data_GDU # _chem_comp.id GDU _chem_comp.name "GALACTOSE-URIDINE-5'-DIPHOSPHATE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type ATOMS _chem_comp.formula "C15 H24 N2 O17 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms UDP-D-GALACTOPYRANOSE _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-08 _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 566.302 _chem_comp.one_letter_code ? _chem_comp.three_letter_code GDU _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 1GUP _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # # 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 GDU N1 N1 N 0 1 N N N -4.190 -9.628 156.134 0.863 -0.669 5.783 N1 GDU 1 GDU C2 C2 C 0 1 N N N -5.510 -9.860 156.451 1.592 0.378 5.358 C2 GDU 2 GDU N3 N3 N 0 1 N N N -6.065 -10.955 155.859 2.872 0.532 5.745 N3 GDU 3 GDU C4 C4 C 0 1 N N N -5.466 -11.822 154.957 3.449 -0.371 6.561 C4 GDU 4 GDU C5 C5 C 0 1 N N N -4.095 -11.515 154.703 2.695 -1.482 7.012 C5 GDU 5 GDU C6 C6 C 0 1 N N N -3.512 -10.481 155.269 1.412 -1.610 6.612 C6 GDU 6 GDU O2 O2 O 0 1 N N N -6.156 -9.185 157.200 1.085 1.201 4.622 O2 GDU 7 GDU O4 O4 O 0 1 N N N -6.143 -12.742 154.506 4.609 -0.235 6.908 O4 GDU 8 GDU C1D C1* C 0 1 N N R -3.495 -8.478 156.729 -0.528 -0.809 5.349 C1D GDU 9 GDU C2D C2* C 0 1 N N R -2.165 -8.841 157.367 -1.344 0.460 5.705 C2D GDU 10 GDU O2D O2* O 0 1 N N N -2.299 -9.525 158.654 -1.854 0.381 7.038 O2D GDU 11 GDU C3D C3* C 0 1 N N S -1.401 -7.474 157.399 -2.496 0.407 4.668 C3D GDU 12 GDU C4D C4* C 0 1 N N R -2.084 -6.710 156.275 -1.950 -0.498 3.548 C4D GDU 13 GDU O4D O4* O 0 1 N N N -3.145 -7.541 155.745 -0.608 -0.868 3.909 O4D GDU 14 GDU O3D O3* O 0 1 N N N -1.557 -6.694 158.596 -3.669 -0.162 5.253 O3D GDU 15 GDU C5D C5* C 0 1 N N N -1.215 -6.035 155.234 -1.940 0.263 2.221 C5D GDU 16 GDU O5D O5* O 0 1 N N N -1.017 -4.635 155.581 -1.425 -0.581 1.190 O5D GDU 17 GDU PA PA P 0 1 N N R 0.448 -3.932 155.456 -1.444 0.279 -0.169 PA GDU 18 GDU O1A O1A O 0 1 N N N 0.938 -3.981 154.049 -2.832 0.692 -0.473 O1A GDU 19 GDU O2A O2A O 0 1 N N N 0.462 -2.499 155.839 -0.522 1.587 0.010 O2A GDU 20 GDU O3A O3A O 0 1 N N N 1.535 -4.658 156.496 -0.874 -0.616 -1.380 O3A GDU 21 GDU PB PB P 0 1 N N S 1.514 -5.563 157.793 -0.921 0.302 -2.701 PB GDU 22 GDU O1B O1B O 0 1 N N N 0.306 -5.237 158.610 -2.317 0.715 -2.965 O1B GDU 23 GDU O2B O2B O 0 1 N N N 1.565 -7.044 157.508 -0.008 1.610 -2.478 O2B GDU 24 GDU O3B O3B O 0 1 N N N 2.882 -5.263 158.629 -0.361 -0.534 -3.957 O3B GDU 25 GDU "C1'" "C1'" C 0 1 N N R 3.544 -4.005 158.412 -0.428 0.329 -5.093 "C1'" GDU 26 GDU "C2'" "C2'" C 0 1 N N R 4.935 -4.060 159.028 -0.656 -0.506 -6.354 "C2'" GDU 27 GDU "C3'" "C3'" C 0 1 N N S 4.860 -4.413 160.500 0.493 -1.508 -6.503 "C3'" GDU 28 GDU "C4'" "C4'" C 0 1 N N R 4.159 -3.255 161.204 1.820 -0.742 -6.459 "C4'" GDU 29 GDU "C5'" "C5'" C 0 1 N N R 2.785 -3.078 160.511 1.861 0.110 -5.188 "C5'" GDU 30 GDU "C6'" "C6'" C 0 1 N N N 1.986 -1.877 160.984 3.197 0.853 -5.117 "C6'" GDU 31 GDU "O2'" "O2'" O 0 1 N N N 5.797 -5.026 158.418 -1.895 -1.209 -6.245 "O2'" GDU 32 GDU "O3'" "O3'" O 0 1 N N N 6.222 -4.533 160.919 0.373 -2.194 -7.751 "O3'" GDU 33 GDU "O4'" "O4'" O 0 1 N N N 4.864 -2.025 161.064 1.924 0.100 -7.608 "O4'" GDU 34 GDU "O5'" "O5'" O 0 1 N N N 2.850 -2.940 159.056 0.793 1.056 -5.208 "O5'" GDU 35 GDU "O6'" "O6'" O 0 1 N N N 2.658 -0.655 160.668 3.237 1.647 -3.930 "O6'" GDU 36 GDU HN3 HN3 H 0 1 N N N -7.032 -11.146 156.118 3.382 1.296 5.432 HN3 GDU 37 GDU H5 H5 H 0 1 N N N -3.451 -12.109 154.032 3.141 -2.216 7.666 H5 GDU 38 GDU H6 H6 H 0 1 N N N -2.449 -10.328 155.017 0.821 -2.450 6.946 H6 GDU 39 GDU H1D H1* H 0 1 N N N -4.214 -8.087 157.486 -0.981 -1.694 5.795 H1D GDU 40 GDU H2D H2* H 0 1 N N N -1.593 -9.609 156.795 -0.741 1.359 5.573 H2D GDU 41 GDU "HO2'" *HO2 H 0 0 N N N -1.467 -9.752 159.053 -2.349 1.197 7.196 "HO2'" GDU 42 GDU H3D H3* H 0 1 N N N -0.303 -7.654 157.321 -2.709 1.404 4.283 H3D GDU 43 GDU H4D H4* H 0 1 N N N -2.508 -5.787 156.734 -2.568 -1.391 3.458 H4D GDU 44 GDU "HO3'" *HO3 H 0 0 N N N -1.093 -5.864 158.615 -3.927 0.417 5.983 "HO3'" GDU 45 GDU "H5'1" 1H5* H 0 0 N N N -0.247 -6.569 155.087 -1.310 1.147 2.314 "H5'1" GDU 46 GDU "H5'2" 2H5* H 0 0 N N N -1.626 -6.156 154.204 -2.956 0.566 1.969 "H5'2" GDU 47 GDU HOA2 2HOA H 0 0 N N N 1.316 -2.089 155.766 0.370 1.274 0.206 HOA2 GDU 48 GDU HOB2 2HOB H 0 0 N N N 1.552 -7.587 158.287 0.891 1.297 -2.309 HOB2 GDU 49 GDU "H1'" "H1'" H 0 1 N N N 3.580 -3.826 157.312 -1.255 1.029 -4.967 "H1'" GDU 50 GDU "H2'" "H2'" H 0 1 N N N 5.356 -3.041 158.863 -0.684 0.148 -7.225 "H2'" GDU 51 GDU "H3'" "H3'" H 0 1 N N N 4.299 -5.350 160.723 0.458 -2.229 -5.686 "H3'" GDU 52 GDU "H4'" "H4'" H 0 1 N N N 4.086 -3.491 162.291 2.649 -1.449 -6.448 "H4'" GDU 53 GDU "H5'" "H5'" H 0 1 N N N 2.284 -4.030 160.802 1.757 -0.534 -4.316 "H5'" GDU 54 GDU "H6'1" "1H6'" H 0 0 N N N 0.946 -1.890 160.580 3.301 1.498 -5.989 "H6'1" GDU 55 GDU "H6'2" "2H6'" H 0 0 N N N 1.747 -1.945 162.071 4.013 0.131 -5.099 "H6'2" GDU 56 GDU HO2A "'HO2" H 0 0 N N N 6.665 -5.060 158.802 -2.587 -0.541 -6.146 HO2A GDU 57 GDU HO3A "'HO3" H 0 0 N N N 6.175 -4.754 161.841 -0.478 -2.650 -7.739 HO3A GDU 58 GDU "HO4'" "'HO4" H 0 0 N N N 4.427 -1.304 161.502 1.888 -0.477 -8.382 "HO4'" GDU 59 GDU "HO6'" "'HO6" H 0 0 N N N 2.158 0.096 160.964 4.093 2.097 -3.923 "HO6'" GDU 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 GDU N1 C2 SING N N 1 GDU N1 C6 SING N N 2 GDU N1 C1D SING N N 3 GDU C2 N3 SING N N 4 GDU C2 O2 DOUB N N 5 GDU N3 C4 SING N N 6 GDU N3 HN3 SING N N 7 GDU C4 C5 SING N N 8 GDU C4 O4 DOUB N N 9 GDU C5 C6 DOUB N N 10 GDU C5 H5 SING N N 11 GDU C6 H6 SING N N 12 GDU C1D C2D SING N N 13 GDU C1D O4D SING N N 14 GDU C1D H1D SING N N 15 GDU C2D O2D SING N N 16 GDU C2D C3D SING N N 17 GDU C2D H2D SING N N 18 GDU O2D "HO2'" SING N N 19 GDU C3D C4D SING N N 20 GDU C3D O3D SING N N 21 GDU C3D H3D SING N N 22 GDU C4D O4D SING N N 23 GDU C4D C5D SING N N 24 GDU C4D H4D SING N N 25 GDU O3D "HO3'" SING N N 26 GDU C5D O5D SING N N 27 GDU C5D "H5'1" SING N N 28 GDU C5D "H5'2" SING N N 29 GDU O5D PA SING N N 30 GDU PA O1A DOUB N N 31 GDU PA O2A SING N N 32 GDU PA O3A SING N N 33 GDU O2A HOA2 SING N N 34 GDU O3A PB SING N N 35 GDU PB O1B DOUB N N 36 GDU PB O2B SING N N 37 GDU PB O3B SING N N 38 GDU O2B HOB2 SING N N 39 GDU O3B "C1'" SING N N 40 GDU "C1'" "C2'" SING N N 41 GDU "C1'" "O5'" SING N N 42 GDU "C1'" "H1'" SING N N 43 GDU "C2'" "C3'" SING N N 44 GDU "C2'" "O2'" SING N N 45 GDU "C2'" "H2'" SING N N 46 GDU "C3'" "C4'" SING N N 47 GDU "C3'" "O3'" SING N N 48 GDU "C3'" "H3'" SING N N 49 GDU "C4'" "C5'" SING N N 50 GDU "C4'" "O4'" SING N N 51 GDU "C4'" "H4'" SING N N 52 GDU "C5'" "C6'" SING N N 53 GDU "C5'" "O5'" SING N N 54 GDU "C5'" "H5'" SING N N 55 GDU "C6'" "O6'" SING N N 56 GDU "C6'" "H6'1" SING N N 57 GDU "C6'" "H6'2" SING N N 58 GDU "O2'" HO2A SING N N 59 GDU "O3'" HO3A SING N N 60 GDU "O4'" "HO4'" SING N N 61 GDU "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 GDU SMILES ACDLabs 10.04 "O=P(OC1OC(C(O)C(O)C1O)CO)(O)OP(=O)(O)OCC3OC(N2C=CC(=O)NC2=O)C(O)C3O" GDU SMILES_CANONICAL CACTVS 3.341 "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" GDU SMILES CACTVS 3.341 "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" GDU 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)CO)O)O)O)O)O" GDU 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)CO)O)O)O)O)O" GDU 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" GDU InChIKey InChI 1.03 HSCJRCZFDFQWRP-ABVWGUQPSA-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 GDU "SYSTEMATIC NAME" ACDLabs 10.04 "[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl dihydrogen diphosphate (non-preferred name)" GDU "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [hydroxy-[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-phosphoryl] 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 GDU "Create component" 1999-07-08 PDBJ GDU "Modify descriptor" 2011-06-04 RCSB GDU "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id GDU _pdbx_chem_comp_synonyms.name UDP-D-GALACTOPYRANOSE _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##