data_UPG # _chem_comp.id UPG _chem_comp.name "URIDINE-5'-DIPHOSPHATE-GLUCOSE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C15 H24 N2 O17 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ;URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER ; _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-08 _chem_comp.pdbx_modified_date 2024-09-27 _chem_comp.pdbx_ambiguous_flag N _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces GUD _chem_comp.formula_weight 566.302 _chem_comp.one_letter_code ? _chem_comp.three_letter_code UPG _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 1EK6 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _chem_comp.pdbx_pcm Y # 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.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _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 UPG N1 N1 N 0 1 N N N N N N 25.413 6.752 43.956 4.871 -1.188 0.165 N1 UPG 1 UPG C2 C2 C 0 1 N N N N N N 24.539 6.200 44.894 5.434 -2.195 0.857 C2 UPG 2 UPG N3 N3 N 0 1 N N N N N N 24.197 7.045 45.917 5.677 -3.384 0.274 N3 UPG 3 UPG C4 C4 C 0 1 N N N N N N 24.620 8.374 46.083 5.358 -3.583 -1.021 C4 UPG 4 UPG C5 C5 C 0 1 N N N N N N 25.498 8.840 45.060 4.766 -2.532 -1.760 C5 UPG 5 UPG C6 C6 C 0 1 N N N N N N 25.855 8.055 44.059 4.533 -1.350 -1.151 C6 UPG 6 UPG O2 O2 O 0 1 N N N N N N 24.106 5.041 44.840 5.726 -2.030 2.026 O2 UPG 7 UPG O4 O4 O 0 1 N N N N N N 24.217 9.023 47.037 5.579 -4.658 -1.549 O4 UPG 8 UPG C1C "C1'A" C 0 1 N N R N N N 25.915 5.905 42.850 4.613 0.093 0.828 C1C UPG 9 UPG C2C "C2'A" C 0 1 N N R N N N 25.525 6.365 41.451 5.477 1.216 0.201 C2C UPG 10 UPG O2C "O2'A" O 0 1 N N N N N N 24.217 5.848 41.079 6.766 1.271 0.814 O2C UPG 11 UPG C3C "C3'A" C 0 1 N N S N N N 26.667 5.791 40.579 4.653 2.484 0.534 C3C UPG 12 UPG C4C "C4'A" C 0 1 N N R N N N 27.850 5.881 41.532 3.231 1.951 0.799 C4C UPG 13 UPG O4C "O4'A" O 0 1 N N N N N N 27.306 5.888 42.894 3.260 0.530 0.580 O4C UPG 14 UPG O3C "O3'A" O 0 1 N N N N N N 26.435 4.438 40.151 5.171 3.126 1.700 O3C UPG 15 UPG C5C "C5'A" C 0 1 N N N N N N 28.721 7.089 41.335 2.242 2.606 -0.167 C5C UPG 16 UPG O5C "O5'A" O 0 1 N N N N N N 27.849 8.218 41.413 0.913 2.195 0.161 O5C UPG 17 UPG PA PA P 0 1 N N N N N N 28.478 9.680 41.403 -0.385 2.693 -0.651 PA UPG 18 UPG O1A O1A O 0 1 N N N N N N 29.568 9.872 42.372 -0.213 2.389 -2.090 O1A UPG 19 UPG O2A O2A O 0 1 N N N N N N 27.398 10.697 41.466 -0.563 4.281 -0.456 O2A UPG 20 UPG O3A O3A O 0 1 N N N N N N 29.280 9.741 39.973 -1.691 1.934 -0.095 O3A UPG 21 UPG PB PB P 0 1 N N N N N N 28.768 9.732 38.482 -3.161 1.656 -0.689 PB UPG 22 UPG O1B O1B O 0 1 N N N N N N 27.329 9.980 38.379 -3.049 1.210 -2.095 O1B UPG 23 UPG O2B O2B O 0 1 N N N N N N 29.251 8.422 37.941 -4.031 3.009 -0.623 O2B UPG 24 UPG O3B O3B O 0 1 N N N N N N 29.518 10.990 37.753 -3.884 0.511 0.182 O3B UPG 25 UPG "C1'" "C1'" C 0 1 N N R N N N 30.770 11.399 38.211 -5.161 -0.034 -0.156 "C1'" UPG 26 UPG "C2'" "C2'" C 0 1 N N R N N N 30.814 12.938 38.266 -5.883 -0.473 1.120 "C2'" UPG 27 UPG "C3'" "C3'" C 0 1 N N S N N N 30.475 13.471 36.893 -5.071 -1.579 1.803 "C3'" UPG 28 UPG "C4'" "C4'" C 0 1 N N S N N N 31.423 12.927 35.834 -4.877 -2.736 0.818 "C4'" UPG 29 UPG "C5'" "C5'" C 0 1 N N R N N N 31.464 11.395 35.905 -4.194 -2.210 -0.447 "C5'" UPG 30 UPG "C6'" "C6'" C 0 1 N N N N N N 32.586 10.815 35.067 -4.051 -3.348 -1.460 "C6'" UPG 31 UPG "O2'" "O2'" O 0 1 N N N N N N 29.878 13.546 39.180 -6.009 0.642 2.005 "O2'" UPG 32 UPG "O3'" "O3'" O 0 1 N N N N N N 30.600 14.902 36.901 -5.774 -2.045 2.956 "O3'" UPG 33 UPG "O4'" "O4'" O 0 1 N N N N N N 30.948 13.293 34.533 -4.060 -3.742 1.419 "O4'" UPG 34 UPG "O5'" "O5'" O 0 1 N N N N N N 31.735 10.926 37.242 -4.985 -1.164 -1.014 "O5'" UPG 35 UPG "O6'" "O6'" O 0 1 N N N N N N 32.414 9.376 35.139 -3.310 -2.887 -2.592 "O6'" UPG 36 UPG HN3 HN3 H 0 1 N N N N N N 23.584 6.678 46.617 6.084 -4.099 0.787 HN3 UPG 37 UPG H5 H5 H 0 1 N N N N N N 25.877 9.850 45.104 4.504 -2.673 -2.799 H5 UPG 38 UPG H6 H6 H 0 1 N N N N N N 26.514 8.446 43.297 4.081 -0.536 -1.699 H6 UPG 39 UPG H1C "H1'A" H 0 1 N N N N N N 25.528 4.885 42.990 4.804 0.015 1.899 H1C UPG 40 UPG H2C "H2'A" H 0 1 N N N N N N 25.540 7.464 41.401 5.567 1.082 -0.877 H2C UPG 41 UPG HO2C "HO2'" H 0 0 N N N N N N 23.995 6.147 40.205 7.344 1.959 0.456 HO2C UPG 42 UPG H3C "H3'A" H 0 1 N N N N N N 26.835 6.452 39.716 4.651 3.171 -0.312 H3C UPG 43 UPG H4C "H4'A" H 0 1 N N N N N N 28.468 4.981 41.399 2.942 2.162 1.828 H4C UPG 44 UPG HO3C "HO3'" H 0 0 N N N N N N 27.167 4.143 39.622 6.085 3.429 1.609 HO3C UPG 45 UPG H5C1 "H5'1" H 0 0 N N N N N N 29.486 7.142 42.123 2.317 3.690 -0.085 H5C1 UPG 46 UPG H5C2 "H5'2" H 0 0 N N N N N N 29.211 7.051 40.351 2.474 2.302 -1.188 H5C2 UPG 47 UPG HOA2 HOA2 H 0 0 N N N N N N 27.596 11.328 42.148 -0.681 4.554 0.465 HOA2 UPG 48 UPG HOB2 HOB2 H 0 0 N N N N N N 28.515 7.930 37.598 -4.146 3.360 0.271 HOB2 UPG 49 UPG "H1'" "H1'" H 0 1 N N N N N N 30.988 10.991 39.209 -5.755 0.722 -0.668 "H1'" UPG 50 UPG "H2'" "H2'" H 0 1 N N N N N N 31.838 13.247 38.523 -6.873 -0.851 0.867 "H2'" UPG 51 UPG "H3'" "H3'" H 0 1 N N N N N N 29.446 13.181 36.637 -4.099 -1.186 2.101 "H3'" UPG 52 UPG "H4'" "H4'" H 0 1 N N N N N N 32.433 13.326 36.006 -5.847 -3.160 0.558 "H4'" UPG 53 UPG "H5'" "H5'" H 0 1 N N N N N N 30.503 10.995 35.549 -3.207 -1.823 -0.193 "H5'" UPG 54 UPG "H6'1" "H6'1" H 0 0 N N N N N N 32.507 11.161 34.026 -3.524 -4.182 -0.997 "H6'1" UPG 55 UPG "H6'2" "H6'2" H 0 0 N N N N N N 33.564 11.107 35.477 -5.040 -3.675 -1.781 "H6'2" UPG 56 UPG "HO2'" HO2A H 0 0 N N N N N N 29.973 14.491 39.150 -6.508 1.383 1.636 "HO2'" UPG 57 UPG "HO3'" HO3A H 0 0 N N N N N N 30.388 15.244 36.040 -5.938 -1.362 3.620 "HO3'" UPG 58 UPG "HO4'" "HO4'" H 0 0 N N N N N N 31.540 12.953 33.872 -4.430 -4.117 2.230 "HO4'" UPG 59 UPG "HO6'" "HO6'" H 0 0 N N N N N N 33.093 8.950 34.629 -3.181 -3.557 -3.277 "HO6'" UPG 60 # 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 UPG N1 C2 SING N N 1 UPG N1 C6 SING N N 2 UPG N1 C1C SING N N 3 UPG C2 N3 SING N N 4 UPG C2 O2 DOUB N N 5 UPG N3 C4 SING N N 6 UPG N3 HN3 SING N N 7 UPG C4 C5 SING N N 8 UPG C4 O4 DOUB N N 9 UPG C5 C6 DOUB N N 10 UPG C5 H5 SING N N 11 UPG C6 H6 SING N N 12 UPG C1C C2C SING N N 13 UPG C1C O4C SING N N 14 UPG C1C H1C SING N N 15 UPG C2C O2C SING N N 16 UPG C2C C3C SING N N 17 UPG C2C H2C SING N N 18 UPG O2C HO2C SING N N 19 UPG C3C C4C SING N N 20 UPG C3C O3C SING N N 21 UPG C3C H3C SING N N 22 UPG C4C O4C SING N N 23 UPG C4C C5C SING N N 24 UPG C4C H4C SING N N 25 UPG O3C HO3C SING N N 26 UPG C5C O5C SING N N 27 UPG C5C H5C1 SING N N 28 UPG C5C H5C2 SING N N 29 UPG O5C PA SING N N 30 UPG PA O1A DOUB N N 31 UPG PA O2A SING N N 32 UPG PA O3A SING N N 33 UPG O2A HOA2 SING N N 34 UPG O3A PB SING N N 35 UPG PB O1B DOUB N N 36 UPG PB O2B SING N N 37 UPG PB O3B SING N N 38 UPG O2B HOB2 SING N N 39 UPG O3B "C1'" SING N N 40 UPG "C1'" "C2'" SING N N 41 UPG "C1'" "O5'" SING N N 42 UPG "C1'" "H1'" SING N N 43 UPG "C2'" "C3'" SING N N 44 UPG "C2'" "O2'" SING N N 45 UPG "C2'" "H2'" SING N N 46 UPG "C3'" "C4'" SING N N 47 UPG "C3'" "O3'" SING N N 48 UPG "C3'" "H3'" SING N N 49 UPG "C4'" "C5'" SING N N 50 UPG "C4'" "O4'" SING N N 51 UPG "C4'" "H4'" SING N N 52 UPG "C5'" "C6'" SING N N 53 UPG "C5'" "O5'" SING N N 54 UPG "C5'" "H5'" SING N N 55 UPG "C6'" "O6'" SING N N 56 UPG "C6'" "H6'1" SING N N 57 UPG "C6'" "H6'2" SING N N 58 UPG "O2'" "HO2'" SING N N 59 UPG "O3'" "HO3'" SING N N 60 UPG "O4'" "HO4'" SING N N 61 UPG "O6'" "HO6'" SING N N 62 # 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 UPG SMILES ACDLabs 12.01 "O=C1C=CN(C(=O)N1)C2OC(C(O)C2O)COP(=O)(OP(=O)(OC3OC(C(O)C(O)C3O)CO)O)O" UPG InChI InChI 1.03 "InChI=1S/C15H24N2O17P2/c18-3-5-8(20)10(22)12(24)14(32-5)33-36(28,29)34-35(26,27)30-4-6-9(21)11(23)13(31-6)17-2-1-7(19)16-15(17)25/h1-2,5-6,8-14,18,20-24H,3-4H2,(H,26,27)(H,28,29)(H,16,19,25)/t5-,6-,8-,9-,10+,11-,12-,13-,14-/m1/s1" UPG InChIKey InChI 1.03 HSCJRCZFDFQWRP-JZMIEXBBSA-N UPG SMILES_CANONICAL CACTVS 3.370 "OC[C@H]1O[C@H](O[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" UPG SMILES CACTVS 3.370 "OC[CH]1O[CH](O[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" UPG SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@](=O)(O)O[P@](=O)(O)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)O)O)O" UPG SMILES "OpenEye OEToolkits" 1.7.6 "C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OC3C(C(C(C(O3)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 UPG "SYSTEMATIC NAME" ACDLabs 12.01 "[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)" UPG "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[[(2R,3S,4R,5R)-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3R,4S,5S,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl] hydrogen phosphate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site UPG "Create component" 1999-07-08 RCSB UPG "Modify descriptor" 2011-06-04 RCSB UPG "Other modification" 2013-05-07 RCSB UPG "Modify synonyms" 2021-03-01 PDBE UPG "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id UPG _pdbx_chem_comp_synonyms.name ;URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER ; _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id UPG _pdbx_chem_comp_pcm.modified_residue_id CYS _pdbx_chem_comp_pcm.type None _pdbx_chem_comp_pcm.category "Covalent chemical modification" _pdbx_chem_comp_pcm.position "Amino-acid side chain" _pdbx_chem_comp_pcm.polypeptide_position "Any position" _pdbx_chem_comp_pcm.comp_id_linking_atom "C6'" _pdbx_chem_comp_pcm.modified_residue_id_linking_atom SG _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #