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 ?
#
_pdbe_chem_comp_drugbank_details.comp_id UPG
_pdbe_chem_comp_drugbank_details.drugbank_id DB01861
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name 'Uridine diphosphate glucose'
_pdbe_chem_comp_drugbank_details.description
'A key intermediate in carbohydrate metabolism. Serves as a precursor of glycogen, can be metabolized into UDPgalactose and UDPglucuronic acid which can then be incorporated into polysaccharides as galactose and glucuronic acid. Also serves as a precursor of sucrose lipopolysaccharides, and glycosphingolipids.'
_pdbe_chem_comp_drugbank_details.cas_number 133-89-1
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
UPG "URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER" wwPDB ?
UPG "5'-Diphosphoglucose" DrugBank ?
UPG Co-galactoisomerase DrugBank ?
UPG Co-waldenase DrugBank ?
UPG Cogalactoisomerase DrugBank ?
UPG UDP-Glucose DrugBank ?
UPG UDPG DrugBank ?
UPG "Uridine 5'-pyrophosphate glucose ester" DrugBank ?
UPG 'Uridine diphosphate glucose' DrugBank ?
UPG "Uridine-5'-Diphosphoglucose" DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id UPG
_pdbe_chem_comp_drugbank_classification.drugbank_id DB01861
_pdbe_chem_comp_drugbank_classification.parent 'Pyrimidine nucleotide sugars'
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Pyrimidine nucleotides'
_pdbe_chem_comp_drugbank_classification.superclass 'Nucleosides, nucleotides, and analogues'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as pyrimidine nucleotide sugars. These are pyrimidine nucleotides bound to a saccharide derivative through the terminal phosphate group.'
#
loop_
_pdbe_chem_comp_drugbank_targets.comp_id
_pdbe_chem_comp_drugbank_targets.drugbank_id
_pdbe_chem_comp_drugbank_targets.name
_pdbe_chem_comp_drugbank_targets.organism
_pdbe_chem_comp_drugbank_targets.uniprot_id
_pdbe_chem_comp_drugbank_targets.pharmacologically_active
_pdbe_chem_comp_drugbank_targets.ordinal
UPG DB01861 'Galactose-1-phosphate uridylyltransferase' 'Escherichia coli (strain K12)' P09148 unknown 1
UPG DB01861 'UDP-glucose 4-epimerase' Humans Q14376 unknown 2
UPG DB01861 'Trehalose-6-phosphate synthase' 'Escherichia coli (strain K12)' P31677 unknown 3
UPG DB01861 'Glucose-1-phosphate thymidylyltransferase' 'Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)' P26393 unknown 4
UPG DB01861 'UDP-glucose 4-epimerase' 'Escherichia coli (strain K12)' P09147 unknown 5
UPG DB01861 'DNA beta-glucosyltransferase' 'Enterobacteria phage T4' P04547 unknown 6
UPG DB01861 'Putative glycosyltransferase 6 domain-containing protein 1' Humans Q7Z4J2 unknown 7
UPG DB01861 'UDP-N-acetyl-alpha-D-glucosaminouronate 4-epimerase' 'Pseudomonas aeruginosa' Q8KN66 unknown 8
UPG DB01861 Glycogenin-1 Humans P46976 unknown 9
UPG DB01861 'Uracil nucleotide/cysteinyl leukotriene receptor' Humans Q13304 unknown 10
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 'Wrapper to provide 2D templates and molecular fragments.'
#
loop_
_pdbe_chem_comp_atom_depiction.comp_id
_pdbe_chem_comp_atom_depiction.atom_id
_pdbe_chem_comp_atom_depiction.element
_pdbe_chem_comp_atom_depiction.model_Cartn_x
_pdbe_chem_comp_atom_depiction.model_Cartn_y
_pdbe_chem_comp_atom_depiction.pdbx_ordinal
UPG N1 N 15.133 5.389 1
UPG C2 C 16.625 5.546 2
UPG N3 N 17.235 6.916 3
UPG C4 C 16.353 8.130 4
UPG C5 C 14.861 7.973 5
UPG C6 C 14.251 6.603 6
UPG O2 O 17.506 4.332 7
UPG O4 O 16.963 9.500 8
UPG C1C C 14.523 4.019 9
UPG C2C C 15.273 2.720 10
UPG O2C O 16.765 2.563 11
UPG C3C C 14.269 1.605 12
UPG C4C C 12.899 2.215 13
UPG O4C O 13.055 3.707 14
UPG O3C O 14.581 0.138 15
UPG C5C C 11.600 1.465 16
UPG O5C O 11.600 -0.035 17
UPG PA P 10.301 -0.785 18
UPG O1A O 9.551 0.514 19
UPG O2A O 11.051 -2.084 20
UPG O3A O 9.002 -1.535 21
UPG PB P 9.002 -3.035 22
UPG O1B O 10.502 -3.035 23
UPG O2B O 7.502 -3.035 24
UPG O3B O 9.002 -4.535 25
UPG "C1'" C 7.702 -5.285 26
UPG "C2'" C 7.702 -6.785 27
UPG "C3'" C 6.404 -7.535 28
UPG "C4'" C 5.104 -6.785 29
UPG "C5'" C 5.104 -5.285 30
UPG "C6'" C 3.805 -4.535 31
UPG "O2'" O 9.002 -7.535 32
UPG "O3'" O 6.404 -9.035 33
UPG "O4'" O 3.805 -7.535 34
UPG "O5'" O 6.404 -4.535 35
UPG "O6'" O 3.805 -3.035 36
#
loop_
_pdbe_chem_comp_bond_depiction.comp_id
_pdbe_chem_comp_bond_depiction.atom_id_1
_pdbe_chem_comp_bond_depiction.atom_id_2
_pdbe_chem_comp_bond_depiction.value_order
_pdbe_chem_comp_bond_depiction.bond_dir
_pdbe_chem_comp_bond_depiction.pdbx_ordinal
UPG N1 C2 SINGLE NONE 1
UPG N1 C6 SINGLE NONE 2
UPG C1C N1 SINGLE BEGINWEDGE 3
UPG C2 N3 SINGLE NONE 4
UPG C2 O2 DOUBLE NONE 5
UPG N3 C4 SINGLE NONE 6
UPG C4 C5 SINGLE NONE 7
UPG C4 O4 DOUBLE NONE 8
UPG C5 C6 DOUBLE NONE 9
UPG C1C C2C SINGLE NONE 10
UPG C1C O4C SINGLE NONE 11
UPG C2C O2C SINGLE BEGINDASH 12
UPG C2C C3C SINGLE NONE 13
UPG C3C C4C SINGLE NONE 14
UPG C3C O3C SINGLE BEGINDASH 15
UPG C4C O4C SINGLE NONE 16
UPG C4C C5C SINGLE BEGINWEDGE 17
UPG C5C O5C SINGLE NONE 18
UPG O5C PA SINGLE NONE 19
UPG PA O1A DOUBLE NONE 20
UPG PA O2A SINGLE BEGINWEDGE 21
UPG PA O3A SINGLE NONE 22
UPG O3A PB SINGLE NONE 23
UPG PB O1B DOUBLE NONE 24
UPG PB O2B SINGLE BEGINDASH 25
UPG PB O3B SINGLE NONE 26
UPG "C1'" O3B SINGLE BEGINDASH 27
UPG "C1'" "C2'" SINGLE NONE 28
UPG "C1'" "O5'" SINGLE NONE 29
UPG "C2'" "C3'" SINGLE NONE 30
UPG "C2'" "O2'" SINGLE BEGINDASH 31
UPG "C3'" "C4'" SINGLE NONE 32
UPG "C3'" "O3'" SINGLE BEGINWEDGE 33
UPG "C4'" "C5'" SINGLE NONE 34
UPG "C4'" "O4'" SINGLE BEGINDASH 35
UPG "C5'" "C6'" SINGLE BEGINWEDGE 36
UPG "C5'" "O5'" SINGLE NONE 37
UPG "C6'" "O6'" SINGLE NONE 38
#
loop_
_pdbe_chem_comp_substructure.comp_id
_pdbe_chem_comp_substructure.substructure_name
_pdbe_chem_comp_substructure.id
_pdbe_chem_comp_substructure.substructure_type
_pdbe_chem_comp_substructure.substructure_smiles
_pdbe_chem_comp_substructure.substructure_inchis
_pdbe_chem_comp_substructure.substructure_inchikeys
UPG MurckoScaffold S1 scaffold 'O=c1ccn([C@H]2CC[C@@H](CO[PH](=O)O[PH](=O)O[C@@H]3CCCCO3)O2)c(=O)[nH]1' InChI=1S/C14H22N2O9P2/c17-11-6-7-16(14(18)15-11)12-5-4-10(23-12)9-22-26(19)25-27(20)24-13-3-1-2-8-21-13/h6-7,10,12-13,26-27H,1-5,8-9H2,(H,15,17,18)/t10-,12+,13+/m0/s1 AKKVBKIXAFLMCT-CYZMBNFOSA-N
UPG phosphate F1 fragment O=P(O)(O)O InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4) NBIIXXVUZAFLBC-UHFFFAOYSA-N
UPG pyranose F2 fragment OC1CCCCO1 InChI=1S/C5H10O2/c6-5-3-1-2-4-7-5/h5-6H,1-4H2 CELWCAITJAEQNL-UHFFFAOYSA-N
UPG pyrimidine F3 fragment c1cncnc1 InChI=1S/C4H4N2/c1-2-5-4-6-3-1/h1-4H CZPWVGJYEJSRLH-UHFFFAOYSA-N
UPG ribose F4 fragment OCC1OCC(O)C1O InChI=1S/C5H10O4/c6-1-4-5(8)3(7)2-9-4/h3-8H,1-2H2 KZVAAIRBJJYZOW-UHFFFAOYSA-N
#
loop_
_pdbe_chem_comp_substructure_mapping.comp_id
_pdbe_chem_comp_substructure_mapping.atom_id
_pdbe_chem_comp_substructure_mapping.substructure_id
_pdbe_chem_comp_substructure_mapping.substructure_ordinal
UPG N1 S1 1
UPG C2 S1 1
UPG N3 S1 1
UPG C4 S1 1
UPG C5 S1 1
UPG C6 S1 1
UPG O2 S1 1
UPG O4 S1 1
UPG C1C S1 1
UPG C2C S1 1
UPG C3C S1 1
UPG C4C S1 1
UPG O4C S1 1
UPG C5C S1 1
UPG O5C S1 1
UPG PA S1 1
UPG O1A S1 1
UPG O3A S1 1
UPG PB S1 1
UPG O1B S1 1
UPG O3B S1 1
UPG "C1'" S1 1
UPG "C2'" S1 1
UPG "C3'" S1 1
UPG "C4'" S1 1
UPG "C5'" S1 1
UPG "O5'" S1 1
UPG O5C F1 1
UPG PA F1 1
UPG O1A F1 1
UPG O2A F1 1
UPG O3A F1 1
UPG O3A F1 2
UPG PB F1 2
UPG O1B F1 2
UPG O2B F1 2
UPG O3B F1 2
UPG "C4'" F2 1
UPG "C5'" F2 1
UPG "O5'" F2 1
UPG "C1'" F2 1
UPG "C2'" F2 1
UPG "C3'" F2 1
UPG O3B F2 1
UPG C5 F3 1
UPG C4 F3 1
UPG N3 F3 1
UPG C2 F3 1
UPG N1 F3 1
UPG C6 F3 1
UPG C2C F4 1
UPG C3C F4 1
UPG C4C F4 1
UPG O4C F4 1
UPG C1C F4 1
UPG C5C F4 1
UPG O5C F4 1
UPG O3C F4 1
UPG O2C F4 1
#
_pdbe_chem_comp_rdkit_properties.comp_id UPG
_pdbe_chem_comp_rdkit_properties.exactmw 566.055
_pdbe_chem_comp_rdkit_properties.amw 566.302
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 19
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 9
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 17
_pdbe_chem_comp_rdkit_properties.NumHBD 9
_pdbe_chem_comp_rdkit_properties.NumHBA 18
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 36
_pdbe_chem_comp_rdkit_properties.NumAtoms 60
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 21
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.733
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 2
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 3
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 11
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 233.898
_pdbe_chem_comp_rdkit_properties.tpsa 296.990
_pdbe_chem_comp_rdkit_properties.CrippenClogP -2.994
_pdbe_chem_comp_rdkit_properties.CrippenMR 109.002
_pdbe_chem_comp_rdkit_properties.chi0v 18.018
_pdbe_chem_comp_rdkit_properties.chi1v 11.108
_pdbe_chem_comp_rdkit_properties.chi2v 5.712
_pdbe_chem_comp_rdkit_properties.chi3v 5.712
_pdbe_chem_comp_rdkit_properties.chi4v 3.789
_pdbe_chem_comp_rdkit_properties.chi0n 40.229
_pdbe_chem_comp_rdkit_properties.chi1n 19.400
_pdbe_chem_comp_rdkit_properties.chi2n 3.408
_pdbe_chem_comp_rdkit_properties.chi3n 3.408
_pdbe_chem_comp_rdkit_properties.chi4n 2.024
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.380
_pdbe_chem_comp_rdkit_properties.kappa1 10.649
_pdbe_chem_comp_rdkit_properties.kappa2 11.159
_pdbe_chem_comp_rdkit_properties.kappa3 6.540
_pdbe_chem_comp_rdkit_properties.Phi 3.301
#
loop_
_pdbe_chem_comp_external_mappings.comp_id
_pdbe_chem_comp_external_mappings.source
_pdbe_chem_comp_external_mappings.resource
_pdbe_chem_comp_external_mappings.resource_id
UPG UniChem DrugBank DB01861
UPG UniChem 'Guide to Pharmacology' 1783
UPG UniChem 'KEGG LIGAND' C00029
UPG UniChem ChEBI 46229
UPG UniChem fdasrs V50K1D7P4Y
UPG UniChem HMDB HMDB0000286
UPG UniChem BindingDb 50423218
UPG UniChem MetaboLights MTBLC46229
UPG UniChem BRENDA 107457
UPG UniChem BRENDA 107464
UPG UniChem BRENDA 129835
UPG UniChem BRENDA 186
UPG UniChem BRENDA 23835
UPG UniChem BRENDA 250247
UPG UniChem BRENDA 253298
UPG UniChem BRENDA 364
UPG UniChem BRENDA 41824
UPG UniChem BRENDA 44923
UPG UniChem BRENDA 64
UPG UniChem BRENDA 7631
UPG UniChem BRENDA 889
UPG UniChem BRENDA 98588
UPG UniChem 'Probes And Drugs' PD049275
UPG UniChem 'EPA CompTox Dashboard' DTXSID00157902
UPG UniChem ZINC ZINC000008215472
UPG UniChem SureChEMBL SCHEMBL454078
UPG UniChem 'PubChem TPHARMA' 14813015
UPG UniChem PubChem 8629
UPG UniChem NMRShiftDB 60081727
UPG UniChem Nikkaji J9.610E
UPG UniChem BindingDb 50209659
#
loop_
_pdbe_chem_comp_rdkit_conformer.comp_id
_pdbe_chem_comp_rdkit_conformer.atom_id
_pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit
_pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit
_pdbe_chem_comp_rdkit_conformer.rdkit_method
_pdbe_chem_comp_rdkit_conformer.rdkit_ordinal
UPG N1 6.022 0.356 -0.259 ETKDGv3 1
UPG C2 7.431 0.344 0.055 ETKDGv3 2
UPG N3 8.355 0.989 -0.823 ETKDGv3 3
UPG C4 7.863 1.673 -1.976 ETKDGv3 4
UPG C5 6.418 1.710 -2.237 ETKDGv3 5
UPG C6 5.565 1.092 -1.415 ETKDGv3 6
UPG O2 7.856 -0.226 1.097 ETKDGv3 7
UPG O4 8.662 2.245 -2.762 ETKDGv3 8
UPG C1C 5.045 -0.261 0.654 ETKDGv3 9
UPG C2C 4.481 0.788 1.625 ETKDGv3 10
UPG O2C 4.588 0.360 2.963 ETKDGv3 11
UPG C3C 3.041 0.935 1.182 ETKDGv3 12
UPG C4C 2.776 -0.391 0.483 ETKDGv3 13
UPG O4C 3.986 -0.836 -0.087 ETKDGv3 14
UPG O3C 2.160 1.121 2.259 ETKDGv3 15
UPG C5C 1.703 -0.262 -0.601 ETKDGv3 16
UPG O5C 1.470 -1.529 -1.170 ETKDGv3 17
UPG PA 0.216 -1.377 -2.316 ETKDGv3 18
UPG O1A -0.003 -2.711 -2.995 ETKDGv3 19
UPG O2A 0.663 -0.246 -3.495 ETKDGv3 20
UPG O3A -1.222 -0.844 -1.574 ETKDGv3 21
UPG PB -1.716 -2.038 -0.463 ETKDGv3 22
UPG O1B -0.629 -2.294 0.558 ETKDGv3 23
UPG O2B -2.078 -3.483 -1.270 ETKDGv3 24
UPG O3B -3.110 -1.503 0.367 ETKDGv3 25
UPG "C1'" -4.100 -1.086 -0.558 ETKDGv3 26
UPG "C2'" -3.972 0.437 -0.896 ETKDGv3 27
UPG "C3'" -5.340 1.160 -0.873 ETKDGv3 28
UPG "C4'" -6.168 0.825 0.398 ETKDGv3 29
UPG "C5'" -5.785 -0.559 0.984 ETKDGv3 30
UPG "C6'" -6.963 -1.202 1.730 ETKDGv3 31
UPG "O2'" -3.049 1.089 -0.056 ETKDGv3 32
UPG "O3'" -6.072 0.865 -2.039 ETKDGv3 33
UPG "O4'" -5.961 1.809 1.381 ETKDGv3 34
UPG "O5'" -5.382 -1.433 -0.053 ETKDGv3 35
UPG "O6'" -7.315 -0.442 2.855 ETKDGv3 36
UPG HN3 9.379 0.971 -0.618 ETKDGv3 37
UPG H5 6.041 2.248 -3.098 ETKDGv3 38
UPG H6 4.506 1.153 -1.633 ETKDGv3 39
UPG H1C 5.534 -1.084 1.221 ETKDGv3 40
UPG H2C 5.007 1.764 1.528 ETKDGv3 41
UPG HO2C 4.114 -0.509 3.050 ETKDGv3 42
UPG H3C 2.958 1.780 0.457 ETKDGv3 43
UPG H4C 2.439 -1.148 1.228 ETKDGv3 44
UPG HO3C 2.291 2.056 2.568 ETKDGv3 45
UPG H5C1 2.060 0.453 -1.376 ETKDGv3 46
UPG H5C2 0.777 0.136 -0.125 ETKDGv3 47
UPG HOA2 1.534 -0.570 -3.838 ETKDGv3 48
UPG HOB2 -2.461 -4.073 -0.572 ETKDGv3 49
UPG "H1'" -4.025 -1.642 -1.523 ETKDGv3 50
UPG "H2'" -3.570 0.525 -1.930 ETKDGv3 51
UPG "H3'" -5.145 2.255 -0.896 ETKDGv3 52
UPG "H4'" -7.248 0.817 0.115 ETKDGv3 53
UPG "H5'" -4.966 -0.443 1.732 ETKDGv3 54
UPG "H6'1" -7.834 -1.338 1.048 ETKDGv3 55
UPG "H6'2" -6.657 -2.212 2.077 ETKDGv3 56
UPG "HO2'" -3.401 1.061 0.870 ETKDGv3 57
UPG "HO3'" -6.285 -0.103 -2.032 ETKDGv3 58
UPG "HO4'" -6.497 2.601 1.115 ETKDGv3 59
UPG "HO6'" -7.986 0.225 2.554 ETKDGv3 60
#