data_URM # _chem_comp.id URM _chem_comp.name ;(((2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl)methyl)phosphonic (((2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl)methyl phosphoric) anhydride ; _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 "Uridine diphospho methylene galactopyranose" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2010-04-14 _chem_comp.pdbx_modified_date 2020-06-17 _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 564.329 _chem_comp.one_letter_code ? _chem_comp.three_letter_code URM _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 3MJ4 _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 URM C1 C1 C 0 1 N N R 79.365 -69.558 35.837 5.026 -0.023 1.075 C1 URM 1 URM C2 C2 C 0 1 N N R 79.467 -68.458 36.925 5.891 1.190 0.667 C2 URM 2 URM C3 C3 C 0 1 N N S 79.700 -69.188 38.239 4.862 2.306 0.383 C3 URM 3 URM C4 C4 C 0 1 N N R 80.390 -70.477 37.785 3.496 1.636 0.653 C4 URM 4 URM C5 C5 C 0 1 N N N 80.357 -71.674 38.756 2.452 2.132 -0.350 C5 URM 5 URM O6 O6 O 0 1 N N N 80.082 -70.680 36.396 3.737 0.224 0.472 O6 URM 6 URM O7 O7 O 0 1 N N N 80.586 -68.422 39.040 5.062 3.409 1.270 O7 URM 7 URM O8 O8 O 0 1 N N N 79.098 -72.344 38.594 1.173 1.591 -0.012 O8 URM 8 URM P9 P9 P 0 1 N N N 78.239 -72.851 39.835 -0.162 1.903 -0.856 P9 URM 9 URM O10 O10 O 0 1 N N N 78.951 -72.520 41.102 -0.017 1.287 -2.336 O10 URM 10 URM O11 O11 O 0 1 N N N 78.212 -74.337 39.716 -0.355 3.367 -0.948 O11 URM 11 URM O12 O12 O 0 1 N N N 76.816 -72.133 39.807 -1.430 1.239 -0.120 O12 URM 12 URM N13 N13 N 0 1 N N N 78.038 -69.876 35.359 5.605 -1.263 0.550 N13 URM 13 URM N15 N15 N 0 1 N N N 76.323 -69.488 33.812 6.247 -2.562 -1.289 N15 URM 14 URM C17 C17 C 0 1 N N N 75.997 -70.958 35.702 6.553 -3.379 0.933 C17 URM 15 URM C18 C18 C 0 1 N N N 77.253 -70.708 36.094 6.019 -2.237 1.416 C18 URM 16 URM C19 C19 C 0 1 N N N 77.464 -69.390 34.345 5.720 -1.434 -0.780 C19 URM 17 URM O19 O19 O 0 1 N N N 78.297 -68.496 33.599 5.340 -0.557 -1.532 O19 URM 18 URM C20 C20 C 0 1 N N N 75.495 -70.308 34.485 6.672 -3.544 -0.468 C20 URM 19 URM O20 O20 O 0 1 N N N 74.342 -70.503 34.129 7.150 -4.566 -0.928 O20 URM 20 URM O21 O21 O 0 1 N N N 80.466 -67.468 36.658 6.759 1.568 1.737 O21 URM 21 URM P22 P22 P 0 1 N N N 76.323 -70.889 40.687 -3.024 1.423 -0.254 P22 URM 22 URM O23 O23 O 0 1 N N N 77.292 -69.824 41.079 -3.417 2.951 0.069 O23 URM 23 URM O24 O24 O 0 1 N N N 75.365 -70.216 39.764 -3.445 1.086 -1.632 O24 URM 24 URM O36 O36 O 0 1 N N N 75.078 -73.543 42.087 -5.705 -0.110 -0.581 O36 URM 25 URM C37 C37 C 0 1 N N R 75.941 -73.821 43.222 -5.302 -1.464 -0.794 C37 URM 26 URM C38 C38 C 0 1 N N R 75.116 -73.792 44.539 -6.011 -2.371 0.215 C38 URM 27 URM C39 C39 C 0 1 N N S 74.471 -72.384 44.685 -5.679 -1.901 1.635 C39 URM 28 URM C40 C40 C 0 1 N N R 73.591 -72.090 43.443 -6.089 -0.433 1.783 C40 URM 29 URM C41 C41 C 0 1 N N S 74.418 -72.255 42.135 -5.377 0.400 0.714 C41 URM 30 URM O42 O42 O 0 1 N N N 74.072 -74.794 44.566 -7.423 -2.303 0.008 O42 URM 31 URM O43 O43 O 0 1 N N N 73.623 -72.324 45.851 -6.394 -2.696 2.582 O43 URM 32 URM O44 O44 O 0 1 N N N 72.924 -70.808 43.512 -5.718 0.038 3.080 O44 URM 33 URM C45 C45 C 0 1 N N N 75.489 -71.307 41.986 -3.865 0.317 0.927 C45 URM 34 URM C46 C46 C 0 1 N N N 76.628 -75.192 42.971 -5.677 -1.890 -2.214 C46 URM 35 URM O47 O47 O 0 1 N N N 77.309 -75.659 44.156 -4.927 -1.120 -3.156 O47 URM 36 URM H1 H1 H 0 1 N N N 79.807 -69.201 34.895 4.934 -0.076 2.159 H1 URM 37 URM H2 H2 H 0 1 N N N 78.538 -67.869 36.954 6.467 0.964 -0.231 H2 URM 38 URM H3 H3 H 0 1 N N N 78.788 -69.364 38.828 4.930 2.634 -0.654 H3 URM 39 URM H4 H4 H 0 1 N N N 81.482 -70.357 37.849 3.169 1.839 1.673 H4 URM 40 URM H5 H5 H 0 1 N N N 81.182 -72.365 38.528 2.406 3.220 -0.318 H5 URM 41 URM H5A H5A H 0 1 N N N 80.463 -71.320 39.792 2.730 1.809 -1.353 H5A URM 42 URM HO7 HO7 H 0 1 N N N 80.737 -68.871 39.864 5.929 3.830 1.184 HO7 URM 43 URM HO10 HO10 H 0 0 N N N 79.219 -73.322 41.534 0.113 0.329 -2.353 HO10 URM 44 URM H17 H17 H 0 1 N N N 75.366 -71.625 36.270 6.885 -4.156 1.605 H17 URM 45 URM H18 H18 H 0 1 N N N 77.641 -71.166 36.992 5.921 -2.093 2.482 H18 URM 46 URM HO21 HO21 H 0 0 N N N 80.474 -66.828 37.360 7.325 2.326 1.535 HO21 URM 47 URM HO23 HO23 H 0 0 N N N 77.057 -69.009 40.651 -3.170 3.241 0.957 HO23 URM 48 URM H37 H37 H 0 1 N N N 76.721 -73.053 43.331 -4.223 -1.547 -0.662 H37 URM 49 URM H38 H38 H 0 1 N N N 75.801 -74.012 45.371 -5.672 -3.399 0.083 H38 URM 50 URM H39 H39 H 0 1 N N N 75.282 -71.646 44.780 -4.607 -2.000 1.811 H39 URM 51 URM H40 H40 H 0 1 N N N 72.784 -72.837 43.432 -7.168 -0.342 1.658 H40 URM 52 URM H41 H41 H 0 1 N N N 73.666 -72.115 41.344 -5.699 1.439 0.788 H41 URM 53 URM HO42 HO42 H 0 0 N N N 73.598 -74.736 45.387 -7.705 -2.583 -0.873 HO42 URM 54 URM HO43 HO43 H 0 0 N N N 73.240 -71.457 45.921 -6.188 -3.639 2.539 HO43 URM 55 URM HO44 HO44 H 0 0 N N N 72.401 -70.680 42.729 -6.129 -0.448 3.808 HO44 URM 56 URM H45 H45 H 0 1 N N N 76.263 -71.697 42.664 -3.530 -0.708 0.766 H45 URM 57 URM H45A H45A H 0 0 N N N 75.028 -70.359 42.302 -3.624 0.622 1.945 H45A URM 58 URM H46 H46 H 0 1 N N N 75.862 -75.928 42.687 -5.450 -2.948 -2.348 H46 URM 59 URM H46A H46A H 0 0 N N N 77.362 -75.080 42.159 -6.742 -1.724 -2.375 H46A URM 60 URM HO47 HO47 H 0 0 N N N 77.720 -76.497 43.976 -5.114 -1.338 -4.080 HO47 URM 61 URM HN15 HN15 H 0 0 N N N 76.062 -69.006 32.976 6.322 -2.670 -2.250 HN15 URM 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 URM N13 C1 SING N N 1 URM C1 O6 SING N N 2 URM C1 C2 SING N N 3 URM C1 H1 SING N N 4 URM O21 C2 SING N N 5 URM C2 C3 SING N N 6 URM C2 H2 SING N N 7 URM C4 C3 SING N N 8 URM C3 O7 SING N N 9 URM C3 H3 SING N N 10 URM O6 C4 SING N N 11 URM C4 C5 SING N N 12 URM C4 H4 SING N N 13 URM O8 C5 SING N N 14 URM C5 H5 SING N N 15 URM C5 H5A SING N N 16 URM O7 HO7 SING N N 17 URM O8 P9 SING N N 18 URM O11 P9 DOUB N N 19 URM O12 P9 SING N N 20 URM P9 O10 SING N N 21 URM O10 HO10 SING N N 22 URM O12 P22 SING N N 23 URM C19 N13 SING N N 24 URM N13 C18 SING N N 25 URM N15 C19 SING N N 26 URM N15 C20 SING N N 27 URM C20 C17 SING N N 28 URM C17 C18 DOUB N N 29 URM C17 H17 SING N N 30 URM C18 H18 SING N N 31 URM O19 C19 DOUB N N 32 URM O20 C20 DOUB N N 33 URM O21 HO21 SING N N 34 URM O24 P22 DOUB N N 35 URM P22 O23 SING N N 36 URM P22 C45 SING N N 37 URM O23 HO23 SING N N 38 URM O36 C41 SING N N 39 URM O36 C37 SING N N 40 URM C46 C37 SING N N 41 URM C37 C38 SING N N 42 URM C37 H37 SING N N 43 URM C38 O42 SING N N 44 URM C38 C39 SING N N 45 URM C38 H38 SING N N 46 URM C40 C39 SING N N 47 URM C39 O43 SING N N 48 URM C39 H39 SING N N 49 URM C41 C40 SING N N 50 URM C40 O44 SING N N 51 URM C40 H40 SING N N 52 URM C45 C41 SING N N 53 URM C41 H41 SING N N 54 URM O42 HO42 SING N N 55 URM O43 HO43 SING N N 56 URM O44 HO44 SING N N 57 URM C45 H45 SING N N 58 URM C45 H45A SING N N 59 URM C46 O47 SING N N 60 URM C46 H46 SING N N 61 URM C46 H46A SING N N 62 URM O47 HO47 SING N N 63 URM N15 HN15 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 URM SMILES_CANONICAL CACTVS 3.370 "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" URM SMILES CACTVS 3.370 "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" URM SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)O[P@@](=O)(C[C@@H]3[C@@H]([C@H]([C@H]([C@H](O3)CO)O)O)O)O)O)O" URM SMILES "OpenEye OEToolkits" 1.7.0 "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" URM 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" URM InChIKey InChI 1.03 WUPLBUVQIJIOHV-PPSAJGQHSA-N # _pdbx_chem_comp_identifier.comp_id URM _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 1.7.0 _pdbx_chem_comp_identifier.identifier "[[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-[[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)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 URM "Create component" 2010-04-14 RCSB URM "Modify descriptor" 2011-06-04 RCSB URM "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id URM _pdbx_chem_comp_synonyms.name "Uridine diphospho methylene galactopyranose" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##