data_A1BIK # _chem_comp.id A1BIK _chem_comp.name "1-(5-amino-3,7-anhydro-5-deoxy-2-O-phosphono-D-threo-beta-D-allo-octofuranuronosyl)pyrimidine-2,4(1H,3H)-dione" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C12 H16 N3 O11 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2024-11-26 _chem_comp.pdbx_modified_date 2025-08-15 _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 409.243 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1BIK _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 9EI7 _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 A1BIK C01 C1 C 0 1 N N R N N N -16.810 15.337 -15.339 -1.852 2.557 -0.720 C01 A1BIK 1 A1BIK C02 C2 C 0 1 N N R N N N -18.277 15.496 -14.944 -0.900 1.401 -0.966 C02 A1BIK 2 A1BIK C03 C3 C 0 1 N N R N N N -19.144 16.006 -16.085 -0.888 0.547 0.333 C03 A1BIK 3 A1BIK C04 C4 C 0 1 N N R N N N -20.396 16.484 -15.360 0.306 -0.371 0.062 C04 A1BIK 4 A1BIK C05 C5 C 0 1 N N R N N N -19.817 16.964 -13.993 1.184 0.470 -0.901 C05 A1BIK 5 A1BIK C06 C6 C 0 1 N N N N N N -19.232 19.262 -14.703 3.602 0.234 -0.821 C06 A1BIK 6 A1BIK C07 C7 C 0 1 N N N N N N -19.790 21.172 -13.336 4.910 1.235 0.836 C07 A1BIK 7 A1BIK C08 C8 C 0 1 N N N N N N -20.401 20.235 -12.377 3.739 1.781 1.415 C08 A1BIK 8 A1BIK C09 C9 C 0 1 N N N N N N -20.401 18.879 -12.601 2.543 1.525 0.843 C09 A1BIK 9 A1BIK C10 C10 C 0 1 N N S N N N -17.893 14.535 -17.564 -3.192 0.908 0.652 C10 A1BIK 10 A1BIK C11 C11 C 0 1 N N N N N N -17.980 13.342 -18.495 -4.523 0.205 0.730 C11 A1BIK 11 A1BIK C12 C12 C 0 1 N N R N N N -16.809 14.285 -16.474 -3.241 1.944 -0.468 C12 A1BIK 12 A1BIK N01 N1 N 0 1 N N N N N N -16.193 16.614 -15.753 -1.417 3.322 0.457 N01 A1BIK 13 A1BIK N02 N2 N 0 1 N N N N N N -19.822 18.444 -13.797 2.481 0.747 -0.281 N02 A1BIK 14 A1BIK N03 N3 N 0 1 N N N N N N -19.257 20.576 -14.406 4.807 0.473 -0.271 N03 A1BIK 15 A1BIK O01 O1 O 0 1 N N N N N N -21.190 15.336 -15.087 -0.120 -1.581 -0.568 O01 A1BIK 16 A1BIK O02 O2 O 0 1 N N N N N N -23.502 15.872 -14.357 -0.371 -4.169 -0.958 O02 A1BIK 17 A1BIK O03 O3 O 0 1 N N N N N N -22.937 16.120 -16.725 1.553 -3.220 0.371 O03 A1BIK 18 A1BIK O04 O4 O 0 1 N N N N N N -23.106 13.922 -15.786 -0.731 -3.160 1.443 O04 A1BIK 19 A1BIK O05 O5 O 0 1 N N N N N N -19.721 22.378 -13.244 6.000 1.451 1.334 O05 A1BIK 20 A1BIK O06 O6 O 0 1 N N N N N N -18.721 18.888 -15.762 3.524 -0.459 -1.817 O06 A1BIK 21 A1BIK O07 O7 O 0 1 N N N N N N -18.424 16.519 -13.933 0.477 1.712 -1.145 O07 A1BIK 22 A1BIK O08 O8 O 0 1 N N N N N N -19.203 14.866 -17.008 -2.159 -0.067 0.431 O08 A1BIK 23 A1BIK O09 O9 O 0 1 N N N N N N -18.941 12.594 -18.439 -5.632 0.898 1.032 O09 A1BIK 24 A1BIK O10 O10 O 0 1 N N N N N N -17.062 13.238 -19.247 -4.592 -0.983 0.519 O10 A1BIK 25 A1BIK O11 O11 O 0 1 N N N N N N -17.062 13.018 -15.870 -3.701 1.316 -1.666 O11 A1BIK 26 A1BIK P01 P1 P 0 1 N N N N N N -22.741 15.322 -15.519 0.114 -3.036 0.078 P01 A1BIK 27 A1BIK H1 H1 H 0 1 N N N N N N -16.257 14.925 -14.482 -1.884 3.206 -1.595 H1 A1BIK 28 A1BIK H2 H2 H 0 1 N N N N N N -18.668 14.533 -14.584 -1.256 0.802 -1.805 H2 A1BIK 29 A1BIK H3 H3 H 0 1 N N N N N N -18.650 16.862 -16.568 -0.693 1.177 1.201 H3 A1BIK 30 A1BIK H4 H4 H 0 1 N N N N N N -20.921 17.288 -15.897 0.843 -0.588 0.986 H4 A1BIK 31 A1BIK H5 H5 H 0 1 N N N N N N -20.393 16.489 -13.185 1.325 -0.067 -1.839 H5 A1BIK 32 A1BIK H6 H6 H 0 1 N N N N N N -20.859 20.622 -11.479 3.802 2.394 2.302 H6 A1BIK 33 A1BIK H7 H7 H 0 1 N N N N N N -20.826 18.186 -11.890 1.639 1.933 1.270 H7 A1BIK 34 A1BIK H8 H8 H 0 1 N N N N N N -17.551 15.393 -18.162 -3.005 1.416 1.598 H8 A1BIK 35 A1BIK H9 H9 H 0 1 N N N N N N -15.820 14.288 -16.956 -3.936 2.737 -0.191 H9 A1BIK 36 A1BIK H10 H10 H 0 1 N N N N N N -16.217 17.259 -14.989 -2.040 4.096 0.635 H10 A1BIK 37 A1BIK H11 H11 H 0 1 N N N N N N -15.244 16.453 -16.024 -1.340 2.726 1.267 H11 A1BIK 38 A1BIK H13 H13 H 0 1 N N N N N N -18.821 21.182 -15.071 5.605 0.095 -0.674 H13 A1BIK 39 A1BIK H14 H14 H 0 1 N N N N N N -23.977 16.649 -14.628 -0.259 -5.073 -0.634 H14 A1BIK 40 A1BIK H15 H15 H 0 1 N N N N N N -23.392 13.835 -16.688 -1.685 -3.050 1.326 H15 A1BIK 41 A1BIK H16 H16 H 0 1 N N N N N N -18.848 11.909 -19.091 -6.462 0.404 1.070 H16 A1BIK 42 A1BIK H17 H17 H 0 1 N N N N N N -16.409 12.849 -15.201 -4.583 0.929 -1.594 H17 A1BIK 43 # 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 A1BIK O10 C11 DOUB N N 1 A1BIK C11 O09 SING N N 2 A1BIK C11 C10 SING N N 3 A1BIK C10 O08 SING N N 4 A1BIK C10 C12 SING N N 5 A1BIK O08 C03 SING N N 6 A1BIK O03 P01 DOUB N N 7 A1BIK C12 O11 SING N N 8 A1BIK C12 C01 SING N N 9 A1BIK C03 C04 SING N N 10 A1BIK C03 C02 SING N N 11 A1BIK O04 P01 SING N N 12 A1BIK O06 C06 DOUB N N 13 A1BIK N01 C01 SING N N 14 A1BIK P01 O01 SING N N 15 A1BIK P01 O02 SING N N 16 A1BIK C04 O01 SING N N 17 A1BIK C04 C05 SING N N 18 A1BIK C01 C02 SING N N 19 A1BIK C02 O07 SING N N 20 A1BIK C06 N03 SING N N 21 A1BIK C06 N02 SING N N 22 A1BIK N03 C07 SING N N 23 A1BIK C05 O07 SING N N 24 A1BIK C05 N02 SING N N 25 A1BIK N02 C09 SING N N 26 A1BIK C07 O05 DOUB N N 27 A1BIK C07 C08 SING N N 28 A1BIK C09 C08 DOUB N N 29 A1BIK C01 H1 SING N N 30 A1BIK C02 H2 SING N N 31 A1BIK C03 H3 SING N N 32 A1BIK C04 H4 SING N N 33 A1BIK C05 H5 SING N N 34 A1BIK C08 H6 SING N N 35 A1BIK C09 H7 SING N N 36 A1BIK C10 H8 SING N N 37 A1BIK C12 H9 SING N N 38 A1BIK N01 H10 SING N N 39 A1BIK N01 H11 SING N N 40 A1BIK N03 H13 SING N N 41 A1BIK O02 H14 SING N N 42 A1BIK O04 H15 SING N N 43 A1BIK O09 H16 SING N N 44 A1BIK O11 H17 SING N N 45 # 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 A1BIK SMILES ACDLabs 14.52 "O=C(O)C1OC2C(OC(C2OP(=O)(O)O)N2C=CC(=O)NC2=O)C(N)C1O" A1BIK InChI InChI 1.06 "InChI=1S/C12H16N3O11P/c13-4-5(17)7(11(18)19)24-8-6(4)25-10(9(8)26-27(21,22)23)15-2-1-3(16)14-12(15)20/h1-2,4-10,17H,13H2,(H,18,19)(H,14,16,20)(H2,21,22,23)/t4-,5-,6-,7+,8-,9-,10-/m1/s1" A1BIK InChIKey InChI 1.06 WKDVCFXFVRNMOM-OLYSFKJBSA-N A1BIK SMILES_CANONICAL CACTVS 3.385 "N[C@@H]1[C@@H](O)[C@H](O[C@@H]2[C@@H]1O[C@H]([C@@H]2O[P](O)(O)=O)N3C=CC(=O)NC3=O)C(O)=O" A1BIK SMILES CACTVS 3.385 "N[CH]1[CH](O)[CH](O[CH]2[CH]1O[CH]([CH]2O[P](O)(O)=O)N3C=CC(=O)NC3=O)C(O)=O" A1BIK SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@H]3[C@H](O2)[C@@H]([C@H]([C@H](O3)C(=O)O)O)N)OP(=O)(O)O" A1BIK SMILES "OpenEye OEToolkits" 3.1.0.0 "C1=CN(C(=O)NC1=O)C2C(C3C(O2)C(C(C(O3)C(=O)O)O)N)OP(=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 A1BIK "SYSTEMATIC NAME" ACDLabs 14.52 "1-(5-amino-3,7-anhydro-5-deoxy-2-O-phosphono-D-threo-beta-D-allo-octofuranuronosyl)pyrimidine-2,4(1H,3H)-dione" A1BIK "SYSTEMATIC NAME" "OpenEye OEToolkits" 3.1.0.0 "(2~{R},3~{R},3~{a}~{R},5~{S},6~{R},7~{R},7~{a}~{R})-7-azanyl-2-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-6-oxidanyl-3-phosphonooxy-3,3~{a},5,6,7,7~{a}-hexahydro-2~{H}-furo[3,2-b]pyran-5-carboxylic acid" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site A1BIK "Create component" 2024-11-26 RCSB A1BIK "Initial release" 2025-08-20 RCSB #