP H51 "Carbohydrate core" 16 07E H52 XYP H52 "Carbohydrate core" 17 07E HO2 XYP HO2 "Carbohydrate core" 18 07E HO3 XYP HO3 "Carbohydrate core" 19 07E 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 07E "CARBOHYDRATE ISOMER" D PDB ? 07E "CARBOHYDRATE RING" pyranose PDB ? 07E "CARBOHYDRATE ANOMER" beta PDB ? 07E "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 07E "Create component" 2011-09-23 RCSB 07E "Initial release" 2017-07-12 RCSB 07E "Other modification" 2020-07-03 RCSB 07E "Modify parent residue" 2020-07-17 RCSB 07E "Modify synonyms" 2020-07-17 RCSB 07E "Modify internal type" 2020-07-17 RCSB 07E "Modify linking type" 2020-07-17 RCSB 07E "Modify atom id" 2020-07-17 RCSB 07E "Modify component atom id" 2020-07-17 RCSB 07E "Modify leaving atom flag" 2020-07-17 RCSB 07E "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id 07E _pdbx_chem_comp_pcm.modified_residue_id GLU _pdbx_chem_comp_pcm.type None _pdbx_chem_comp_pcm.category Carbohydrate _pdbx_chem_comp_pcm.position "Amino-acid side chain" _pdbx_chem_comp_pcm.polypeptide_position "Any position" _pdbx_chem_comp_pcm.comp_id_linking_atom "C4'" _pdbx_chem_comp_pcm.modified_residue_id_linking_atom OE2 _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #