data_660 # _chem_comp.id 660 _chem_comp.name "[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-[[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]methyl]phosphinic acid" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C16 H26 N2 O16 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "UDP-glucose phosphonate" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2016-02-02 _chem_comp.pdbx_modified_date 2021-03-01 _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 564.329 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 660 _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 5EIY _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # # 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 660 C1 C1 C 0 1 N N R 3.713 8.018 102.643 -5.032 0.124 -0.800 C1 660 1 660 C2 C2 C 0 1 N N R 4.158 9.183 101.840 -5.762 1.313 -0.124 C2 660 2 660 C3 C3 C 0 1 N N S 3.039 9.450 100.932 -4.784 2.484 -0.386 C3 660 3 660 C4 C4 C 0 1 N N R 2.317 8.158 100.759 -3.435 1.795 -0.665 C4 660 4 660 C5 C5 C 0 1 N N N 2.423 7.687 99.343 -2.387 2.276 0.341 C5 660 5 660 O6 O1 O 0 1 N N N 2.937 7.188 101.694 -3.638 0.378 -0.522 O6 660 6 660 O7 O2 O 0 1 N N N 2.158 10.415 101.543 -5.204 3.241 -1.523 O7 660 7 660 O8 O3 O 0 1 N N N 3.578 6.917 99.163 -1.114 1.723 0.004 O8 660 8 660 P9 P1 P 0 1 N N N 4.648 7.331 97.975 0.223 2.018 0.852 P9 660 9 660 O10 O4 O 0 1 N N N 5.955 6.734 98.239 0.069 1.399 2.330 O10 660 10 660 O11 O5 O 0 1 N N N 4.970 8.755 98.017 0.433 3.480 0.949 O11 660 11 660 O12 O6 O 0 1 N N N 4.114 6.889 96.476 1.485 1.343 0.116 O12 660 12 660 N13 N1 N 0 1 N N N 4.814 7.302 103.187 -5.454 -1.146 -0.204 N13 660 13 660 N15 N2 N 0 1 N N N 5.964 6.353 105.189 -6.484 -3.236 -0.441 N15 660 14 660 C17 C6 C 0 1 N N N 6.933 6.111 102.845 -5.595 -2.560 1.669 C17 660 15 660 C18 C7 C 0 1 N N N 5.898 6.790 102.309 -5.206 -1.389 1.120 C18 660 16 660 C19 C8 C 0 1 N N N 4.875 7.069 104.622 -6.085 -2.061 -0.962 C19 660 17 660 O19 O7 O 0 1 N N N 4.009 7.476 105.323 -6.299 -1.822 -2.135 O19 660 18 660 C20 C9 C 0 1 N N N 6.998 5.866 104.350 -6.254 -3.515 0.858 C20 660 19 660 O20 O8 O 0 1 N N N 7.910 5.268 104.821 -6.611 -4.580 1.330 O20 660 20 660 O21 O9 O 0 1 N N N 4.377 10.322 102.694 -7.026 1.554 -0.746 O21 660 21 660 P22 P2 P 0 1 N N N 2.785 7.504 95.716 3.081 1.509 0.254 P22 660 22 660 O23 O10 O 0 1 N N N 2.717 8.953 95.857 3.491 3.033 -0.063 O23 660 23 660 O24 O11 O 0 1 N N N 2.897 7.378 94.265 3.496 1.163 1.632 O24 660 24 660 O36 O12 O 0 1 N N N 0.909 4.669 95.093 5.745 -0.054 0.581 O36 660 25 660 C37 C10 C 0 1 N N R 0.800 3.905 96.264 5.327 -1.404 0.790 C37 660 26 660 C38 C11 C 0 1 N N S -0.655 3.837 96.716 6.028 -2.316 -0.221 C38 660 27 660 C39 C12 C 0 1 N N S -1.227 5.248 96.842 5.703 -1.837 -1.639 C39 660 28 660 C40 C13 C 0 1 N N R -1.008 6.014 95.539 6.131 -0.373 -1.783 C40 660 29 660 C41 C14 C 0 1 N N S 0.480 5.996 95.216 5.425 0.463 -0.712 C41 660 30 660 O42 O13 O 0 1 N N N -0.719 3.194 97.961 5.568 -3.658 -0.052 O42 660 31 660 O43 O14 O 0 1 N N N -2.597 5.174 97.108 6.413 -2.638 -2.588 O43 660 32 660 O44 O15 O 0 1 N N N -1.433 7.338 95.692 5.767 0.105 -3.079 O44 660 33 660 C45 C15 C 0 1 N N N 1.239 6.683 96.346 3.912 0.398 -0.928 C45 660 34 660 C46 C16 C 0 1 N N N 1.297 2.485 95.997 5.694 -1.839 2.210 C46 660 35 660 O47 O16 O 0 1 N N N 2.696 2.470 95.973 4.951 -1.063 3.152 O47 660 36 660 H1 H1 H 0 1 N N N 3.050 8.365 103.450 -5.215 0.122 -1.875 H1 660 37 660 H2 H2 H 0 1 N N N 5.067 8.934 101.273 -5.883 1.138 0.945 H2 660 38 660 H3 H3 H 0 1 N N N 3.407 9.813 99.961 -4.713 3.125 0.492 H3 660 39 660 H4 H4 H 0 1 N N N 1.257 8.294 101.020 -3.107 2.019 -1.680 H4 660 40 660 H5 H5 H 0 1 N N N 2.463 8.559 98.674 -2.329 3.364 0.313 H5 660 41 660 H6 H6 H 0 1 N N N 1.541 7.077 99.098 -2.670 1.953 1.343 H6 660 42 660 H7 H7 H 0 1 N N N 2.618 11.239 101.654 -6.075 3.649 -1.425 H7 660 43 660 H8 H8 H 0 1 N N N 6.600 7.422 98.355 -0.072 0.442 2.343 H8 660 44 660 H9 H9 H 0 1 N N N 6.001 6.193 106.175 -6.939 -3.884 -1.001 H9 660 45 660 H10 H10 H 0 1 N N N 7.720 5.739 102.206 -5.402 -2.766 2.711 H10 660 46 660 H11 H11 H 0 1 N N N 5.857 6.961 101.243 -4.702 -0.648 1.722 H11 660 47 660 H12 H12 H 0 1 N N N 5.103 10.144 103.280 -7.521 2.289 -0.358 H12 660 48 660 H13 H13 H 0 1 N N N 2.764 9.358 94.999 3.249 3.329 -0.952 H13 660 49 660 H14 H14 H 0 1 N N N 1.403 4.346 97.071 4.247 -1.475 0.655 H14 660 50 660 H15 H15 H 0 1 N N N -1.236 3.283 95.964 7.105 -2.276 -0.061 H15 660 51 660 H16 H16 H 0 1 N N N -0.702 5.772 97.654 4.632 -1.925 -1.817 H16 660 52 660 H17 H17 H 0 1 N N N -1.560 5.514 94.729 7.210 -0.295 -1.656 H17 660 53 660 H18 H18 H 0 1 N N N 0.651 6.550 94.281 5.758 1.499 -0.782 H18 660 54 660 H19 H19 H 0 1 N N N -1.623 3.148 98.248 5.736 -4.024 0.826 H19 660 55 660 H20 H20 H 0 1 N N N -2.737 4.698 97.918 6.196 -3.579 -2.548 H20 660 56 660 H21 H21 H 0 1 N N N -2.361 7.352 95.894 6.174 -0.383 -3.808 H21 660 57 660 H22 H22 H 0 1 N N N 0.590 7.444 96.804 3.567 -0.624 -0.771 H22 660 58 660 H23 H23 H 0 1 N N N 1.514 5.933 97.102 3.677 0.708 -1.946 H23 660 59 660 H24 H24 H 0 1 N N N 0.911 2.139 95.027 5.456 -2.894 2.340 H24 660 60 660 H25 H25 H 0 1 N N N 0.938 1.817 96.793 6.761 -1.684 2.372 H25 660 61 660 H26 H26 H 0 1 N N N 3.001 1.586 95.807 5.134 -1.285 4.076 H26 660 62 # # 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 660 O24 P22 DOUB N N 1 660 O36 C41 SING N N 2 660 O36 C37 SING N N 3 660 C41 C40 SING N N 4 660 C41 C45 SING N N 5 660 C40 O44 SING N N 6 660 C40 C39 SING N N 7 660 P22 O23 SING N N 8 660 P22 C45 SING N N 9 660 P22 O12 SING N N 10 660 O47 C46 SING N N 11 660 C46 C37 SING N N 12 660 C37 C38 SING N N 13 660 O12 P9 SING N N 14 660 C38 C39 SING N N 15 660 C38 O42 SING N N 16 660 C39 O43 SING N N 17 660 P9 O11 DOUB N N 18 660 P9 O10 SING N N 19 660 P9 O8 SING N N 20 660 O8 C5 SING N N 21 660 C5 C4 SING N N 22 660 C4 C3 SING N N 23 660 C4 O6 SING N N 24 660 C3 O7 SING N N 25 660 C3 C2 SING N N 26 660 O6 C1 SING N N 27 660 C2 C1 SING N N 28 660 C2 O21 SING N N 29 660 C18 C17 DOUB N N 30 660 C18 N13 SING N N 31 660 C1 N13 SING N N 32 660 C17 C20 SING N N 33 660 N13 C19 SING N N 34 660 C20 O20 DOUB N N 35 660 C20 N15 SING N N 36 660 C19 N15 SING N N 37 660 C19 O19 DOUB N N 38 660 C1 H1 SING N N 39 660 C2 H2 SING N N 40 660 C3 H3 SING N N 41 660 C4 H4 SING N N 42 660 C5 H5 SING N N 43 660 C5 H6 SING N N 44 660 O7 H7 SING N N 45 660 O10 H8 SING N N 46 660 N15 H9 SING N N 47 660 C17 H10 SING N N 48 660 C18 H11 SING N N 49 660 O21 H12 SING N N 50 660 O23 H13 SING N N 51 660 C37 H14 SING N N 52 660 C38 H15 SING N N 53 660 C39 H16 SING N N 54 660 C40 H17 SING N N 55 660 C41 H18 SING N N 56 660 O42 H19 SING N N 57 660 O43 H20 SING N N 58 660 O44 H21 SING N N 59 660 C45 H22 SING N N 60 660 C45 H23 SING N N 61 660 C46 H24 SING N N 62 660 C46 H25 SING N N 63 660 O47 H26 SING N N 64 # # 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 660 InChI InChI 1.03 "InChI=1S/C16H26N2O16P2/c19-3-6-10(21)13(24)12(23)8(32-6)5-35(27,28)34-36(29,30)31-4-7-11(22)14(25)15(33-7)18-2-1-9(20)17-16(18)26/h1-2,6-8,10-15,19,21-25H,3-5H2,(H,27,28)(H,29,30)(H,17,20,26)/t6-,7-,8-,10-,11-,12+,13+,14-,15-/m1/s1" 660 InChIKey InChI 1.03 WUPLBUVQIJIOHV-RIDHHKDKSA-N 660 SMILES_CANONICAL CACTVS 3.385 "OC[C@H]1O[C@H](C[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O)[C@H](O)[C@@H](O)[C@@H]1O" 660 SMILES CACTVS 3.385 "OC[CH]1O[CH](C[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O)[CH](O)[CH](O)[CH]1O" 660 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.4 "C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)OP(=O)(C[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)O)O)O)O" 660 SMILES "OpenEye OEToolkits" 2.0.4 "C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(CC3C(C(C(C(O3)CO)O)O)O)O)O)O" # _pdbx_chem_comp_identifier.comp_id 660 _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.4 _pdbx_chem_comp_identifier.identifier "[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-[[(2~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]methyl]phosphinic acid" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 660 "Create component" 2016-02-02 RCSB 660 "Modify synonyms" 2016-03-03 RCSB 660 "Initial release" 2016-03-09 RCSB 660 "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 660 _pdbx_chem_comp_synonyms.name "UDP-glucose phosphonate" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##