data_A1CU0 # _chem_comp.id A1CU0 _chem_comp.name ;2'-deoxycytidine-5'-(alpha-thio)-triphosphate, Sp isomer ; _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C9 H16 N3 O12 P3 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "[[(2~{R},3~{S},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphinothioyl] phosphono hydrogen phosphate, Sp isomer" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2025-09-22 _chem_comp.pdbx_modified_date 2026-06-12 _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 483.223 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1CU0 _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 9Y62 _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 A1CU0 "O4'" O1 O 0 1 N N N N N N 3.426 7.460 11.249 2.912 -0.313 -0.633 "O4'" A1CU0 1 A1CU0 O2 O2 O 0 1 N N N N N N 6.295 7.892 8.466 4.540 0.049 1.411 O2 A1CU0 2 A1CU0 "O5'" O3 O 0 1 N N N N N N 3.047 6.110 14.078 0.170 -1.184 -0.176 "O5'" A1CU0 3 A1CU0 "C2'" C1 C 0 1 N N N N N N 3.948 5.799 9.659 4.855 -1.630 -0.954 "C2'" A1CU0 4 A1CU0 "C3'" C2 C 0 1 N N S N N N 3.305 5.120 10.861 3.641 -2.564 -0.751 "C3'" A1CU0 5 A1CU0 "C4'" C3 C 0 1 N N R N N N 2.897 6.247 11.763 2.419 -1.637 -0.935 "C4'" A1CU0 6 A1CU0 "C1'" C4 C 0 1 N N R N N N 4.322 7.180 10.189 4.223 -0.249 -1.236 "C1'" A1CU0 7 A1CU0 N1 N1 N 0 1 N N N N N N 5.731 7.176 10.601 5.018 0.813 -0.614 N1 A1CU0 8 A1CU0 C5 C5 C 0 1 N N N N N N 6.143 6.777 11.844 5.652 1.731 -1.396 C5 A1CU0 9 A1CU0 C1 C6 C 0 1 N N N N N N 7.487 6.779 12.168 6.384 2.708 -0.809 C1 A1CU0 10 A1CU0 C4 C7 C 0 1 N N N N N N 8.397 7.142 11.176 6.469 2.746 0.598 C4 A1CU0 11 A1CU0 N4 N2 N 0 1 N N N N N N 7.991 7.521 9.940 5.835 1.831 1.318 N4 A1CU0 12 A1CU0 C2 C8 C 0 1 N N N N N N 6.669 7.539 9.642 5.114 0.879 0.727 C2 A1CU0 13 A1CU0 N2 N3 N 0 1 N N N N N N 9.719 7.144 11.450 7.206 3.727 1.219 N2 A1CU0 14 A1CU0 "C5'" C9 C 0 1 N N N N N N 3.799 6.006 12.940 1.305 -2.025 0.040 "C5'" A1CU0 15 A1CU0 PA P1 P 0 1 N N S N N N 3.504 4.857 14.879 -1.191 -1.312 0.676 PA A1CU0 16 A1CU0 S1 S1 S 0 1 N N N N N N 5.411 4.929 15.471 -1.664 -3.109 0.824 S1 A1CU0 17 A1CU0 O2A O4 O 0 1 N N N N N N 2.691 4.813 16.135 -0.964 -0.694 2.145 O2A A1CU0 18 A1CU0 O3A O5 O 0 1 N N N N N N 3.464 3.620 13.923 -2.368 -0.507 -0.069 O3A A1CU0 19 A1CU0 PB P2 P 0 1 N N N N N N 2.580 2.345 14.109 -3.925 -0.250 0.252 PB A1CU0 20 A1CU0 O2B O6 O 0 1 N N N N N N 1.141 2.566 14.435 -4.765 -1.587 -0.060 O2B A1CU0 21 A1CU0 O1B O7 O 0 1 N N N N N N 2.495 1.752 12.727 -4.081 0.109 1.679 O1B A1CU0 22 A1CU0 O3B O8 O 0 1 N N N N N N 3.425 1.507 15.117 -4.471 0.954 -0.667 O3B A1CU0 23 A1CU0 PG P3 P 0 1 N N N N N N 2.735 0.343 15.932 -5.735 1.947 -0.574 PG A1CU0 24 A1CU0 O2G O9 O 0 1 N N N N N N 3.769 -0.023 16.945 -7.074 1.150 -0.979 O2G A1CU0 25 A1CU0 O1G O10 O 0 1 N N N N N N 2.534 -0.782 14.941 -5.863 2.455 0.810 O1G A1CU0 26 A1CU0 O3G O11 O 0 1 N N N N N N 1.407 0.681 16.603 -5.521 3.184 -1.582 O3G A1CU0 27 A1CU0 "O3'" O12 O 0 1 N N N N N N 2.169 4.340 10.579 3.636 -3.600 -1.736 "O3'" A1CU0 28 A1CU0 "H2'1" H1 H 0 0 N N N N N N 3.236 5.878 8.824 5.464 -1.594 -0.051 "H2'1" A1CU0 29 A1CU0 "H2'2" H2 H 0 0 N N N N N N 4.842 5.249 9.328 5.451 -1.958 -1.805 "H2'2" A1CU0 30 A1CU0 "H3'" H3 H 0 1 N N N N N N 4.067 4.512 11.371 3.650 -2.990 0.252 "H3'" A1CU0 31 A1CU0 "H4'" H4 H 0 1 N N N N N N 1.826 6.261 12.012 2.059 -1.683 -1.962 "H4'" A1CU0 32 A1CU0 "H1'" H5 H 0 1 N N N N N N 4.185 7.912 9.379 4.141 -0.081 -2.310 "H1'" A1CU0 33 A1CU0 H6 H6 H 0 1 N N N N N N 5.414 6.459 12.575 5.572 1.680 -2.472 H6 A1CU0 34 A1CU0 H5 H7 H 0 1 N N N N N N 7.822 6.508 13.158 6.895 3.446 -1.410 H5 A1CU0 35 A1CU0 HN41 H8 H 0 0 N N N N N N 10.375 7.421 10.748 7.669 4.395 0.690 HN41 A1CU0 36 A1CU0 HN42 H9 H 0 0 N N N N N N 10.042 6.868 12.355 7.263 3.751 2.188 HN42 A1CU0 37 A1CU0 "H5'1" H10 H 0 0 N N N N N N 4.238 5.000 12.874 1.659 -1.903 1.063 "H5'1" A1CU0 38 A1CU0 "H5'2" H11 H 0 0 N N N N N N 4.603 6.757 12.954 1.023 -3.065 -0.126 "H5'2" A1CU0 39 A1CU0 H12 H12 H 0 1 N N N N N N 3.270 4.830 16.888 -0.715 0.240 2.145 H12 A1CU0 40 A1CU0 H13 H13 H 0 1 N N N N N N 0.603 2.281 13.706 -4.709 -1.882 -0.979 H13 A1CU0 41 A1CU0 H14 H14 H 0 1 N N N N N N 4.096 -0.896 16.763 -7.061 0.789 -1.876 H14 A1CU0 42 A1CU0 H15 H15 H 0 1 N N N N N N 0.725 0.115 16.260 -6.246 3.824 -1.578 H15 A1CU0 43 A1CU0 "HO3'" H16 H 0 0 N N N N N N 1.839 3.958 11.384 4.412 -4.175 -1.705 "HO3'" A1CU0 44 # 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 A1CU0 O2 C2 DOUB N N 1 A1CU0 C2 N4 SING N N 2 A1CU0 C2 N1 SING N N 3 A1CU0 "C2'" "C1'" SING N N 4 A1CU0 "C2'" "C3'" SING N N 5 A1CU0 N4 C4 DOUB N N 6 A1CU0 "C1'" N1 SING N N 7 A1CU0 "C1'" "O4'" SING N N 8 A1CU0 "O3'" "C3'" SING N N 9 A1CU0 N1 C5 SING N N 10 A1CU0 "C3'" "C4'" SING N N 11 A1CU0 C4 N2 SING N N 12 A1CU0 C4 C1 SING N N 13 A1CU0 "O4'" "C4'" SING N N 14 A1CU0 "C4'" "C5'" SING N N 15 A1CU0 C5 C1 DOUB N N 16 A1CU0 O1B PB DOUB N N 17 A1CU0 "C5'" "O5'" SING N N 18 A1CU0 O3A PB SING N N 19 A1CU0 O3A PA SING N N 20 A1CU0 "O5'" PA SING N N 21 A1CU0 PB O2B SING N N 22 A1CU0 PB O3B SING N N 23 A1CU0 PA S1 DOUB N N 24 A1CU0 PA O2A SING N N 25 A1CU0 O1G PG DOUB N N 26 A1CU0 O3B PG SING N N 27 A1CU0 PG O3G SING N N 28 A1CU0 PG O2G SING N N 29 A1CU0 "C2'" "H2'1" SING N N 30 A1CU0 "C2'" "H2'2" SING N N 31 A1CU0 "C3'" "H3'" SING N N 32 A1CU0 "C4'" "H4'" SING N N 33 A1CU0 "C1'" "H1'" SING N N 34 A1CU0 C5 H6 SING N N 35 A1CU0 C1 H5 SING N N 36 A1CU0 N2 HN41 SING N N 37 A1CU0 N2 HN42 SING N N 38 A1CU0 "C5'" "H5'1" SING N N 39 A1CU0 "C5'" "H5'2" SING N N 40 A1CU0 O2B H13 SING N N 41 A1CU0 O2G H14 SING N N 42 A1CU0 O3G H15 SING N N 43 A1CU0 "O3'" "HO3'" SING N N 44 A1CU0 O2A H12 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 A1CU0 InChI InChI 1.06 "InChI=1S/C9H16N3O12P3S/c10-7-1-2-12(9(14)11-7)8-3-5(13)6(22-8)4-21-27(20,28)24-26(18,19)23-25(15,16)17/h1-2,5-6,8,13H,3-4H2,(H,18,19)(H,20,28)(H2,10,11,14)(H2,15,16,17)/t5-,6+,8+,27-/m0/s1" A1CU0 InChIKey InChI 1.06 CBYOGVVSAABFCZ-HAHHPWOESA-N A1CU0 SMILES_CANONICAL CACTVS 3.385 "NC1=NC(=O)N(C=C1)[C@H]2C[C@H](O)[C@@H](CO[P@](O)(=S)O[P](O)(=O)O[P](O)(O)=O)O2" A1CU0 SMILES CACTVS 3.385 "NC1=NC(=O)N(C=C1)[CH]2C[CH](O)[CH](CO[P](O)(=S)O[P](O)(=O)O[P](O)(O)=O)O2" A1CU0 SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)CO[P@@](=S)(O)OP(=O)(O)OP(=O)(O)O)O" A1CU0 SMILES "OpenEye OEToolkits" 3.1.0.0 "C1C(C(OC1N2C=CC(=NC2=O)N)COP(=S)(O)OP(=O)(O)OP(=O)(O)O)O" # _pdbx_chem_comp_identifier.comp_id A1CU0 _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 3.1.0.0 _pdbx_chem_comp_identifier.identifier "[[(2~{R},3~{S},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphinothioyl] phosphono hydrogen phosphate" # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id A1CU0 _pdbx_chem_comp_synonyms.name "[[(2~{R},3~{S},5~{R})-5-(4-azanyl-2-oxidanylidene-pyrimidin-1-yl)-3-oxidanyl-oxolan-2-yl]methoxy-oxidanyl-phosphinothioyl] phosphono hydrogen phosphate, Sp isomer" _pdbx_chem_comp_synonyms.provenance PDB _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 A1CU0 "Create component" 2025-09-22 RCSB A1CU0 "Initial release" 2026-06-17 RCSB #