data_A1DI0 # _chem_comp.id A1DI0 _chem_comp.name "[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl dihydrogen diphosphate" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C15 H24 N2 O17 P2" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2026-06-01 _chem_comp.pdbx_modified_date 2026-10-02 _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 A1DI0 _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 36CA _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _chem_comp.pdbx_pcm ? _chem_comp.pdbx_comp_type ? # 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 A1DI0 C02 C1 C 0 1 N N N N N N -13.995 11.750 6.377 -6.866 -3.297 0.824 C02 A1DI0 1 A1DI0 C03 C2 C 0 1 N N N N N N -13.353 10.516 6.520 -7.103 -3.124 -0.561 C03 A1DI0 2 A1DI0 C04 C3 C 0 1 N N N N N N -12.125 10.480 7.165 -6.621 -2.023 -1.177 C04 A1DI0 3 A1DI0 C06 C4 C 0 1 N N R N N N -10.307 11.572 8.313 -5.394 0.097 -1.125 C06 A1DI0 4 A1DI0 C08 C5 C 0 1 N N R N N N -8.528 10.054 8.550 -3.706 1.681 -1.047 C08 A1DI0 5 A1DI0 C09 C6 C 0 1 N N N N N N -8.645 8.592 8.123 -2.670 2.180 -0.039 C09 A1DI0 6 A1DI0 C19 C7 C 0 1 N N S N N N -3.848 4.710 7.123 4.769 -0.684 -0.035 C19 A1DI0 7 A1DI0 C21 C8 C 0 1 N N R N N N -1.640 4.380 8.069 7.029 0.103 0.124 C21 A1DI0 8 A1DI0 C22 C9 C 0 1 N N N N N N -0.254 4.876 7.888 7.886 1.363 -0.014 C22 A1DI0 9 A1DI0 C24 C10 C 0 1 N N S N N N -1.669 2.901 7.628 7.519 -0.959 -0.864 C24 A1DI0 10 A1DI0 C26 C11 C 0 1 N N S N N N -3.006 2.356 7.285 6.618 -2.194 -0.762 C26 A1DI0 11 A1DI0 C28 C12 C 0 1 N N R N N N -3.845 3.308 6.522 5.168 -1.778 -1.028 C28 A1DI0 12 A1DI0 C30 C13 C 0 1 N N S N N N -8.939 10.263 9.786 -5.022 2.465 -0.879 C30 A1DI0 13 A1DI0 C32 C14 C 0 1 N N R N N N -10.387 10.734 9.615 -6.077 1.374 -0.572 C32 A1DI0 14 A1DI0 C34 C15 C 0 1 N N N N N N -12.251 12.783 7.487 -5.699 -1.274 0.859 C34 A1DI0 15 A1DI0 N05 N1 N 0 1 N N N N N N -11.621 11.614 7.629 -5.917 -1.097 -0.457 N05 A1DI0 16 A1DI0 N36 N2 N 0 1 N N N N N N -13.422 12.843 6.871 -6.167 -2.362 1.498 N36 A1DI0 17 A1DI0 O01 O1 O 0 1 N N N N N N -15.051 11.816 5.824 -7.295 -4.280 1.402 O01 A1DI0 18 A1DI0 O07 O2 O 0 1 N N N N N N -9.445 10.968 7.575 -4.000 0.295 -0.804 O07 A1DI0 19 A1DI0 O10 O3 O 0 1 N N N N N N -7.650 7.884 8.861 -1.420 1.531 -0.278 O10 A1DI0 20 A1DI0 O12 O4 O 0 1 N N N N N N -6.852 5.763 10.153 0.369 3.341 0.380 O12 A1DI0 21 A1DI0 O13 O5 O 0 1 N N N N N N -8.966 5.532 8.836 -0.402 1.594 2.031 O13 A1DI0 22 A1DI0 O14 O6 O 0 1 N N N N N N -6.690 5.761 7.591 1.077 0.821 0.137 O14 A1DI0 23 A1DI0 O16 O7 O 0 1 N N N N N N -4.777 7.530 7.993 2.103 -0.872 1.867 O16 A1DI0 24 A1DI0 O17 O8 O 0 1 N N N N N N -6.044 7.593 5.838 3.087 1.429 1.539 O17 A1DI0 25 A1DI0 O18 O9 O 0 1 N N N N N N -4.499 5.540 6.260 3.435 -0.251 -0.312 O18 A1DI0 26 A1DI0 O20 O10 O 0 1 N N N N N N -2.473 5.251 7.255 5.665 0.422 -0.160 O20 A1DI0 27 A1DI0 O23 O11 O 0 1 N N N N N N -0.287 6.245 8.162 7.504 2.311 0.985 O23 A1DI0 28 A1DI0 O25 O12 O 0 1 N N N N N N -1.054 2.104 8.662 8.864 -1.321 -0.546 O25 A1DI0 29 A1DI0 O27 O13 O 0 1 N N N N N N -2.815 1.193 6.389 7.025 -3.163 -1.731 O27 A1DI0 30 A1DI0 O29 O14 O 0 1 N N N N N N -5.212 2.828 6.446 4.309 -2.908 -0.865 O29 A1DI0 31 A1DI0 O31 O15 O 0 1 N N N N N N -8.081 11.323 10.453 -5.351 3.154 -2.087 O31 A1DI0 32 A1DI0 O33 O16 O 0 1 N N N N N N -10.839 11.529 10.635 -7.299 1.639 -1.263 O33 A1DI0 33 A1DI0 O35 O17 O 0 1 N N N N N N -11.776 13.788 7.914 -5.070 -0.438 1.480 O35 A1DI0 34 A1DI0 P11 P1 P 0 1 N N N N N N -7.609 6.203 8.903 -0.101 1.817 0.599 P11 A1DI0 35 A1DI0 P15 P2 P 0 1 N N N N N N -5.479 6.711 6.932 2.440 0.306 0.823 P15 A1DI0 36 A1DI0 H1 H1 H 0 1 N N N N N N -13.803 9.612 6.137 -7.661 -3.863 -1.118 H1 A1DI0 37 A1DI0 H2 H2 H 0 1 N N N N N N -11.592 9.549 7.286 -6.792 -1.874 -2.233 H2 A1DI0 38 A1DI0 H3 H3 H 0 1 N N N N N N -9.997 12.595 8.574 -5.533 0.024 -2.204 H3 A1DI0 39 A1DI0 H4 H4 H 0 1 N N N N N N -7.484 10.374 8.413 -3.327 1.806 -2.061 H4 A1DI0 40 A1DI0 H5 H5 H 0 1 N N N N N N -9.646 8.203 8.362 -2.546 3.258 -0.148 H5 A1DI0 41 A1DI0 H6 H6 H 0 1 N N N N N N -8.461 8.494 7.043 -3.009 1.955 0.973 H6 A1DI0 42 A1DI0 H7 H7 H 0 1 N N N N N N -4.336 4.683 8.109 4.819 -1.079 0.980 H7 A1DI0 43 A1DI0 H8 H8 H 0 1 N N N N N N -1.930 4.449 9.128 7.108 -0.281 1.140 H8 A1DI0 44 A1DI0 H9 H9 H 0 1 N N N N N N 0.427 4.365 8.584 8.937 1.103 0.115 H9 A1DI0 45 A1DI0 H10 H10 H 0 1 N N N N N N 0.080 4.703 6.854 7.738 1.797 -1.003 H10 A1DI0 46 A1DI0 H11 H11 H 0 1 N N N N N N -1.043 2.827 6.727 7.479 -0.560 -1.878 H11 A1DI0 47 A1DI0 H12 H12 H 0 1 N N N N N N -3.530 2.043 8.200 6.697 -2.621 0.237 H12 A1DI0 48 A1DI0 H13 H13 H 0 1 N N N N N N -3.441 3.382 5.502 5.080 -1.396 -2.046 H13 A1DI0 49 A1DI0 H14 H14 H 0 1 N N N N N N -8.926 9.346 10.394 -4.944 3.167 -0.049 H14 A1DI0 50 A1DI0 H15 H15 H 0 1 N N N N N N -11.040 9.865 9.449 -6.249 1.290 0.501 H15 A1DI0 51 A1DI0 H16 H16 H 0 1 N N N N N N -13.883 13.725 6.776 -6.001 -2.474 2.447 H16 A1DI0 52 A1DI0 H17 H17 H 0 1 N N N N N N -7.384 5.150 10.647 0.584 3.559 -0.537 H17 A1DI0 53 A1DI0 H18 H18 H 0 1 N N N N N N -4.826 8.451 7.766 1.677 -1.642 1.467 H18 A1DI0 54 A1DI0 H19 H19 H 0 1 N N N N N N 0.584 6.610 8.059 8.008 3.136 0.957 H19 A1DI0 55 A1DI0 H20 H20 H 0 1 N N N N N N -0.200 2.462 8.873 9.240 -1.992 -1.133 H20 A1DI0 56 A1DI0 H21 H21 H 0 1 N N N N N N -2.280 0.541 6.826 6.496 -3.973 -1.723 H21 A1DI0 57 A1DI0 H22 H22 H 0 1 N N N N N N -5.221 1.955 6.073 3.374 -2.716 -1.014 H22 A1DI0 58 A1DI0 H23 H23 H 0 1 N N N N N N -8.386 11.465 11.341 -6.171 3.664 -2.037 H23 A1DI0 59 A1DI0 H24 H24 H 0 1 N N N N N N -10.890 11.020 11.435 -7.764 2.428 -0.953 H24 A1DI0 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 A1DI0 O01 C02 DOUB N N 1 A1DI0 O17 P15 DOUB N N 2 A1DI0 O18 P15 SING N N 3 A1DI0 O18 C19 SING N N 4 A1DI0 C02 C03 SING N N 5 A1DI0 C02 N36 SING N N 6 A1DI0 O27 C26 SING N N 7 A1DI0 O29 C28 SING N N 8 A1DI0 C03 C04 DOUB N N 9 A1DI0 C28 C19 SING N N 10 A1DI0 C28 C26 SING N N 11 A1DI0 N36 C34 SING N N 12 A1DI0 P15 O14 SING N N 13 A1DI0 P15 O16 SING N N 14 A1DI0 C19 O20 SING N N 15 A1DI0 C04 N05 SING N N 16 A1DI0 O20 C21 SING N N 17 A1DI0 C26 C24 SING N N 18 A1DI0 C34 N05 SING N N 19 A1DI0 C34 O35 DOUB N N 20 A1DI0 O07 C06 SING N N 21 A1DI0 O07 C08 SING N N 22 A1DI0 O14 P11 SING N N 23 A1DI0 C24 C21 SING N N 24 A1DI0 C24 O25 SING N N 25 A1DI0 N05 C06 SING N N 26 A1DI0 C22 C21 SING N N 27 A1DI0 C22 O23 SING N N 28 A1DI0 C09 C08 SING N N 29 A1DI0 C09 O10 SING N N 30 A1DI0 C06 C32 SING N N 31 A1DI0 C08 C30 SING N N 32 A1DI0 O13 P11 DOUB N N 33 A1DI0 O10 P11 SING N N 34 A1DI0 P11 O12 SING N N 35 A1DI0 C32 C30 SING N N 36 A1DI0 C32 O33 SING N N 37 A1DI0 C30 O31 SING N N 38 A1DI0 C03 H1 SING N N 39 A1DI0 C04 H2 SING N N 40 A1DI0 C06 H3 SING N N 41 A1DI0 C08 H4 SING N N 42 A1DI0 C09 H5 SING N N 43 A1DI0 C09 H6 SING N N 44 A1DI0 C19 H7 SING N N 45 A1DI0 C21 H8 SING N N 46 A1DI0 C22 H9 SING N N 47 A1DI0 C22 H10 SING N N 48 A1DI0 C24 H11 SING N N 49 A1DI0 C26 H12 SING N N 50 A1DI0 C28 H13 SING N N 51 A1DI0 C30 H14 SING N N 52 A1DI0 C32 H15 SING N N 53 A1DI0 N36 H16 SING N N 54 A1DI0 O12 H17 SING N N 55 A1DI0 O16 H18 SING N N 56 A1DI0 O23 H19 SING N N 57 A1DI0 O25 H20 SING N N 58 A1DI0 O27 H21 SING N N 59 A1DI0 O29 H22 SING N N 60 A1DI0 O31 H23 SING N N 61 A1DI0 O33 H24 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 A1DI0 SMILES ACDLabs 14.52 "O=C1C=CN(C(=O)N1)C1OC(COP(=O)(O)OP(=O)(O)OC2OC(CO)C(O)C(O)C2O)C(O)C1O" A1DI0 InChI InChI 1.06 "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" A1DI0 InChIKey InChI 1.06 HSCJRCZFDFQWRP-VQFSATMJSA-N A1DI0 SMILES_CANONICAL CACTVS 3.385 "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" A1DI0 SMILES CACTVS 3.385 "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" A1DI0 SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)OP(=O)(O)O[C@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)O)O)O" A1DI0 SMILES "OpenEye OEToolkits" 3.1.0.0 "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" # 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 A1DI0 "SYSTEMATIC NAME" ACDLabs 14.52 "[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2S,3R,4S,5S,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)oxan-2-yl dihydrogen diphosphate (non-preferred name)" A1DI0 "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~{S},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl] 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 A1DI0 "Create component" 2026-06-01 RCSB A1DI0 "Initial release" 2026-10-07 RCSB #