data_UD2 # _chem_comp.id UD2 _chem_comp.name URIDINE-DIPHOSPHATE-N-ACETYLGALACTOSAMINE _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C17 H27 N3 O17 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ;(2R,3R,4R,5R,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate ; _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2001-02-21 _chem_comp.pdbx_modified_date 2020-06-17 _chem_comp.pdbx_ambiguous_flag ? _chem_comp.pdbx_release_status REL _chem_comp.pdbx_replaced_by ? _chem_comp.pdbx_replaces ? _chem_comp.formula_weight 607.354 _chem_comp.one_letter_code ? _chem_comp.three_letter_code UD2 _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 1OMZ _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 UD2 "C1'" "C1'" C 0 1 N N R -21.840 -55.954 -41.771 4.577 0.429 -0.412 "C1'" UD2 1 UD2 "C2'" "C2'" C 0 1 N N R -22.855 -56.648 -40.824 5.330 0.789 0.871 "C2'" UD2 2 UD2 "C3'" "C3'" C 0 1 N N R -23.963 -57.332 -41.660 4.496 1.788 1.679 "C3'" UD2 3 UD2 "C4'" "C4'" C 0 1 N N R -24.679 -56.265 -42.531 4.208 3.016 0.811 "C4'" UD2 4 UD2 "C5'" "C5'" C 0 1 N N R -23.627 -55.592 -43.464 3.498 2.570 -0.470 "C5'" UD2 5 UD2 "C6'" "C6'" C 0 1 N N N -24.204 -54.489 -44.350 3.260 3.784 -1.370 "C6'" UD2 6 UD2 "C7'" "C7'" C 0 1 N N N -21.395 -57.257 -38.911 6.614 -1.209 1.416 "C7'" UD2 7 UD2 "C8'" "C8'" C 0 1 N N N -21.163 -58.317 -37.842 6.840 -2.454 2.233 "C8'" UD2 8 UD2 "N2'" "N2'" N 0 1 N N N -22.149 -57.621 -39.965 5.549 -0.422 1.666 "N2'" UD2 9 UD2 "O1'" "O1'" O 0 1 N N N -20.989 -56.938 -42.384 3.342 -0.207 -0.078 "O1'" UD2 10 UD2 "O3'" "O3'" O 0 1 N N N -24.901 -57.956 -40.798 5.224 2.186 2.843 "O3'" UD2 11 UD2 "O4'" "O4'" O 0 1 N N N -25.295 -55.274 -41.693 5.437 3.663 0.476 "O4'" UD2 12 UD2 "O5'" "O5'" O 0 1 N N N -22.515 -55.015 -42.683 4.313 1.619 -1.158 "O5'" UD2 13 UD2 "O6'" "O6'" O 0 1 N N N -23.546 -54.430 -45.610 2.497 3.389 -2.512 "O6'" UD2 14 UD2 "O7'" "O7'" O 0 1 N N N -20.885 -56.129 -38.777 7.391 -0.914 0.532 "O7'" UD2 15 UD2 N1 N1 N 0 1 N N N -24.294 -60.063 -48.284 -5.477 1.043 0.383 N1 UD2 16 UD2 C2 C2 C 0 1 N N N -25.218 -60.200 -49.343 -6.056 1.956 1.183 C2 UD2 17 UD2 N3 N3 N 0 1 N N N -24.855 -59.492 -50.500 -6.384 3.176 0.718 N3 UD2 18 UD2 C4 C4 C 0 1 N N N -23.699 -58.694 -50.685 -6.133 3.503 -0.566 C4 UD2 19 UD2 C5 C5 C 0 1 N N N -22.811 -58.610 -49.547 -5.523 2.552 -1.419 C5 UD2 20 UD2 C6 C6 C 0 1 N N N -23.120 -59.272 -48.422 -5.201 1.338 -0.925 C6 UD2 21 UD2 O2 O2 O 0 1 N N N -26.246 -60.869 -49.273 -6.288 1.675 2.343 O2 UD2 22 UD2 O4 O4 O 0 1 N N N -23.498 -58.130 -51.747 -6.429 4.607 -0.988 O4 UD2 23 UD2 C1B C1* C 0 1 N N R -24.595 -60.780 -47.012 -5.132 -0.276 0.918 C1B UD2 24 UD2 C2B C2* C 0 1 N N R -23.456 -61.744 -46.672 -5.967 -1.382 0.224 C2B UD2 25 UD2 "O2'" O2* O 0 1 N N N -23.578 -63.019 -47.276 -7.226 -1.556 0.877 "O2'" UD2 26 UD2 C3B C3* C 0 1 N N S -23.463 -61.792 -45.152 -5.071 -2.631 0.410 C3B UD2 27 UD2 C4B C4* C 0 1 N N R -24.008 -60.427 -44.741 -3.667 -2.052 0.669 C4B UD2 28 UD2 O4B O4* O 0 1 N N N -24.699 -59.859 -45.902 -3.771 -0.622 0.581 O4B UD2 29 UD2 O3B O3* O 0 1 N N N -24.318 -62.812 -44.594 -5.511 -3.398 1.532 O3B UD2 30 UD2 C5B C5* C 0 1 N N N -22.901 -59.489 -44.304 -2.688 -2.569 -0.388 C5B UD2 31 UD2 O5B O5* O 0 1 N N N -21.944 -59.321 -45.336 -1.368 -2.122 -0.073 O5B UD2 32 UD2 PA PA P 0 1 N N S -20.393 -59.122 -45.021 -0.083 -2.481 -0.975 PA UD2 33 UD2 O1A O1A O 0 1 N N N -19.947 -59.871 -43.811 0.177 -4.069 -0.930 O1A UD2 34 UD2 O2A O2A O 0 1 N N N -19.612 -59.327 -46.241 -0.328 -2.060 -2.372 O2A UD2 35 UD2 O3A O3A O 0 1 N N N -20.222 -57.590 -44.680 1.208 -1.709 -0.400 O3A UD2 36 UD2 PB PB P 0 1 N N R -19.783 -56.724 -43.442 2.638 -1.306 -1.021 PB UD2 37 UD2 O1B O1B O 0 1 N N N -18.642 -57.385 -42.803 3.572 -2.615 -1.110 O1B UD2 38 UD2 O2B O2B O 0 1 N N N -19.775 -55.288 -43.869 2.447 -0.744 -2.376 O2B UD2 39 UD2 "H1'" "H1'" H 0 1 N N N -21.158 -55.307 -41.200 5.184 -0.249 -1.012 "H1'" UD2 40 UD2 "H2'" "H2'" H 0 1 N N N -23.331 -55.900 -40.173 6.290 1.236 0.616 "H2'" UD2 41 UD2 "H3'" "H3'" H 0 1 N N N -23.513 -58.096 -42.310 3.557 1.322 1.978 "H3'" UD2 42 UD2 "H4'" "H4'" H 0 1 N N N -25.462 -56.746 -43.135 3.570 3.709 1.360 "H4'" UD2 43 UD2 "H5'" "H5'" H 0 1 N N N -23.271 -56.403 -44.116 2.542 2.113 -0.216 "H5'" UD2 44 UD2 "H6'1" "1H6'" H 0 0 N N N -24.078 -53.523 -43.839 2.714 4.547 -0.815 "H6'1" UD2 45 UD2 "H6'2" "2H6'" H 0 0 N N N -25.267 -54.709 -44.526 4.219 4.188 -1.696 "H6'2" UD2 46 UD2 "H8'1" "1H8'" H 0 0 N N N -21.107 -59.309 -38.314 7.743 -2.957 1.888 "H8'1" UD2 47 UD2 "H8'2" "2H8'" H 0 0 N N N -20.219 -58.107 -37.317 6.952 -2.184 3.283 "H8'2" UD2 48 UD2 "H8'3" "3H8'" H 0 0 N N N -21.995 -58.300 -37.123 5.986 -3.123 2.120 "H8'3" UD2 49 UD2 "HN2'" "HN2'" H 0 0 N N N -22.235 -58.595 -40.176 4.927 -0.658 2.372 "HN2'" UD2 50 UD2 "HO3'" "HO3'" H 0 0 N N N -24.505 -58.095 -39.946 4.754 2.819 3.403 "HO3'" UD2 51 UD2 "HO4'" "HO4'" H 0 0 N N N -25.431 -55.633 -40.824 5.330 4.451 -0.075 "HO4'" UD2 52 UD2 "HO6'" "HO6'" H 0 0 N N N -24.193 -54.417 -46.305 2.308 4.110 -3.128 "HO6'" UD2 53 UD2 HN3 HN3 H 0 1 N N N -25.480 -59.558 -51.278 -6.802 3.822 1.308 HN3 UD2 54 UD2 H5 H5 H 0 1 N N N -21.908 -58.020 -49.602 -5.315 2.796 -2.450 H5 UD2 55 UD2 H6 H6 H 0 1 N N N -22.446 -59.201 -47.581 -4.734 0.600 -1.561 H6 UD2 56 UD2 H1B H1* H 0 1 N N N -25.547 -61.311 -47.161 -5.281 -0.303 1.997 H1B UD2 57 UD2 H2B H2* H 0 1 N N N -22.494 -61.396 -47.076 -6.107 -1.158 -0.834 H2B UD2 58 UD2 "HO2'" HO2* H 0 0 N N N -23.605 -62.921 -48.221 -7.785 -2.237 0.479 "HO2'" UD2 59 UD2 H3B H3* H 0 1 N N N -22.453 -62.026 -44.785 -5.073 -3.240 -0.494 H3B UD2 60 UD2 H4B H4* H 0 1 N N N -24.689 -60.551 -43.886 -3.325 -2.341 1.663 H4B UD2 61 UD2 HO3A HO3* H 0 0 N N N -24.506 -63.466 -45.257 -6.412 -3.738 1.448 HO3A UD2 62 UD2 "H5'1" 1H5* H 0 0 N N N -22.403 -59.911 -43.419 -2.710 -3.659 -0.401 "H5'1" UD2 63 UD2 "H5'2" 2H5* H 0 0 N N N -23.342 -58.509 -44.069 -2.977 -2.188 -1.367 "H5'2" UD2 64 UD2 HOA2 HO1A H 0 0 N N N -19.852 -60.792 -44.025 0.346 -4.415 -0.043 HOA2 UD2 65 UD2 HOB2 HO1B H 0 0 N N N -17.957 -57.528 -43.446 3.740 -3.036 -0.256 HOB2 UD2 66 # # 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 UD2 O4 C4 DOUB N N 1 UD2 C4 N3 SING N N 2 UD2 C4 C5 SING N N 3 UD2 N3 C2 SING N N 4 UD2 C5 C6 DOUB N N 5 UD2 C2 O2 DOUB N N 6 UD2 C2 N1 SING N N 7 UD2 C6 N1 SING N N 8 UD2 N1 C1B SING N N 9 UD2 "O2'" C2B SING N N 10 UD2 C1B C2B SING N N 11 UD2 C1B O4B SING N N 12 UD2 C2B C3B SING N N 13 UD2 O2A PA DOUB N N 14 UD2 O4B C4B SING N N 15 UD2 "O6'" "C6'" SING N N 16 UD2 O5B PA SING N N 17 UD2 O5B C5B SING N N 18 UD2 C3B C4B SING N N 19 UD2 C3B O3B SING N N 20 UD2 PA O3A SING N N 21 UD2 PA O1A SING N N 22 UD2 C4B C5B SING N N 23 UD2 O3A PB SING N N 24 UD2 "C6'" "C5'" SING N N 25 UD2 O2B PB DOUB N N 26 UD2 "C5'" "O5'" SING N N 27 UD2 "C5'" "C4'" SING N N 28 UD2 PB O1B SING N N 29 UD2 PB "O1'" SING N N 30 UD2 "O5'" "C1'" SING N N 31 UD2 "C4'" "O4'" SING N N 32 UD2 "C4'" "C3'" SING N N 33 UD2 "O1'" "C1'" SING N N 34 UD2 "C1'" "C2'" SING N N 35 UD2 "C3'" "C2'" SING N N 36 UD2 "C3'" "O3'" SING N N 37 UD2 "C2'" "N2'" SING N N 38 UD2 "N2'" "C7'" SING N N 39 UD2 "C7'" "O7'" DOUB N N 40 UD2 "C7'" "C8'" SING N N 41 UD2 "C1'" "H1'" SING N N 42 UD2 "C2'" "H2'" SING N N 43 UD2 "C3'" "H3'" SING N N 44 UD2 "C4'" "H4'" SING N N 45 UD2 "C5'" "H5'" SING N N 46 UD2 "C6'" "H6'1" SING N N 47 UD2 "C6'" "H6'2" SING N N 48 UD2 "C8'" "H8'1" SING N N 49 UD2 "C8'" "H8'2" SING N N 50 UD2 "C8'" "H8'3" SING N N 51 UD2 "N2'" "HN2'" SING N N 52 UD2 "O3'" "HO3'" SING N N 53 UD2 "O4'" "HO4'" SING N N 54 UD2 "O6'" "HO6'" SING N N 55 UD2 N3 HN3 SING N N 56 UD2 C5 H5 SING N N 57 UD2 C6 H6 SING N N 58 UD2 C1B H1B SING N N 59 UD2 C2B H2B SING N N 60 UD2 "O2'" "HO2'" SING N N 61 UD2 C3B H3B SING N N 62 UD2 C4B H4B SING N N 63 UD2 O3B HO3A SING N N 64 UD2 C5B "H5'1" SING N N 65 UD2 C5B "H5'2" SING N N 66 UD2 O1A HOA2 SING N N 67 UD2 O1B HOB2 SING N N 68 # # 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 UD2 SMILES ACDLabs 10.04 "O=P(OC1OC(C(O)C(O)C1NC(=O)C)CO)(O)OP(=O)(O)OCC3OC(N2C=CC(=O)NC2=O)C(O)C3O" UD2 SMILES_CANONICAL CACTVS 3.341 "CC(=O)N[C@@H]1[C@@H](O)[C@@H](O)[C@@H](CO)O[C@@H]1O[P@](O)(=O)O[P@](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O" UD2 SMILES CACTVS 3.341 "CC(=O)N[CH]1[CH](O)[CH](O)[CH](CO)O[CH]1O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O" UD2 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC(=O)N[C@@H]1[C@H]([C@H]([C@H](O[C@@H]1O[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=O)NC3=O)O)O)CO)O)O" UD2 SMILES "OpenEye OEToolkits" 1.5.0 "CC(=O)NC1C(C(C(OC1OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=O)NC3=O)O)O)CO)O)O" UD2 InChI InChI 1.03 "InChI=1S/C17H27N3O17P2/c1-6(22)18-10-13(26)11(24)7(4-21)35-16(10)36-39(31,32)37-38(29,30)33-5-8-12(25)14(27)15(34-8)20-3-2-9(23)19-17(20)28/h2-3,7-8,10-16,21,24-27H,4-5H2,1H3,(H,18,22)(H,29,30)(H,31,32)(H,19,23,28)/t7-,8-,10-,11+,12-,13-,14-,15-,16-/m1/s1" UD2 InChIKey InChI 1.03 LFTYTUAZOPRMMI-NESSUJCYSA-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 UD2 "SYSTEMATIC NAME" ACDLabs 10.04 "(2R,3R,4R,5R,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)" UD2 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[[(2R,3R,4R,5R,6R)-3-acetamido-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-hydroxy-phosphoryl] [(2R,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl 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 UD2 "Create component" 2001-02-21 RCSB UD2 "Modify descriptor" 2011-06-04 RCSB UD2 "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id UD2 _pdbx_chem_comp_synonyms.name "(2R,3R,4R,5R,6R)-3-(acetylamino)-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##