data_PRDCC_900087 # _chem_comp.id PRD_900087 _chem_comp.name "(1S)-1,5-anhydro-4-O-alpha-D-glucopyranosyl-1-(phosphonomethyl)-D-glucitol" _chem_comp.type saccharide _chem_comp.formula "C13 H25 O13 P" _chem_comp.pdbx_release_status REF_ONLY _chem_comp.formula_weight 420.304 _chem_comp.pdbx_type ? _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge ? _chem_comp.pdbx_initial_date ? _chem_comp.pdbx_modified_date ? _chem_comp.pdbx_ambiguous_flag ? _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.one_letter_code ? _chem_comp.three_letter_code ? _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag ? _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag ? _chem_comp.pdbx_model_coordinates_db_code ? _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_pcm ? _chem_comp.pdbx_processing_site ? # 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_comp_id _chem_comp_atom.pdbx_residue_numbering _chem_comp_atom.pdbx_component_atom_id _chem_comp_atom.pdbx_polymer_type _chem_comp_atom.pdbx_ref_id _chem_comp_atom.pdbx_component_id _chem_comp_atom.pdbx_ordinal _chem_comp_atom.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag PRD_900087 "C1'" C10 C 0 1 N N S 24.429 -30.556 282.115 2.892 0.844 -0.820 GPM 1 C1 polymer 1 1 1 ? ? ? PRD_900087 "C2'" C9 C 0 1 N N R 23.635 -29.909 281.014 2.157 2.171 -1.032 GPM 1 C2 polymer 1 1 2 ? ? ? PRD_900087 "C3'" C8 C 0 1 N N R 23.613 -30.805 279.889 0.824 2.133 -0.278 GPM 1 C3 polymer 1 1 3 ? ? ? PRD_900087 "C4'" C7 C 0 1 N N S 24.987 -31.029 279.368 0.008 0.933 -0.766 GPM 1 C4 polymer 1 1 4 ? ? ? PRD_900087 "C5'" C12 C 0 1 N N R 26.027 -31.326 280.438 0.826 -0.346 -0.565 GPM 1 C5 polymer 1 1 5 ? ? ? PRD_900087 "C6'" C13 C 0 1 N N N 27.439 -30.900 280.055 0.041 -1.544 -1.105 GPM 1 C6 polymer 1 1 6 ? ? ? PRD_900087 C C11 C 0 1 N N N 23.865 -31.903 282.587 3.204 0.666 0.667 GPM 1 C7 polymer 1 1 7 ? ? ? PRD_900087 "O2'" O11 O 0 1 N N N 22.320 -29.594 281.510 2.958 3.245 -0.533 GPM 1 O2 polymer 1 1 8 ? ? ? PRD_900087 "O3'" O12 O 0 1 N N N 22.826 -30.163 278.913 0.099 3.339 -0.530 GPM 1 O3 polymer 1 1 9 ? ? ? PRD_900087 "O4'" O5 O 0 1 N N N 25.053 -32.203 278.548 -1.207 0.845 -0.019 GPM 1 O4 polymer 1 1 10 ? ? ? PRD_900087 "O5'" O9 O 0 1 N N N 25.823 -30.709 281.703 2.066 -0.233 -1.266 GPM 1 O5 polymer 1 1 11 ? ? ? PRD_900087 "O6'" O10 O 0 1 N N N 27.603 -29.535 279.790 0.740 -2.750 -0.794 GPM 1 O6 polymer 1 1 12 ? ? ? PRD_900087 P P1 P 0 1 N N N 24.755 -32.728 283.961 4.207 -0.839 0.901 GPM 1 P polymer 1 1 13 ? ? ? PRD_900087 OP2 O6 O 0 1 N N N 23.971 -33.937 284.385 5.415 -0.763 0.050 GPM 1 O1P polymer 1 1 14 ? ? ? PRD_900087 OP1 O8 O 0 1 N N N 26.207 -33.088 283.569 3.340 -2.131 0.490 GPM 1 O2P polymer 1 1 15 ? ? ? PRD_900087 OP3 O7 O 0 1 N N N 24.809 -31.702 285.142 4.645 -0.956 2.446 GPM 1 O3P polymer 1 1 16 ? ? ? PRD_900087 C1 C3 C 0 1 N N R 24.728 -31.993 277.182 -2.388 0.924 -0.819 GLC 2 C1 polymer 1 1 17 ? ? ? PRD_900087 C2 C2 C 0 1 N N R 24.398 -33.354 276.597 -3.529 1.519 0.012 GLC 2 C2 polymer 1 1 18 ? ? ? PRD_900087 C3 C1 C 0 1 N N S 25.592 -34.196 276.434 -3.828 0.590 1.192 GLC 2 C3 polymer 1 1 19 ? ? ? PRD_900087 C4 C5 C 0 1 N N S 26.638 -33.490 275.657 -4.165 -0.806 0.657 GLC 2 C4 polymer 1 1 20 ? ? ? PRD_900087 C5 C4 C 0 1 N N R 26.988 -32.190 276.353 -3.000 -1.310 -0.199 GLC 2 C5 polymer 1 1 21 ? ? ? PRD_900087 C6 C6 C 0 1 N N N 28.107 -31.366 275.725 -3.353 -2.678 -0.787 GLC 2 C6 polymer 1 1 22 ? ? ? PRD_900087 O2 O13 O 0 1 N N N 23.468 -34.007 277.460 -3.143 2.804 0.502 GLC 2 O2 polymer 1 1 23 ? ? ? PRD_900087 O3 O1 O 0 1 N N N 25.241 -35.398 275.776 -4.940 1.099 1.931 GLC 2 O3 polymer 1 1 24 ? ? ? PRD_900087 O4 O3 O 0 1 N N N 27.763 -34.319 275.461 -4.375 -1.699 1.752 GLC 2 O4 polymer 1 1 25 ? ? ? PRD_900087 O5 O2 O 0 1 N N N 25.804 -31.344 276.448 -2.754 -0.385 -1.260 GLC 2 O5 polymer 1 1 26 ? ? ? PRD_900087 O6 O4 O 0 1 N N N 27.755 -30.801 274.482 -2.234 -3.187 -1.516 GLC 2 O6 polymer 1 1 27 ? ? ? PRD_900087 H14 H14 H 0 1 N N N 24.405 -29.877 282.980 3.822 0.849 -1.388 GPM 1 H1 polymer 1 1 28 ? ? ? PRD_900087 H13 H13 H 0 1 N N N 24.143 -28.978 280.724 1.971 2.319 -2.095 GPM 1 H2 polymer 1 1 29 ? ? ? PRD_900087 H12 H12 H 0 1 N N N 23.166 -31.768 280.177 1.011 2.037 0.791 GPM 1 H3 polymer 1 1 30 ? ? ? PRD_900087 H11 H11 H 0 1 N N N 25.308 -30.147 278.794 -0.223 1.054 -1.825 GPM 1 H4 polymer 1 1 31 ? ? ? PRD_900087 H19 H19 H 0 1 N N N 26.044 -32.416 280.581 1.021 -0.489 0.498 GPM 1 H5 polymer 1 1 32 ? ? ? PRD_900087 H20 H20 H 0 1 N N N 28.111 -31.168 280.884 -0.947 -1.567 -0.646 GPM 1 H61 polymer 1 1 33 ? ? ? PRD_900087 H21 H21 H 0 1 N N N 27.729 -31.458 279.153 -0.062 -1.452 -2.186 GPM 1 H62 polymer 1 1 34 ? ? ? PRD_900087 H15 H15 H 0 1 N N N 23.871 -32.588 281.726 2.272 0.572 1.225 GPM 1 H71 polymer 1 1 35 ? ? ? PRD_900087 H16 H16 H 0 1 N N N 22.828 -31.735 282.914 3.758 1.532 1.029 GPM 1 H72 polymer 1 1 36 ? ? ? PRD_900087 H23 H23 H 0 1 N N N 22.393 -29.002 282.249 2.551 4.116 -0.630 GPM 1 HO2 polymer 1 1 37 ? ? ? PRD_900087 H24 H24 H 0 1 N N N 21.950 -30.024 279.253 0.558 4.141 -0.245 GPM 1 HO3 polymer 1 1 38 ? ? ? PRD_900087 H22 H22 H 0 1 N N N 28.509 -29.363 279.561 0.256 -3.556 -1.023 GPM 1 HO6 polymer 1 1 39 ? ? ? PRD_900087 H18 H18 H 0 1 N N N 26.340 -34.023 283.670 2.531 -2.244 1.008 GPM 1 HOP2 polymer 1 1 40 ? ? ? PRD_900087 H17 H17 H 0 1 N N N 24.335 -32.051 285.888 5.183 -1.735 2.644 GPM 1 HOP3 polymer 1 1 41 ? ? ? PRD_900087 H4 H4 H 0 1 N N N 23.826 -31.367 277.116 -2.200 1.560 -1.684 GLC 2 H1 polymer 1 1 42 ? ? ? PRD_900087 H3 H3 H 0 1 N N N 23.935 -33.201 275.611 -4.419 1.618 -0.609 GLC 2 H2 polymer 1 1 43 ? ? ? PRD_900087 H2 H2 H 0 1 N N N 25.996 -34.430 277.430 -2.955 0.530 1.841 GLC 2 H3 polymer 1 1 44 ? ? ? PRD_900087 H6 H6 H 0 1 N N N 26.213 -33.234 274.676 -5.068 -0.754 0.049 GLC 2 H4 polymer 1 1 45 ? ? ? PRD_900087 H5 H5 H 0 1 N N N 27.306 -32.443 277.375 -2.106 -1.400 0.419 GLC 2 H5 polymer 1 1 46 ? ? ? PRD_900087 H8 H8 H 0 1 N N N 28.371 -30.552 276.416 -3.604 -3.366 0.020 GLC 2 H61 polymer 1 1 47 ? ? ? PRD_900087 H9 H9 H 0 1 N N N 28.980 -32.019 275.577 -4.207 -2.576 -1.456 GLC 2 H62 polymer 1 1 48 ? ? ? PRD_900087 H25 H25 H 0 1 N N N 22.697 -33.463 277.565 -2.938 3.445 -0.193 GLC 2 HO2 polymer 1 1 49 ? ? ? PRD_900087 H1 H1 H 0 1 N N N 24.571 -35.849 276.276 -4.796 1.981 2.300 GLC 2 HO3 polymer 1 1 50 ? ? ? PRD_900087 H7 H7 H 0 1 N N N 28.420 -33.849 274.962 -5.097 -1.438 2.339 GLC 2 HO4 polymer 1 1 51 ? ? ? PRD_900087 H10 H10 H 0 1 N N N 28.488 -30.302 274.142 -2.412 -4.015 -1.981 GLC 2 HO6 polymer 1 1 52 ? ? ? # 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 PRD_900087 P OP2 DOUB N N 1 PRD_900087 P C SING N N 2 PRD_900087 P OP1 SING N N 3 PRD_900087 P OP3 SING N N 4 PRD_900087 O3 C3 SING N N 5 PRD_900087 C3 C4 SING N N 6 PRD_900087 C3 C2 SING N N 7 PRD_900087 C2 O2 SING N N 8 PRD_900087 C2 C1 SING N N 9 PRD_900087 C1 O5 SING N N 10 PRD_900087 C1 "O4'" SING N N 11 PRD_900087 O5 C5 SING N N 12 PRD_900087 C5 C4 SING N N 13 PRD_900087 C5 C6 SING N N 14 PRD_900087 C4 O4 SING N N 15 PRD_900087 C6 O6 SING N N 16 PRD_900087 "O4'" "C4'" SING N N 17 PRD_900087 "C4'" "C5'" SING N N 18 PRD_900087 "C4'" "C3'" SING N N 19 PRD_900087 "C3'" "O3'" SING N N 20 PRD_900087 "C3'" "C2'" SING N N 21 PRD_900087 "C2'" "O2'" SING N N 22 PRD_900087 "C2'" "C1'" SING N N 23 PRD_900087 "C1'" "O5'" SING N N 24 PRD_900087 "C1'" C SING N N 25 PRD_900087 "O5'" "C5'" SING N N 26 PRD_900087 "C5'" "C6'" SING N N 27 PRD_900087 "C6'" "O6'" SING N N 28 PRD_900087 O3 H1 SING N N 29 PRD_900087 C3 H2 SING N N 30 PRD_900087 C2 H3 SING N N 31 PRD_900087 C1 H4 SING N N 32 PRD_900087 C5 H5 SING N N 33 PRD_900087 C4 H6 SING N N 34 PRD_900087 O4 H7 SING N N 35 PRD_900087 C6 H8 SING N N 36 PRD_900087 C6 H9 SING N N 37 PRD_900087 O6 H10 SING N N 38 PRD_900087 "C4'" H11 SING N N 39 PRD_900087 "C3'" H12 SING N N 40 PRD_900087 "C2'" H13 SING N N 41 PRD_900087 "C1'" H14 SING N N 42 PRD_900087 C H15 SING N N 43 PRD_900087 C H16 SING N N 44 PRD_900087 OP3 H17 SING N N 45 PRD_900087 OP1 H18 SING N N 46 PRD_900087 "C5'" H19 SING N N 47 PRD_900087 "C6'" H20 SING N N 48 PRD_900087 "C6'" H21 SING N N 49 PRD_900087 "O6'" H22 SING N N 50 PRD_900087 "O2'" H23 SING N N 51 PRD_900087 "O3'" H24 SING N N 52 PRD_900087 O2 H25 SING N N 53 # 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 PRD_900087 InChI InChI 1.06 "InChI=1S/C13H25O13P/c14-1-4-7(16)9(18)11(20)13(25-4)26-12-5(2-15)24-6(3-27(21,22)23)8(17)10(12)19/h4-20H,1-3H2,(H2,21,22,23)/t4-,5-,6-,7-,8+,9+,10-,11-,12-,13-/m1/s1" PRD_900087 InChIKey InChI 1.06 LIGBAXRYIYXSON-NVYKSAHZSA-N PRD_900087 SMILES_CANONICAL CACTVS 3.385 "OC[C@H]1O[C@H](O[C@H]2[C@H](O)[C@@H](O)[C@@H](C[P](O)(O)=O)O[C@@H]2CO)[C@H](O)[C@@H](O)[C@@H]1O" PRD_900087 SMILES CACTVS 3.385 "OC[CH]1O[CH](O[CH]2[CH](O)[CH](O)[CH](C[P](O)(O)=O)O[CH]2CO)[CH](O)[CH](O)[CH]1O" PRD_900087 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O[C@@H]2[C@H](O[C@@H]([C@@H]([C@H]2O)O)CP(=O)(O)O)CO)O)O)O)O" PRD_900087 SMILES "OpenEye OEToolkits" 2.0.7 "C(C1C(C(C(C(O1)OC2C(OC(C(C2O)O)CP(=O)(O)O)CO)O)O)O)O" # _pdbx_chem_comp_identifier.comp_id PRD_900087 _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier ;[(2~{S},3~{R},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-5-[(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxid anyl)oxan-2-yl]oxy-3,4-bis(oxidanyl)oxan-2-yl]methylphosphonic acid ; #