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      ? 
# 
