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 
# 
