data_UGA
#
_chem_comp.id UGA
_chem_comp.name "URIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C15 H22 N2 O18 P2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "UDP-GLUCURONIC ACID"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-12-13
_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 580.285
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code UGA
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1DLJ
_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
UGA "C1'" "C1'" C 0 1 N N R -16.924 14.694 55.748 0.767 0.386 4.945 "C1'" UGA 1
UGA "C2'" "C2'" C 0 1 N N R -18.004 14.883 54.666 1.013 -0.445 6.205 "C2'" UGA 2
UGA "O2'" "O2'" O 0 1 N N N -17.897 16.200 54.150 2.225 -1.188 6.061 "O2'" UGA 3
UGA "C3'" "C3'" C 0 1 N N S -19.398 14.685 55.264 -0.159 -1.411 6.404 "C3'" UGA 4
UGA "O3'" "O3'" O 0 1 N N N -20.406 14.802 54.248 -0.019 -2.086 7.655 "O3'" UGA 5
UGA "C4'" "C4'" C 0 1 N N S -19.474 13.310 55.919 -1.466 -0.609 6.396 "C4'" UGA 6
UGA "O4'" "O4'" O 0 1 N N N -20.759 13.143 56.512 -2.582 -1.501 6.427 "O4'" UGA 7
UGA "C5'" "C5'" C 0 1 N N S -18.375 13.242 56.991 -1.523 0.237 5.122 "C5'" UGA 8
UGA "O5'" "O5'" O 0 1 N N N -17.083 13.444 56.385 -0.427 1.150 5.096 "O5'" UGA 9
UGA "C6'" "C6'" C 0 1 N N N -18.346 11.867 57.651 -2.817 1.008 5.092 "C6'" UGA 10
UGA "O'P" "O6'1" O 0 1 N N N -18.688 10.853 56.983 -2.801 2.215 5.052 "O'P" UGA 11
UGA "O'Q" "O6'2" O 0 1 N N N -17.979 11.798 58.850 -3.989 0.352 5.110 "O'Q" UGA 12
UGA PB PB P 0 1 N N S -15.764 16.080 57.620 1.166 0.328 2.536 PB UGA 13
UGA O1B O1B O 0 1 N N N -15.017 14.825 57.911 2.582 0.705 2.743 O1B UGA 14
UGA O2B O2B O 0 1 N N N -16.298 16.901 58.764 0.280 1.658 2.338 O2B UGA 15
UGA O3B O3B O 0 1 N N N -16.990 15.746 56.660 0.633 -0.484 3.820 O3B UGA 16
UGA O3A O3A O 0 1 N N N -14.765 17.002 56.797 1.043 -0.598 1.225 O3A UGA 17
UGA PA PA P 0 1 N N R -14.620 17.701 55.363 1.590 0.273 -0.012 PA UGA 18
UGA O1A O1A O 0 1 N N N -14.970 19.128 55.494 3.000 0.650 0.233 O1A UGA 19
UGA O2A O2A O 0 1 N N N -15.302 16.864 54.350 0.698 1.603 -0.168 O2A UGA 20
UGA O5D O5* O 0 1 N N N -13.045 17.572 55.105 1.496 -0.597 -1.364 O5D UGA 21
UGA C5D C5* C 0 1 N N N -12.428 16.273 55.128 1.993 0.226 -2.421 C5D UGA 22
UGA C4D C4* C 0 1 N N R -10.922 16.375 54.974 1.931 -0.545 -3.740 C4D UGA 23
UGA O4D O4* O 0 1 N N N -10.588 16.739 53.602 0.568 -0.880 -4.047 O4D UGA 24
UGA C3D C3* C 0 1 N N S -10.363 17.471 55.875 2.458 0.337 -4.889 C3D UGA 25
UGA O3D O3* O 0 1 N N N -9.106 17.031 56.418 3.592 -0.267 -5.513 O3D UGA 26
UGA C2D C2* C 0 1 N N R -10.195 18.656 54.924 1.268 0.413 -5.881 C2D UGA 27
UGA O2D O2* O 0 1 N N N -9.130 19.545 55.349 1.724 0.311 -7.231 O2D UGA 28
UGA C1D C1* C 0 1 N N R -9.827 17.973 53.610 0.434 -0.830 -5.483 C1D UGA 29
UGA N1 N1 N 0 1 Y N N -10.181 18.878 52.514 -0.969 -0.657 -5.865 N1 UGA 30
UGA C6 C6 C 0 1 Y N N -11.505 19.106 52.200 -1.574 -1.588 -6.664 C6 UGA 31
UGA C2 C2 C 0 1 Y N N -9.161 19.512 51.826 -1.653 0.413 -5.421 C2 UGA 32
UGA O2 O2 O 0 1 N N N -7.966 19.331 52.061 -1.096 1.228 -4.711 O2 UGA 33
UGA N3 N3 N 0 1 Y N N -9.581 20.371 50.833 -2.943 0.599 -5.760 N3 UGA 34
UGA C4 C4 C 0 1 Y N N -10.886 20.652 50.475 -3.575 -0.295 -6.546 C4 UGA 35
UGA O4 O4 O 0 1 N N N -11.124 21.476 49.593 -4.743 -0.129 -6.849 O4 UGA 36
UGA C5 C5 C 0 1 Y N N -11.872 19.945 51.230 -2.868 -1.428 -7.015 C5 UGA 37
UGA "H1'1" "1H1'" H 0 0 N N N -15.914 14.703 55.275 1.609 1.059 4.784 "H1'1" UGA 38
UGA "H2'1" "1H2'" H 0 0 N N N -17.854 14.131 53.855 1.091 0.215 7.069 "H2'1" UGA 39
UGA "HO'2" "2HO'" H 0 0 N N N -18.563 16.316 53.482 2.936 -0.544 5.939 "HO'2" UGA 40
UGA "H3'1" "1H3'" H 0 0 N N N -19.580 15.475 56.029 -0.173 -2.141 5.594 "H3'1" UGA 41
UGA "HO'3" "3HO'" H 0 0 N N N -21.271 14.679 54.619 0.816 -2.572 7.618 "HO'3" UGA 42
UGA "H4'1" "1H4'" H 0 0 N N N -19.324 12.498 55.169 -1.495 0.042 7.269 "H4'1" UGA 43
UGA "HO'4" "4HO'" H 0 0 N N N -20.806 12.286 56.920 -3.378 -0.952 6.416 "HO'4" UGA 44
UGA "H5'1" "1H5'" H 0 0 N N N -18.595 14.032 57.746 -1.470 -0.416 4.252 "H5'1" UGA 45
UGA "HO'6" "6HO'" H 0 0 N N N -17.960 10.941 59.261 -4.820 0.847 5.090 "HO'6" UGA 46
UGA HOB2 2HOB H 0 0 N N N -16.774 17.701 58.578 -0.632 1.368 2.206 HOB2 UGA 47
UGA HOA2 2HOA H 0 0 N N N -15.216 17.278 53.499 -0.210 1.313 -0.327 HOA2 UGA 48
UGA H5A1 1H5* H 0 0 N N N -12.707 15.703 56.044 1.384 1.126 -2.497 H5A1 UGA 49
UGA "H5'2" 2H5* H 0 0 N N N -12.872 15.595 54.362 3.026 0.503 -2.210 "H5'2" UGA 50
UGA H4A1 1H4* H 0 0 N N N -10.486 15.385 55.246 2.529 -1.453 -3.667 H4A1 UGA 51
UGA H3A1 1H3* H 0 0 N N N -11.007 17.731 56.746 2.712 1.331 -4.520 H3A1 UGA 52
UGA HOA3 3HO* H 0 0 N N N -8.757 17.713 56.979 3.837 0.299 -6.258 HOA3 UGA 53
UGA H2A1 1H2* H 0 0 N N N -11.105 19.297 54.867 0.696 1.329 -5.734 H2A1 UGA 54
UGA HOC2 2HO* H 0 0 N N N -9.025 20.281 54.758 2.234 1.112 -7.415 HOC2 UGA 55
UGA H1A1 1H1* H 0 0 N N N -8.742 17.742 53.494 0.846 -1.730 -5.939 H1A1 UGA 56
UGA H61 1H6 H 0 1 N N N -12.310 18.592 52.751 -1.019 -2.446 -7.013 H61 UGA 57
UGA HN3 HN3 H 0 1 N N N -8.848 20.849 50.307 -3.420 1.378 -5.434 HN3 UGA 58
UGA H51 1H5 H 0 1 N N N -12.956 20.050 51.057 -3.358 -2.155 -7.646 H51 UGA 59
# #
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
UGA "C1'" "C2'" SING N N 1
UGA "C1'" "O5'" SING N N 2
UGA "C1'" O3B SING N N 3
UGA "C1'" "H1'1" SING N N 4
UGA "C2'" "O2'" SING N N 5
UGA "C2'" "C3'" SING N N 6
UGA "C2'" "H2'1" SING N N 7
UGA "O2'" "HO'2" SING N N 8
UGA "C3'" "O3'" SING N N 9
UGA "C3'" "C4'" SING N N 10
UGA "C3'" "H3'1" SING N N 11
UGA "O3'" "HO'3" SING N N 12
UGA "C4'" "O4'" SING N N 13
UGA "C4'" "C5'" SING N N 14
UGA "C4'" "H4'1" SING N N 15
UGA "O4'" "HO'4" SING N N 16
UGA "C5'" "O5'" SING N N 17
UGA "C5'" "C6'" SING N N 18
UGA "C5'" "H5'1" SING N N 19
UGA "C6'" "O'P" DOUB N N 20
UGA "C6'" "O'Q" SING N N 21
UGA "O'Q" "HO'6" SING N N 22
UGA PB O1B DOUB N N 23
UGA PB O2B SING N N 24
UGA PB O3B SING N N 25
UGA PB O3A SING N N 26
UGA O2B HOB2 SING N N 27
UGA O3A PA SING N N 28
UGA PA O1A DOUB N N 29
UGA PA O2A SING N N 30
UGA PA O5D SING N N 31
UGA O2A HOA2 SING N N 32
UGA O5D C5D SING N N 33
UGA C5D C4D SING N N 34
UGA C5D H5A1 SING N N 35
UGA C5D "H5'2" SING N N 36
UGA C4D O4D SING N N 37
UGA C4D C3D SING N N 38
UGA C4D H4A1 SING N N 39
UGA O4D C1D SING N N 40
UGA C3D O3D SING N N 41
UGA C3D C2D SING N N 42
UGA C3D H3A1 SING N N 43
UGA O3D HOA3 SING N N 44
UGA C2D O2D SING N N 45
UGA C2D C1D SING N N 46
UGA C2D H2A1 SING N N 47
UGA O2D HOC2 SING N N 48
UGA C1D N1 SING N N 49
UGA C1D H1A1 SING N N 50
UGA N1 C6 SING Y N 51
UGA N1 C2 SING Y N 52
UGA C6 C5 DOUB Y N 53
UGA C6 H61 SING N N 54
UGA C2 O2 DOUB N N 55
UGA C2 N3 SING Y N 56
UGA N3 C4 SING Y N 57
UGA N3 HN3 SING N N 58
UGA C4 O4 DOUB N N 59
UGA C4 C5 SING Y N 60
UGA C5 H51 SING N N 61
# #
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
UGA SMILES ACDLabs 10.04 "O=C(O)C3OC(OP(=O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(O)C2O)C(O)C(O)C3O"
UGA SMILES_CANONICAL CACTVS 3.341 "O[C@@H]1[C@@H](O)[C@H](O[C@@H]([C@H]1O)C(O)=O)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"
UGA SMILES CACTVS 3.341 "O[CH]1[CH](O)[CH](O[CH]([CH]1O)C(O)=O)O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O"
UGA SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "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)C(=O)O)O)O)O)O)O"
UGA SMILES "OpenEye OEToolkits" 1.5.0 "C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OC3C(C(C(C(O3)C(=O)O)O)O)O)O)O"
UGA InChI InChI 1.03 "InChI=1S/C15H22N2O18P2/c18-5-1-2-17(15(26)16-5)12-9(22)6(19)4(32-12)3-31-36(27,28)35-37(29,30)34-14-10(23)7(20)8(21)11(33-14)13(24)25/h1-2,4,6-12,14,19-23H,3H2,(H,24,25)(H,27,28)(H,29,30)(H,16,18,26)/t4-,6-,7+,8+,9-,10-,11+,12-,14-/m1/s1"
UGA InChIKey InChI 1.03 HDYANYHVCAPMJV-LXQIFKJMSA-N
# #
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
UGA "SYSTEMATIC NAME" ACDLabs 10.04 "(2S,3S,4S,5R,6R)-6-{[(S)-{[(R)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-3,4,5-trihydroxytetrahydro-2H-pyran-2-carboxylic acid (non-preferred name)"
UGA "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2S,3S,4S,5R,6R)-6-[[[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxy-3,4,5-trihydroxy-oxane-2-carboxylic 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
UGA "Create component" 1999-12-13 RCSB
UGA "Modify descriptor" 2011-06-04 RCSB
UGA "Modify synonyms" 2021-03-01 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id UGA
_pdbx_chem_comp_synonyms.name "UDP-GLUCURONIC ACID"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
##