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 
# 
