data_A1CVS # _chem_comp.id A1CVS _chem_comp.name "1-{5-O-[(R)-hydroxy(phosphonomethyl)phosphoryl]-beta-D-ribofuranosyl}-2-sulfanylidene-2,3-dihydropyrimidin-4(1H)-one" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C10 H16 N2 O10 P2 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2025-09-24 _chem_comp.pdbx_modified_date 2025-11-14 _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 418.254 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1CVS _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 9YDV _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 A1CVS C1 C1 C 0 1 N N N N N N 132.483 119.327 159.189 5.107 -2.487 -0.816 C1 A1CVS 1 A1CVS C10 C2 C 0 1 N N N N N N 130.551 118.025 158.570 4.399 -0.935 0.780 C10 A1CVS 2 A1CVS C2 C3 C 0 1 N N N N N N 132.177 119.075 160.552 4.171 -1.953 -1.734 C2 A1CVS 3 A1CVS C3 C4 C 0 1 N N N N N N 131.087 118.327 160.865 3.385 -0.925 -1.348 C3 A1CVS 4 A1CVS C4 C5 C 0 1 N N R N N N 129.066 117.013 160.254 2.653 0.697 0.336 C4 A1CVS 5 A1CVS C5 C6 C 0 1 N N R N N N 127.114 117.248 161.509 0.583 1.655 0.071 C5 A1CVS 6 A1CVS C6 C7 C 0 1 N N N N N N 126.903 118.194 162.667 -0.758 1.522 -0.652 C6 A1CVS 7 A1CVS C7 C8 C 0 1 N N N N N N 127.341 119.005 165.812 -3.931 -0.699 0.920 C7 A1CVS 8 A1CVS C8 C9 C 0 1 N N S N N N 127.779 115.908 161.848 1.531 2.584 -0.719 C8 A1CVS 9 A1CVS C9 C10 C 0 1 N N R N N N 129.237 116.233 161.550 2.924 1.940 -0.541 C9 A1CVS 10 A1CVS N1 N1 N 0 1 N N N N N N 130.269 117.819 159.896 3.506 -0.418 -0.083 N1 A1CVS 11 A1CVS N2 N2 N 0 1 N N N N N N 131.643 118.755 158.236 5.194 -1.960 0.422 N2 A1CVS 12 A1CVS O1 O1 O 0 1 N N N N N N 133.443 120.014 158.797 5.822 -3.418 -1.139 O1 A1CVS 13 A1CVS O10 O2 O 0 1 N N N N N N 130.087 115.105 161.409 3.810 2.841 0.126 O10 A1CVS 14 A1CVS O2 O3 O 0 1 N N N N N N 127.995 117.877 160.544 1.263 0.381 0.108 O2 A1CVS 15 A1CVS O3 O4 O 0 1 N N N N N N 128.181 118.564 163.239 -1.658 0.755 0.150 O3 A1CVS 16 A1CVS O4 O5 O 0 1 N N N N N N 127.694 120.920 163.958 -3.147 -0.243 -1.627 O4 A1CVS 17 A1CVS O5 O6 O 0 1 N N N N N N 129.750 119.699 164.847 -4.018 1.779 -0.393 O5 A1CVS 18 A1CVS O6 O7 O 0 1 N N N N N N 128.898 120.055 167.684 -5.617 -1.799 -1.034 O6 A1CVS 19 A1CVS O7 O8 O 0 1 N N N N N N 126.584 119.409 168.329 -6.314 -2.068 1.487 O7 A1CVS 20 A1CVS O8 O9 O 0 1 N N N N N N 126.964 121.403 166.886 -6.422 0.170 0.324 O8 A1CVS 21 A1CVS O9 O10 O 0 1 N N N N N N 127.309 114.906 160.956 1.512 3.903 -0.169 O9 A1CVS 22 A1CVS P1 P1 P 0 1 N N N N N N 128.314 119.628 164.409 -3.166 0.416 -0.302 P1 A1CVS 23 A1CVS P2 P2 P 0 1 N N N N N N 127.454 120.039 167.279 -5.638 -1.083 0.407 P2 A1CVS 24 A1CVS S1 S1 S 0 1 N N N N N N 129.576 117.379 157.392 4.526 -0.278 2.356 S1 A1CVS 25 A1CVS H1 H1 H 0 1 N N N N N N 132.806 119.475 161.334 4.086 -2.362 -2.730 H1 A1CVS 26 A1CVS H2 H2 H 0 1 N N N N N N 130.862 118.130 161.903 2.666 -0.504 -2.034 H2 A1CVS 27 A1CVS H3 H3 H 0 1 N N N N N N 128.815 116.322 159.435 2.822 0.931 1.387 H3 A1CVS 28 A1CVS H4 H4 H 0 1 N N N N N N 126.141 117.043 161.039 0.433 2.036 1.081 H4 A1CVS 29 A1CVS H5 H5 H 0 1 N N N N N N 126.387 119.098 162.311 -1.179 2.513 -0.823 H5 A1CVS 30 A1CVS H6 H6 H 0 1 N N N N N N 126.289 117.700 163.434 -0.608 1.021 -1.608 H6 A1CVS 31 A1CVS H7 H7 H 0 1 N N N N N N 126.286 118.949 165.506 -3.354 -1.622 0.981 H7 A1CVS 32 A1CVS H8 H8 H 0 1 N N N N N N 127.703 117.998 166.067 -3.945 -0.214 1.896 H8 A1CVS 33 A1CVS H9 H9 H 0 1 N N N N N N 127.633 115.646 162.906 1.252 2.607 -1.773 H9 A1CVS 34 A1CVS H10 H10 H 0 1 N N N N N N 129.620 116.909 162.328 3.334 1.644 -1.506 H10 A1CVS 35 A1CVS H11 H11 H 0 1 N N N N N N 131.854 118.888 157.268 5.833 -2.320 1.057 H11 A1CVS 36 A1CVS H12 H12 H 0 1 N N N N N N 130.159 114.656 162.243 4.014 3.639 -0.380 H12 A1CVS 37 A1CVS H13 H13 H 0 1 N N N N N N 130.062 120.593 164.768 -4.073 2.265 0.442 H13 A1CVS 38 A1CVS H14 H14 H 0 1 N N N N N N 129.237 120.940 167.615 -5.120 -2.629 -1.054 H14 A1CVS 39 A1CVS H15 H15 H 0 1 N N N N N N 125.875 120.002 168.551 -7.225 -2.315 1.278 H15 A1CVS 40 A1CVS H16 H16 H 0 1 N N N N N N 127.721 114.076 161.166 2.089 4.529 -0.628 H16 A1CVS 41 # 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 A1CVS S1 C10 DOUB N N 1 A1CVS N2 C10 SING N N 2 A1CVS N2 C1 SING N N 3 A1CVS C10 N1 SING N N 4 A1CVS O1 C1 DOUB N N 5 A1CVS C1 C2 SING N N 6 A1CVS N1 C4 SING N N 7 A1CVS N1 C3 SING N N 8 A1CVS C4 O2 SING N N 9 A1CVS C4 C9 SING N N 10 A1CVS O2 C5 SING N N 11 A1CVS C2 C3 DOUB N N 12 A1CVS O9 C8 SING N N 13 A1CVS O10 C9 SING N N 14 A1CVS C5 C8 SING N N 15 A1CVS C5 C6 SING N N 16 A1CVS C9 C8 SING N N 17 A1CVS C6 O3 SING N N 18 A1CVS O3 P1 SING N N 19 A1CVS O4 P1 DOUB N N 20 A1CVS P1 O5 SING N N 21 A1CVS P1 C7 SING N N 22 A1CVS C7 P2 SING N N 23 A1CVS O8 P2 DOUB N N 24 A1CVS P2 O6 SING N N 25 A1CVS P2 O7 SING N N 26 A1CVS C2 H1 SING N N 27 A1CVS C3 H2 SING N N 28 A1CVS C4 H3 SING N N 29 A1CVS C5 H4 SING N N 30 A1CVS C6 H5 SING N N 31 A1CVS C6 H6 SING N N 32 A1CVS C7 H7 SING N N 33 A1CVS C7 H8 SING N N 34 A1CVS C8 H9 SING N N 35 A1CVS C9 H10 SING N N 36 A1CVS N2 H11 SING N N 37 A1CVS O10 H12 SING N N 38 A1CVS O5 H13 SING N N 39 A1CVS O6 H14 SING N N 40 A1CVS O7 H15 SING N N 41 A1CVS O9 H16 SING N N 42 # 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 A1CVS SMILES ACDLabs 14.52 "O=P(O)(O)CP(=O)(O)OCC1OC(N2C=CC(=O)NC2=S)C(O)C1O" A1CVS InChI InChI 1.06 "InChI=1S/C10H16N2O10P2S/c13-6-1-2-12(10(25)11-6)9-8(15)7(14)5(22-9)3-21-24(19,20)4-23(16,17)18/h1-2,5,7-9,14-15H,3-4H2,(H,19,20)(H,11,13,25)(H2,16,17,18)/t5-,7-,8-,9-/m1/s1" A1CVS InChIKey InChI 1.06 VAZIBAQQXATRMK-ZOQUXTDFSA-N A1CVS SMILES_CANONICAL CACTVS 3.385 "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)C[P](O)(O)=O)N2C=CC(=O)NC2=S" A1CVS SMILES CACTVS 3.385 "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)C[P](O)(O)=O)N2C=CC(=O)NC2=S" A1CVS SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "C1=CN(C(=S)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(CP(=O)(O)O)O)O)O" A1CVS SMILES "OpenEye OEToolkits" 3.1.0.0 "C1=CN(C(=S)NC1=O)C2C(C(C(O2)COP(=O)(CP(=O)(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 A1CVS "SYSTEMATIC NAME" ACDLabs 14.52 "1-{5-O-[(R)-hydroxy(phosphonomethyl)phosphoryl]-beta-D-ribofuranosyl}-2-sulfanylidene-2,3-dihydropyrimidin-4(1H)-one" A1CVS "SYSTEMATIC NAME" "OpenEye OEToolkits" 3.1.0.0 "[[(2~{R},3~{S},4~{R},5~{R})-3,4-bis(oxidanyl)-5-(4-oxidanylidene-2-sulfanylidene-pyrimidin-1-yl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]methylphosphonic 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 A1CVS "Create component" 2025-09-24 RCSB A1CVS "Initial release" 2025-11-19 RCSB #