data_RZM # _chem_comp.id RZM _chem_comp.name "(2R,3R,4R,5R)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-3-yl alpha-D-glucopyranoside" _chem_comp.type D-saccharide _chem_comp.pdbx_type ATOMS _chem_comp.formula "C12 H23 N O9" _chem_comp.mon_nstd_parent_comp_id GLC _chem_comp.pdbx_synonyms ;(2R,3R,4R,5R)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-3-yl alpha-D-glucoside; (2R,3R,4R,5R)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-3-yl D-glucoside; (2R,3R,4R,5R)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-3-yl glucoside ; _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2014-07-24 _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 325.312 _chem_comp.one_letter_code ? _chem_comp.three_letter_code RZM _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 4U2Y _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 RZM "(2R,3R,4R,5R)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-3-yl alpha-D-glucoside" PDB ? 2 RZM "(2R,3R,4R,5R)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-3-yl D-glucoside" PDB ? 3 RZM "(2R,3R,4R,5R)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-3-yl glucoside" 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 RZM "O6'" "O6'" O 0 1 N N N 27.377 -29.467 278.987 -1.835 3.145 1.620 "O6'" RZM 1 RZM "C6'" "C6'" C 0 1 N N N 27.245 -30.745 279.614 -1.352 2.313 0.563 "C6'" RZM 2 RZM "C5'" "C5'" C 0 1 N N R 25.817 -31.076 280.038 -1.720 0.856 0.851 "C5'" RZM 3 RZM "C2'" "C2'" C 0 1 N N R 23.807 -30.122 280.421 -3.505 -0.271 -0.285 "C2'" RZM 4 RZM "C1'" "C1'" C 0 1 N N N 23.001 -30.388 281.516 -4.683 -1.157 0.124 "C1'" RZM 5 RZM "O1'" "O1'" O 0 1 N N N 22.476 -29.096 281.922 -5.864 -0.360 0.232 "O1'" RZM 6 RZM "C3'" "C3'" C 0 1 N N R 23.671 -31.228 279.271 -2.222 -1.122 -0.453 "C3'" RZM 7 RZM "O3'" "O3'" O 0 1 N N N 22.529 -30.815 278.373 -2.144 -1.677 -1.768 "O3'" RZM 8 RZM "C4'" "C4'" C 0 1 N N R 24.793 -31.139 278.719 -1.111 -0.063 -0.229 "C4'" RZM 9 RZM O1 "O4'" O 0 1 N N N 25.143 -32.278 277.850 0.086 -0.679 0.248 O1 RZM 10 RZM C1 C1 C 0 1 N N S 24.700 -32.030 276.542 0.993 -1.066 -0.786 C1 RZM 11 RZM C2 C2 C 0 1 N N R 24.367 -33.357 275.937 2.109 -1.928 -0.191 C2 RZM 12 RZM O2 O2 O 0 1 N N N 23.340 -33.969 276.754 1.539 -3.067 0.456 O2 RZM 13 RZM C3 C3 C 0 1 N N S 25.591 -34.192 275.830 2.895 -1.099 0.831 C3 RZM 14 RZM O3 O3 O 0 1 N N N 25.316 -35.529 275.325 3.983 -1.873 1.339 O3 RZM 15 RZM C4 C4 C 0 1 N N S 26.574 -33.507 274.959 3.435 0.159 0.144 C4 RZM 16 RZM O4 O4 O 0 1 N N N 27.751 -34.348 274.772 4.108 0.975 1.104 O4 RZM 17 RZM C5 C5 C 0 1 N N R 26.935 -32.214 275.636 2.268 0.940 -0.465 C5 RZM 18 RZM C6 C6 C 0 1 N N N 28.029 -31.448 274.963 2.806 2.167 -1.205 C6 RZM 19 RZM O6 O6 O 0 1 N N N 27.506 -30.774 273.831 1.712 2.958 -1.673 O6 RZM 20 RZM O5 O5 O 0 1 N N N 25.754 -31.328 275.786 1.562 0.102 -1.382 O5 RZM 21 RZM "N5'" "N5'" N 0 1 N N N 25.297 -30.139 280.783 -3.184 0.688 0.793 "N5'" RZM 22 RZM H1A H1 H 0 1 N N N 28.285 -29.323 278.749 -1.637 4.084 1.503 H1A RZM 23 RZM H2A H2 H 0 1 N N N 27.585 -31.516 278.906 -1.804 2.623 -0.379 H2A RZM 24 RZM H3A H3 H 0 1 N N N 27.885 -30.761 280.508 -0.268 2.407 0.494 H3A RZM 25 RZM H4A H4 H 0 1 N N N 25.799 -32.064 280.521 -1.352 0.569 1.836 H4A RZM 26 RZM H5A H5 H 0 1 N N N 23.561 -29.144 279.982 -3.734 0.260 -1.209 H5A RZM 27 RZM H6 H6 H 0 1 N N N 22.182 -31.067 281.237 -4.834 -1.931 -0.629 H6 RZM 28 RZM H7 H7 H 0 1 N N N 23.590 -30.838 282.329 -4.470 -1.623 1.086 H7 RZM 29 RZM H8 H8 H 0 1 N N N 21.909 -29.207 282.676 -6.653 -0.858 0.489 H8 RZM 30 RZM H9 H9 H 0 1 N N N 23.461 -32.204 279.732 -2.172 -1.906 0.303 H9 RZM 31 RZM H10 H10 H 0 1 N N N 21.708 -30.903 278.843 -2.874 -2.272 -1.987 H10 RZM 32 RZM H11 H11 H 0 1 N N N 24.925 -30.200 278.162 -0.920 0.495 -1.146 H11 RZM 33 RZM H1 H12 H 0 1 N N N 23.793 -31.408 276.559 0.458 -1.637 -1.544 H1 RZM 34 RZM H2 H13 H 0 1 N N N 23.969 -33.188 274.926 2.779 -2.257 -0.986 H2 RZM 35 RZM HO2 H14 H 0 1 N Y N 22.582 -33.398 276.791 1.023 -3.636 -0.132 HO2 RZM 36 RZM H3 H15 H 0 1 N N N 26.030 -34.283 276.834 2.236 -0.812 1.651 H3 RZM 37 RZM HO3 H16 H 0 1 N Y N 24.685 -35.958 275.891 3.711 -2.689 1.783 HO3 RZM 38 RZM H4 H17 H 0 1 N N N 26.112 -33.289 273.985 4.132 -0.128 -0.644 H4 RZM 39 RZM HO4 H18 H 0 1 N Y N 27.498 -35.157 274.343 4.861 0.543 1.530 HO4 RZM 40 RZM H5 H19 H 0 1 N N N 27.288 -32.465 276.647 1.593 1.261 0.328 H5 RZM 41 RZM H61 H20 H 0 1 N N N 28.820 -32.142 274.643 3.420 2.760 -0.527 H61 RZM 42 RZM H62 H21 H 0 1 N N N 28.448 -30.713 275.666 3.410 1.844 -2.053 H62 RZM 43 RZM HO6 H22 H 0 1 N Y N 28.200 -30.287 273.403 1.979 3.754 -2.152 HO6 RZM 44 RZM H23 H23 H 0 1 N N N 25.420 -30.352 281.752 -3.546 0.370 1.680 H23 RZM 45 # # 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 RZM O6 C6 SING N N 1 RZM O4 C4 SING N N 2 RZM C4 C5 SING N N 3 RZM C4 C3 SING N N 4 RZM C6 C5 SING N N 5 RZM O3 C3 SING N N 6 RZM C5 O5 SING N N 7 RZM O5 C1 SING N N 8 RZM C3 C2 SING N N 9 RZM C2 C1 SING N N 10 RZM C2 O2 SING N N 11 RZM C1 O1 SING N N 12 RZM O1 "C4'" SING N N 13 RZM "O3'" "C3'" SING N N 14 RZM "C4'" "C3'" SING N N 15 RZM "C4'" "C5'" SING N N 16 RZM "O6'" "C6'" SING N N 17 RZM "C3'" "C2'" SING N N 18 RZM "C6'" "C5'" SING N N 19 RZM "C5'" "N5'" SING N N 20 RZM "C2'" "N5'" SING N N 21 RZM "C2'" "C1'" SING N N 22 RZM "C1'" "O1'" SING N N 23 RZM "O6'" H1A SING N N 24 RZM "C6'" H2A SING N N 25 RZM "C6'" H3A SING N N 26 RZM "C5'" H4A SING N N 27 RZM "C2'" H5A SING N N 28 RZM "C1'" H6 SING N N 29 RZM "C1'" H7 SING N N 30 RZM "O1'" H8 SING N N 31 RZM "C3'" H9 SING N N 32 RZM "O3'" H10 SING N N 33 RZM "C4'" H11 SING N N 34 RZM C1 H1 SING N N 35 RZM C2 H2 SING N N 36 RZM O2 HO2 SING N N 37 RZM C3 H3 SING N N 38 RZM O3 HO3 SING N N 39 RZM C4 H4 SING N N 40 RZM O4 HO4 SING N N 41 RZM C5 H5 SING N N 42 RZM C6 H61 SING N N 43 RZM C6 H62 SING N N 44 RZM O6 HO6 SING N N 45 RZM "N5'" H23 SING N N 46 # # 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 RZM SMILES ACDLabs 12.01 "O(C1C(O)C(NC1CO)CO)C2OC(C(O)C(O)C2O)CO" RZM InChI InChI 1.03 "InChI=1S/C12H23NO9/c14-1-4-7(17)11(5(2-15)13-4)22-12-10(20)9(19)8(18)6(3-16)21-12/h4-20H,1-3H2/t4-,5-,6-,7-,8-,9+,10-,11-,12-/m1/s1" RZM InChIKey InChI 1.03 AZDBETUGBOOBRU-BBFNFCGLSA-N RZM SMILES_CANONICAL CACTVS 3.385 "OC[C@H]1N[C@H](CO)[C@@H](O[C@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O)[C@@H]1O" RZM SMILES CACTVS 3.385 "OC[CH]1N[CH](CO)[CH](O[CH]2O[CH](CO)[CH](O)[CH](O)[CH]2O)[CH]1O" RZM SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "C([C@@H]1[C@H]([C@@H]([C@H](N1)CO)O[C@@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O)O)O" RZM SMILES "OpenEye OEToolkits" 1.9.2 "C(C1C(C(C(N1)CO)OC2C(C(C(C(O2)CO)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 RZM "SYSTEMATIC NAME" ACDLabs 12.01 "(2R,3R,4R,5R)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-3-yl alpha-D-glucopyranoside" RZM "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 ;(2S,3R,4S,5S,6R)-2-[(2R,3R,4R,5R)-2,5-bis(hydroxymethyl)-4-oxidanyl-pyrrolidin-3-yl]oxy-6-(hydroxymethyl)oxane-3,4,5-tr iol ; # _pdbx_chem_comp_related.comp_id RZM _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 RZM C1 GLC C1 "Carbohydrate core" 2 RZM C2 GLC C2 "Carbohydrate core" 3 RZM C3 GLC C3 "Carbohydrate core" 4 RZM C4 GLC C4 "Carbohydrate core" 5 RZM C5 GLC C5 "Carbohydrate core" 6 RZM C6 GLC C6 "Carbohydrate core" 7 RZM O2 GLC O2 "Carbohydrate core" 8 RZM O3 GLC O3 "Carbohydrate core" 9 RZM O4 GLC O4 "Carbohydrate core" 10 RZM O1 GLC O1 "Carbohydrate core" 11 RZM O5 GLC O5 "Carbohydrate core" 12 RZM O6 GLC O6 "Carbohydrate core" 13 RZM H1 GLC H1 "Carbohydrate core" 14 RZM H2 GLC H2 "Carbohydrate core" 15 RZM HO2 GLC HO2 "Carbohydrate core" 16 RZM H3 GLC H3 "Carbohydrate core" 17 RZM HO3 GLC HO3 "Carbohydrate core" 18 RZM H4 GLC H4 "Carbohydrate core" 19 RZM HO4 GLC HO4 "Carbohydrate core" 20 RZM H5 GLC H5 "Carbohydrate core" 21 RZM H61 GLC H61 "Carbohydrate core" 22 RZM H62 GLC H62 "Carbohydrate core" 23 RZM HO6 GLC HO6 "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 RZM "CARBOHYDRATE ISOMER" D PDB ? RZM "CARBOHYDRATE RING" pyranose PDB ? RZM "CARBOHYDRATE ANOMER" alpha PDB ? RZM "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 RZM "Create component" 2014-07-24 RCSB RZM "Other modification" 2014-08-05 RCSB RZM "Modify descriptor" 2014-09-05 RCSB RZM "Initial release" 2015-08-12 RCSB RZM "Other modification" 2020-07-03 RCSB RZM "Modify parent residue" 2020-07-17 RCSB RZM "Modify synonyms" 2020-07-17 RCSB RZM "Modify linking type" 2020-07-17 RCSB RZM "Modify atom id" 2020-07-17 RCSB RZM "Modify component atom id" 2020-07-17 RCSB RZM "Modify leaving atom flag" 2020-07-17 RCSB ##