data_A1BCU # _chem_comp.id A1BCU _chem_comp.name "(2R,3R,4R)-3,4-dihydroxy-5-oxooxan-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxyoxolan-2-yl]methyl dihydrogen diphosphate (non-preferred name)" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C14 H20 N2 O16 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms Uridine-diphosphate-4-keto-D-xylose _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2024-10-06 _chem_comp.pdbx_modified_date 2025-02-28 _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 534.260 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1BCU _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 9DH0 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _chem_comp.pdbx_pcm ? # 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_n_terminal_atom_flag _chem_comp_atom.pdbx_backbone_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 A1BCU N1 N1 N 0 1 N N N N N N 105.111 109.661 64.490 -5.490 -1.119 -0.155 N1 A1BCU 1 A1BCU C5 C1 C 0 1 N N N N N N 104.612 108.387 62.562 -6.212 -2.167 1.821 C5 A1BCU 2 A1BCU C6 C2 C 0 1 N N N N N N 104.354 109.484 63.305 -5.617 -1.122 1.207 C6 A1BCU 3 A1BCU N3 N2 N 0 1 N N N N N N 106.339 107.609 64.117 -6.544 -3.205 -0.302 N3 A1BCU 4 A1BCU C4 C3 C 0 1 N N N N N N 105.590 107.455 62.966 -6.694 -3.243 1.037 C4 A1BCU 5 A1BCU O4 O1 O 0 1 N N N N N N 105.798 106.471 62.275 -7.233 -4.197 1.569 O4 A1BCU 6 A1BCU C2 C4 C 0 1 N N N N N N 106.096 108.731 64.899 -5.951 -2.148 -0.888 C2 A1BCU 7 A1BCU O2 O2 O 0 1 N N N N N N 106.753 108.877 65.932 -5.832 -2.123 -2.098 O2 A1BCU 8 A1BCU "C1'" C5 C 0 1 N N R N N N 97.324 112.788 63.389 5.355 -0.401 -0.205 "C1'" A1BCU 9 A1BCU C1D C6 C 0 1 N N R N N N 104.842 110.854 65.320 -4.850 0.018 -0.822 C1D A1BCU 10 A1BCU "C2'" C7 C 0 1 N N R N N N 96.872 111.720 62.438 5.763 -1.262 -1.403 "C2'" A1BCU 11 A1BCU C2D C8 C 0 1 N N R N N N 104.904 112.123 64.496 -5.648 1.314 -0.560 C2D A1BCU 12 A1BCU "C3'" C9 C 0 1 N N R N N N 95.919 112.399 61.419 7.279 -1.495 -1.358 "C3'" A1BCU 13 A1BCU C3D C10 C 0 1 N N S N N N 104.111 113.093 65.401 -4.560 2.401 -0.409 C3D A1BCU 14 A1BCU "C4'" C11 C 0 1 N N N N N N 94.798 113.203 62.155 7.630 -2.020 0.019 "C4'" A1BCU 15 A1BCU C4D C12 C 0 1 N N R N N N 102.985 112.211 65.875 -3.233 1.632 -0.598 C4D A1BCU 16 A1BCU "C5'" C13 C 0 1 N N N N N N 95.294 114.217 63.138 7.073 -1.284 1.219 "C5'" A1BCU 17 A1BCU C5D C14 C 0 1 N N N N N N 101.804 112.434 64.953 -2.158 2.188 0.338 C5D A1BCU 18 A1BCU O1A O3 O 0 1 N N N N N N 101.841 112.294 61.141 0.714 3.339 0.783 O1A A1BCU 19 A1BCU O1B O4 O 0 1 N N N N N N 99.219 114.417 64.766 3.780 2.458 -0.526 O1B A1BCU 20 A1BCU "O2'" O5 O 0 1 N N N N N N 98.045 111.110 61.861 5.083 -2.518 -1.342 "O2'" A1BCU 21 A1BCU O2A O6 O 0 1 N N N N N N 100.027 111.431 62.703 0.277 1.459 2.410 O2A A1BCU 22 A1BCU O2B O7 O 0 1 N N N N N N 99.218 115.887 62.601 3.659 1.359 1.743 O2B A1BCU 23 A1BCU O2D O8 O 0 1 N N N N N N 106.253 112.498 64.346 -6.501 1.609 -1.668 O2D A1BCU 24 A1BCU "O3'" O9 O 0 1 N N N N N N 95.383 111.435 60.552 7.964 -0.264 -1.595 "O3'" A1BCU 25 A1BCU O3A O10 O 0 1 N N N N N N 100.634 113.995 62.637 1.671 1.073 0.214 O3A A1BCU 26 A1BCU O3B O11 O 0 1 N N N N N N 98.070 113.697 62.576 3.949 -0.152 -0.258 O3B A1BCU 27 A1BCU O3D O12 O 0 1 N N N N N N 104.900 113.467 66.533 -4.708 3.401 -1.419 O3D A1BCU 28 A1BCU "O4'" O13 O 0 1 N N N N N N 93.620 113.025 61.944 8.332 -2.994 0.155 "O4'" A1BCU 29 A1BCU O4D O14 O 0 1 N N N N N N 103.447 110.801 65.716 -3.546 0.266 -0.252 O4D A1BCU 30 A1BCU "O5'" O15 O 0 1 N N N N N N 96.223 113.525 63.995 5.671 -1.080 1.011 "O5'" A1BCU 31 A1BCU O5D O16 O 0 1 N N N N N N 102.162 112.212 63.601 -0.911 1.545 0.067 O5D A1BCU 32 A1BCU PA P1 P 0 1 N N N N N N 101.119 112.498 62.421 0.444 1.886 0.867 PA A1BCU 33 A1BCU PB P2 P 0 1 N N N N N N 99.203 114.475 63.283 3.273 1.188 0.324 PB A1BCU 34 A1BCU H1 H1 H 0 1 N N N N N N 104.063 108.221 61.647 -6.323 -2.180 2.895 H1 A1BCU 35 A1BCU H2 H2 H 0 1 N N N N N N 103.601 110.199 63.008 -5.243 -0.292 1.789 H2 A1BCU 36 A1BCU H3 H3 H 0 1 N N N N N N 107.032 106.936 64.378 -6.872 -3.938 -0.846 H3 A1BCU 37 A1BCU H4 H4 H 0 1 N N N N N N 97.963 112.346 64.168 5.892 0.547 -0.241 H4 A1BCU 38 A1BCU H5 H5 H 0 1 N N N N N N 105.518 110.909 66.186 -4.766 -0.169 -1.892 H5 A1BCU 39 A1BCU H6 H6 H 0 1 N N N N N N 96.298 110.965 62.996 5.500 -0.749 -2.327 H6 A1BCU 40 A1BCU H7 H7 H 0 1 N N N N N N 104.392 111.991 63.531 -6.229 1.225 0.358 H7 A1BCU 41 A1BCU H8 H8 H 0 1 N N N N N N 96.514 113.121 60.840 7.562 -2.227 -2.115 H8 A1BCU 42 A1BCU H9 H9 H 0 1 N N N N N N 103.740 113.957 64.830 -4.604 2.850 0.583 H9 A1BCU 43 A1BCU H10 H10 H 0 1 N N N N N N 102.719 112.432 66.919 -2.902 1.695 -1.635 H10 A1BCU 44 A1BCU H11 H11 H 0 1 N N N N N N 95.800 115.041 62.613 7.229 -1.878 2.119 H11 A1BCU 45 A1BCU H12 H12 H 0 1 N N N N N N 94.457 114.618 63.728 7.572 -0.320 1.323 H12 A1BCU 46 A1BCU H13 H13 H 0 1 N N N N N N 101.451 113.470 65.066 -2.056 3.262 0.177 H13 A1BCU 47 A1BCU H14 H14 H 0 1 N N N N N N 100.997 111.740 65.229 -2.445 2.002 1.373 H14 A1BCU 48 A1BCU H15 H15 H 0 1 N N N N N N 99.237 115.299 65.118 3.561 2.414 -1.467 H15 A1BCU 49 A1BCU H16 H16 H 0 1 N N N N N N 98.571 110.720 62.549 5.295 -3.115 -2.072 H16 A1BCU 50 A1BCU H17 H17 H 0 1 N N N N N N 100.002 110.806 61.988 0.098 0.517 2.540 H17 A1BCU 51 A1BCU H18 H18 H 0 1 N N N N N N 106.305 113.294 63.830 -7.026 2.414 -1.556 H18 A1BCU 52 A1BCU H19 H19 H 0 1 N N N N N N 94.434 111.478 60.577 8.928 -0.337 -1.558 H19 A1BCU 53 A1BCU H20 H20 H 0 1 N N N N N N 104.404 114.063 67.082 -5.551 3.873 -1.385 H20 A1BCU 54 # 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 A1BCU "O3'" "C3'" SING N N 1 A1BCU O1A PA DOUB N N 2 A1BCU "C3'" "C4'" SING N N 3 A1BCU "C3'" "C2'" SING N N 4 A1BCU "O2'" "C2'" SING N N 5 A1BCU "O4'" "C4'" DOUB N N 6 A1BCU "C4'" "C5'" SING N N 7 A1BCU O4 C4 DOUB N N 8 A1BCU PA O3A SING N N 9 A1BCU PA O2A SING N N 10 A1BCU PA O5D SING N N 11 A1BCU "C2'" "C1'" SING N N 12 A1BCU C5 C4 SING N N 13 A1BCU C5 C6 DOUB N N 14 A1BCU O3B PB SING N N 15 A1BCU O3B "C1'" SING N N 16 A1BCU O2B PB DOUB N N 17 A1BCU O3A PB SING N N 18 A1BCU C4 N3 SING N N 19 A1BCU "C5'" "O5'" SING N N 20 A1BCU PB O1B SING N N 21 A1BCU C6 N1 SING N N 22 A1BCU "C1'" "O5'" SING N N 23 A1BCU O5D C5D SING N N 24 A1BCU N3 C2 SING N N 25 A1BCU O2D C2D SING N N 26 A1BCU N1 C2 SING N N 27 A1BCU N1 C1D SING N N 28 A1BCU C2D C1D SING N N 29 A1BCU C2D C3D SING N N 30 A1BCU C2 O2 DOUB N N 31 A1BCU C5D C4D SING N N 32 A1BCU C1D O4D SING N N 33 A1BCU C3D C4D SING N N 34 A1BCU C3D O3D SING N N 35 A1BCU O4D C4D SING N N 36 A1BCU C5 H1 SING N N 37 A1BCU C6 H2 SING N N 38 A1BCU N3 H3 SING N N 39 A1BCU "C1'" H4 SING N N 40 A1BCU C1D H5 SING N N 41 A1BCU "C2'" H6 SING N N 42 A1BCU C2D H7 SING N N 43 A1BCU "C3'" H8 SING N N 44 A1BCU C3D H9 SING N N 45 A1BCU C4D H10 SING N N 46 A1BCU "C5'" H11 SING N N 47 A1BCU "C5'" H12 SING N N 48 A1BCU C5D H13 SING N N 49 A1BCU C5D H14 SING N N 50 A1BCU O1B H15 SING N N 51 A1BCU "O2'" H16 SING N N 52 A1BCU O2A H17 SING N N 53 A1BCU O2D H18 SING N N 54 A1BCU "O3'" H19 SING N N 55 A1BCU O3D H20 SING N N 56 # 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 A1BCU SMILES ACDLabs 14.52 "O=C1C=CN(C(=O)N1)C1OC(COP(=O)(O)OP(=O)(O)OC2OCC(=O)C(O)C2O)C(O)C1O" A1BCU InChI InChI 1.06 "InChI=1S/C14H20N2O16P2/c17-5-3-28-13(11(22)8(5)19)31-34(26,27)32-33(24,25)29-4-6-9(20)10(21)12(30-6)16-2-1-7(18)15-14(16)23/h1-2,6,8-13,19-22H,3-4H2,(H,24,25)(H,26,27)(H,15,18,23)/t6-,8+,9-,10-,11-,12-,13-/m1/s1" A1BCU InChIKey InChI 1.06 URJZIQLTPCJVMW-QNSCKLTRSA-N A1BCU SMILES_CANONICAL CACTVS 3.385 "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(=O)O[C@H]2OCC(=O)[C@H](O)[C@H]2O)N3C=CC(=O)NC3=O" A1BCU SMILES CACTVS 3.385 "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(=O)O[CH]2OCC(=O)[CH](O)[CH]2O)N3C=CC(=O)NC3=O" A1BCU SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "C1C(=O)[C@@H]([C@H]([C@H](O1)OP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=O)NC3=O)O)O)O)O" A1BCU SMILES "OpenEye OEToolkits" 3.1.0.0 "C1C(=O)C(C(C(O1)OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=O)NC3=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 A1BCU "SYSTEMATIC NAME" ACDLabs 14.52 "(2R,3R,4R)-3,4-dihydroxy-5-oxooxan-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxyoxolan-2-yl]methyl dihydrogen diphosphate (non-preferred name)" A1BCU "SYSTEMATIC NAME" "OpenEye OEToolkits" 3.1.0.0 "[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R})-3,4-bis(oxidanyl)-5-oxidanylidene-oxan-2-yl] hydrogen phosphate" # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id A1BCU _pdbx_chem_comp_synonyms.name Uridine-diphosphate-4-keto-D-xylose _pdbx_chem_comp_synonyms.provenance AUTHOR _pdbx_chem_comp_synonyms.type ? # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site A1BCU "Create component" 2024-10-06 RCSB A1BCU "Initial release" 2025-03-05 RCSB #