data_9KJ # _chem_comp.id 9KJ _chem_comp.name "{[(2R,3R,4R,5R)-3-(alpha-D-glucopyranosyloxy)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-1-yl]methyl}phosphonic acid" _chem_comp.type D-saccharide _chem_comp.pdbx_type ATOMS _chem_comp.formula "C13 H26 N O12 P" _chem_comp.mon_nstd_parent_comp_id GLC _chem_comp.pdbx_synonyms ;{[(2R,3R,4R,5R)-3-(alpha-D-glucosyloxy)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-1-yl]methyl}phosphonic acid; {[(2R,3R,4R,5R)-3-(D-glucosyloxy)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-1-yl]methyl}phosphonic acid; {[(2R,3R,4R,5R)-3-(glucosyloxy)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-1-yl]methyl}phosphonic acid ; _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-05-17 _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 419.319 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 9KJ _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 5VT4 _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 9KJ "{[(2R,3R,4R,5R)-3-(alpha-D-glucosyloxy)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-1-yl]methyl}phosphonic acid" PDB ? 2 9KJ "{[(2R,3R,4R,5R)-3-(D-glucosyloxy)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-1-yl]methyl}phosphonic acid" PDB ? 3 9KJ "{[(2R,3R,4R,5R)-3-(glucosyloxy)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-1-yl]methyl}phosphonic acid" 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 9KJ C20 C20 C 0 1 N N N 140.158 145.642 -342.805 0.508 1.741 -0.219 C20 9KJ 1 9KJ C2 C22 C 0 1 N N R 136.887 148.539 -346.317 -3.746 -1.533 -0.083 C2 9KJ 2 9KJ C3 C24 C 0 1 N N S 135.876 147.410 -346.589 -4.139 -0.472 -1.115 C3 9KJ 3 9KJ C4 C26 C 0 1 N N S 136.579 146.156 -347.133 -4.467 0.835 -0.387 C4 9KJ 4 9KJ O4 O27 O 0 1 N N N 135.650 145.051 -347.198 -4.765 1.853 -1.345 O4 9KJ 5 9KJ O6 O01 O 0 1 N N N 139.797 145.016 -347.184 -2.438 2.994 1.921 O6 9KJ 6 9KJ C6 C02 C 0 1 N N N 138.492 144.560 -346.838 -3.600 2.533 1.229 C6 9KJ 7 9KJ C5 C03 C 0 1 N N R 137.780 145.783 -346.246 -3.259 1.260 0.452 C5 9KJ 8 9KJ O5 O04 O 0 1 N N N 138.727 146.854 -346.098 -2.928 0.216 1.369 O5 9KJ 9 9KJ C1 C05 C 0 1 N N S 138.164 148.076 -345.608 -2.566 -1.017 0.744 C1 9KJ 10 9KJ O1 O06 O 0 1 N N N 137.858 147.931 -344.225 -1.441 -0.806 -0.111 O1 9KJ 11 9KJ C07 C07 C 0 1 N N R 139.095 147.805 -343.525 -0.222 -0.541 0.587 C07 9KJ 12 9KJ C08 C08 C 0 1 N N R 139.399 149.028 -342.627 0.560 -1.853 0.859 C08 9KJ 13 9KJ O09 O09 O 0 1 N N N 140.244 149.972 -343.272 0.141 -2.445 2.090 O09 9KJ 14 9KJ C10 C10 C 0 1 N N R 140.162 148.294 -341.528 2.023 -1.373 0.954 C10 9KJ 15 9KJ C11 C11 C 0 1 N N N 140.514 149.238 -340.373 2.951 -2.395 0.295 C11 9KJ 16 9KJ O12 O12 O 0 1 N N N 141.814 148.862 -339.915 2.471 -2.697 -1.017 O12 9KJ 17 9KJ N13 N13 N 0 1 N N N 139.189 147.250 -341.197 2.107 -0.085 0.240 N13 9KJ 18 9KJ C14 C14 C 0 1 N N N 137.882 147.840 -340.855 3.117 -0.140 -0.826 C14 9KJ 19 9KJ P15 P15 P 0 1 N N N 137.670 147.996 -338.985 4.604 0.775 -0.302 P15 9KJ 20 9KJ O16 O16 O 0 1 N N N 137.410 149.440 -338.561 5.300 0.007 0.930 O16 9KJ 21 9KJ O17 O17 O 0 1 N N N 138.928 147.506 -338.365 5.639 0.866 -1.532 O17 9KJ 22 9KJ O18 O18 O 0 1 N N N 136.524 147.127 -338.567 4.220 2.140 0.122 O18 9KJ 23 9KJ C19 C19 C 0 1 N N R 139.024 146.634 -342.520 0.773 0.236 -0.310 C19 9KJ 24 9KJ O21 O21 O 0 1 N N N 140.275 144.821 -341.656 1.357 2.430 -1.140 O21 9KJ 25 9KJ O2 O23 O 0 1 N N N 136.272 149.484 -345.427 -3.368 -2.736 -0.756 O2 9KJ 26 9KJ O3 O25 O 0 1 N N N 134.934 147.858 -347.568 -5.285 -0.915 -1.845 O3 9KJ 27 9KJ H1A H1 H 0 1 N N N 139.914 145.030 -343.686 -0.534 1.942 -0.466 H1A 9KJ 28 9KJ H2A H2 H 0 1 N N N 141.099 146.182 -342.983 0.715 2.086 0.794 H2A 9KJ 29 9KJ H2 H3 H 0 1 N N N 137.155 149.021 -347.269 -4.592 -1.734 0.574 H2 9KJ 30 9KJ H3 H4 H 0 1 N N N 135.363 147.155 -345.650 -3.310 -0.308 -1.804 H3 9KJ 31 9KJ H4 H5 H 0 1 N N N 136.953 146.381 -348.143 -5.328 0.684 0.264 H4 9KJ 32 9KJ HO4 H6 H 0 1 N Y N 136.095 144.282 -347.535 -5.518 1.648 -1.916 HO4 9KJ 33 9KJ HO6 H7 H 0 1 N Y N 140.294 144.299 -347.560 -2.581 3.800 2.436 HO6 9KJ 34 9KJ H61 H8 H 0 1 N N N 137.960 144.199 -347.731 -4.390 2.319 1.949 H61 9KJ 35 9KJ H62 H9 H 0 1 N N N 138.551 143.751 -346.095 -3.939 3.302 0.535 H62 9KJ 36 9KJ H5 H10 H 0 1 N N N 137.393 145.503 -345.255 -2.410 1.451 -0.204 H5 9KJ 37 9KJ H1 H11 H 0 1 N N N 138.910 148.876 -345.722 -2.310 -1.751 1.508 H1 9KJ 38 9KJ H12 H12 H 0 1 N N N 139.932 147.643 -344.220 -0.415 -0.003 1.515 H12 9KJ 39 9KJ H13 H13 H 0 1 N N N 138.471 149.475 -342.241 0.437 -2.553 0.032 H13 9KJ 40 9KJ H14 H14 H 0 1 N N N 140.405 150.704 -342.688 0.600 -3.269 2.306 H14 9KJ 41 9KJ H15 H15 H 0 1 N N N 141.081 147.853 -341.941 2.301 -1.236 1.999 H15 9KJ 42 9KJ H16 H16 H 0 1 N N N 140.523 150.280 -340.725 3.957 -1.983 0.228 H16 9KJ 43 9KJ H17 H17 H 0 1 N N N 139.781 149.132 -339.560 2.970 -3.306 0.893 H17 9KJ 44 9KJ H18 H18 H 0 1 N N N 142.072 149.426 -339.195 3.012 -3.340 -1.495 H18 9KJ 45 9KJ H20 H20 H 0 1 N N N 137.810 148.839 -341.309 3.380 -1.179 -1.024 H20 9KJ 46 9KJ H21 H21 H 0 1 N N N 137.083 147.198 -341.254 2.713 0.312 -1.732 H21 9KJ 47 9KJ H22 H22 H 0 1 N N N 136.572 149.494 -338.117 5.513 -0.919 0.747 H22 9KJ 48 9KJ H23 H23 H 0 1 N N N 138.742 146.742 -337.832 6.456 1.341 -1.324 H23 9KJ 49 9KJ H24 H24 H 0 1 N N N 138.050 146.129 -342.601 0.695 -0.100 -1.343 H24 9KJ 50 9KJ H25 H25 H 0 1 N N N 140.970 144.187 -341.789 1.243 3.390 -1.136 H25 9KJ 51 9KJ HO2 H26 H 0 1 N Y N 136.880 150.191 -345.245 -3.102 -3.452 -0.162 HO2 9KJ 52 9KJ HO3 H27 H 0 1 N Y N 134.489 148.634 -347.248 -5.149 -1.743 -2.326 HO3 9KJ 53 # # 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 9KJ O3 C3 SING N N 1 9KJ O4 C4 SING N N 2 9KJ O6 C6 SING N N 3 9KJ C4 C3 SING N N 4 9KJ C4 C5 SING N N 5 9KJ C6 C5 SING N N 6 9KJ C3 C2 SING N N 7 9KJ C2 C1 SING N N 8 9KJ C2 O2 SING N N 9 9KJ C5 O5 SING N N 10 9KJ O5 C1 SING N N 11 9KJ C1 O1 SING N N 12 9KJ O1 C07 SING N N 13 9KJ C07 C08 SING N N 14 9KJ C07 C19 SING N N 15 9KJ O09 C08 SING N N 16 9KJ C20 C19 SING N N 17 9KJ C20 O21 SING N N 18 9KJ C08 C10 SING N N 19 9KJ C19 N13 SING N N 20 9KJ C10 N13 SING N N 21 9KJ C10 C11 SING N N 22 9KJ N13 C14 SING N N 23 9KJ C14 P15 SING N N 24 9KJ C11 O12 SING N N 25 9KJ P15 O18 DOUB N N 26 9KJ P15 O16 SING N N 27 9KJ P15 O17 SING N N 28 9KJ C20 H1A SING N N 29 9KJ C20 H2A SING N N 30 9KJ C2 H2 SING N N 31 9KJ C3 H3 SING N N 32 9KJ C4 H4 SING N N 33 9KJ O4 HO4 SING N N 34 9KJ O6 HO6 SING N N 35 9KJ C6 H61 SING N N 36 9KJ C6 H62 SING N N 37 9KJ C5 H5 SING N N 38 9KJ C1 H1 SING N N 39 9KJ C07 H12 SING N N 40 9KJ C08 H13 SING N N 41 9KJ O09 H14 SING N N 42 9KJ C10 H15 SING N N 43 9KJ C11 H16 SING N N 44 9KJ C11 H17 SING N N 45 9KJ O12 H18 SING N N 46 9KJ C14 H20 SING N N 47 9KJ C14 H21 SING N N 48 9KJ O16 H22 SING N N 49 9KJ O17 H23 SING N N 50 9KJ C19 H24 SING N N 51 9KJ O21 H25 SING N N 52 9KJ O2 HO2 SING N N 53 9KJ O3 HO3 SING N N 54 # # 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 9KJ SMILES ACDLabs 12.01 "C(C2C(OC1C(O)C(C(C(CO)O1)O)O)C(C(N2CP(=O)(O)O)CO)O)O" 9KJ InChI InChI 1.03 "InChI=1S/C13H26NO12P/c15-1-5-8(18)12(6(2-16)14(5)4-27(22,23)24)26-13-11(21)10(20)9(19)7(3-17)25-13/h5-13,15-21H,1-4H2,(H2,22,23,24)/t5-,6-,7-,8-,9-,10+,11-,12-,13-/m1/s1" 9KJ InChIKey InChI 1.03 QVTCDBMCRXGRKE-DFIZWEOJSA-N 9KJ SMILES_CANONICAL CACTVS 3.385 "OC[C@H]1O[C@H](O[C@H]2[C@H](O)[C@@H](CO)N(C[P](O)(O)=O)[C@@H]2CO)[C@H](O)[C@@H](O)[C@@H]1O" 9KJ SMILES CACTVS 3.385 "OC[CH]1O[CH](O[CH]2[CH](O)[CH](CO)N(C[P](O)(O)=O)[CH]2CO)[CH](O)[CH](O)[CH]1O" 9KJ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "C([C@@H]1[C@H]([C@@H]([C@H](N1CP(=O)(O)O)CO)O[C@@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O)O)O" 9KJ SMILES "OpenEye OEToolkits" 2.0.6 "C(C1C(C(C(N1CP(=O)(O)O)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 9KJ "SYSTEMATIC NAME" ACDLabs 12.01 "{[(2R,3R,4R,5R)-3-(alpha-D-glucopyranosyloxy)-4-hydroxy-2,5-bis(hydroxymethyl)pyrrolidin-1-yl]methyl}phosphonic acid" 9KJ "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 ;[(2~{R},3~{R},4~{R},5~{R})-2,5-bis(hydroxymethyl)-3-[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxida nyl)oxan-2-yl]oxy-4-oxidanyl-pyrrolidin-1-yl]methylphosphonic acid ; # _pdbx_chem_comp_related.comp_id 9KJ _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 9KJ C6 GLC C6 "Carbohydrate core" 2 9KJ C5 GLC C5 "Carbohydrate core" 3 9KJ C1 GLC C1 "Carbohydrate core" 4 9KJ C2 GLC C2 "Carbohydrate core" 5 9KJ C3 GLC C3 "Carbohydrate core" 6 9KJ C4 GLC C4 "Carbohydrate core" 7 9KJ O6 GLC O6 "Carbohydrate core" 8 9KJ O5 GLC O5 "Carbohydrate core" 9 9KJ O1 GLC O1 "Carbohydrate core" 10 9KJ O2 GLC O2 "Carbohydrate core" 11 9KJ O3 GLC O3 "Carbohydrate core" 12 9KJ O4 GLC O4 "Carbohydrate core" 13 9KJ H5 GLC H5 "Carbohydrate core" 14 9KJ H1 GLC H1 "Carbohydrate core" 15 9KJ HO2 GLC HO2 "Carbohydrate core" 16 9KJ HO3 GLC HO3 "Carbohydrate core" 17 9KJ H2 GLC H2 "Carbohydrate core" 18 9KJ H3 GLC H3 "Carbohydrate core" 19 9KJ H4 GLC H4 "Carbohydrate core" 20 9KJ HO4 GLC HO4 "Carbohydrate core" 21 9KJ HO6 GLC HO6 "Carbohydrate core" 22 9KJ H61 GLC H61 "Carbohydrate core" 23 9KJ H62 GLC H62 "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 9KJ "CARBOHYDRATE ISOMER" D PDB ? 9KJ "CARBOHYDRATE RING" pyranose PDB ? 9KJ "CARBOHYDRATE ANOMER" alpha PDB ? 9KJ "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 9KJ "Create component" 2017-05-17 RCSB 9KJ "Initial release" 2017-06-07 RCSB 9KJ "Other modification" 2020-07-03 RCSB 9KJ "Modify parent residue" 2020-07-17 RCSB 9KJ "Modify synonyms" 2020-07-17 RCSB 9KJ "Modify internal type" 2020-07-17 RCSB 9KJ "Modify linking type" 2020-07-17 RCSB 9KJ "Modify atom id" 2020-07-17 RCSB 9KJ "Modify component atom id" 2020-07-17 RCSB 9KJ "Modify leaving atom flag" 2020-07-17 RCSB ##