data_A1CY0 # _chem_comp.id A1CY0 _chem_comp.name "1-(5-deoxy-3-O-phosphono-alpha-L-arabinofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H15 N2 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2025-10-20 _chem_comp.pdbx_modified_date 2026-10-16 _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 322.208 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1CY0 _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 9YRD _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 A1CY0 "C1'" C1 C 0 1 N N R N N N 15.206 32.746 14.828 -0.738 -0.665 -0.739 "C1'" A1CY0 1 A1CY0 C2 C2 C 0 1 N N N N N N 13.425 31.147 13.559 -2.298 -0.134 1.048 C2 A1CY0 2 A1CY0 "C2'" C3 C 0 1 N N R N N N 15.901 32.859 16.251 0.314 0.399 -0.338 "C2'" A1CY0 3 A1CY0 "C3'" C4 C 0 1 N N R N N N 17.302 33.385 15.904 1.609 -0.458 -0.321 "C3'" A1CY0 4 A1CY0 C4 C5 C 0 1 N N N N N N 13.887 28.763 13.762 -4.520 0.463 0.643 C4 A1CY0 5 A1CY0 "C4'" C6 C 0 1 N N S N N N 17.216 33.948 14.721 1.090 -1.825 0.173 "C4'" A1CY0 6 A1CY0 C5 C7 C 0 1 N N N N N N 15.119 28.910 14.599 -4.293 0.324 -0.747 C5 A1CY0 7 A1CY0 "C5'" C8 C 0 1 N N N N N N 16.770 35.369 14.852 1.796 -2.953 -0.583 "C5'" A1CY0 8 A1CY0 C6 C9 C 0 1 N N N N N N 15.586 30.128 14.963 -3.066 -0.041 -1.179 C6 A1CY0 9 A1CY0 C7 C10 C 0 1 N N N N N N 15.927 27.667 15.084 -5.404 0.581 -1.732 C7 A1CY0 10 A1CY0 N1 N1 N 0 1 N N N N N N 14.787 31.361 14.485 -2.069 -0.269 -0.271 N1 A1CY0 11 A1CY0 N3 N2 N 0 1 N N N N N N 13.136 29.684 13.301 -3.510 0.229 1.506 N3 A1CY0 12 A1CY0 O2 O1 O 0 1 N N N N N N 12.756 32.047 13.151 -1.398 -0.347 1.838 O2 A1CY0 13 A1CY0 "O2'" O2 O 0 1 N N N N N N 15.261 33.738 17.014 0.395 1.437 -1.317 "O2'" A1CY0 14 A1CY0 "O3'" O3 O 0 1 N N N N N N 18.205 32.268 15.854 2.566 0.084 0.592 "O3'" A1CY0 15 A1CY0 O4 O4 O 0 1 N N N N N N 13.536 27.657 13.478 -5.618 0.791 1.057 O4 A1CY0 16 A1CY0 "O4'" O5 O 0 1 N N N N N N 16.250 33.208 13.920 -0.318 -1.873 -0.084 "O4'" A1CY0 17 A1CY0 OP1 O6 O 0 1 N N N N N N 20.594 31.386 16.432 4.724 -0.523 -0.567 OP1 A1CY0 18 A1CY0 OP2 O7 O 0 1 N N N N N N 20.029 33.920 16.527 3.887 1.842 -0.848 OP2 A1CY0 19 A1CY0 P P1 P 0 1 N N N N N N 19.867 32.581 15.831 4.029 0.577 0.138 P A1CY0 20 A1CY0 "H1'1" H1 H 0 0 N N N N N N 14.340 33.423 14.800 -0.744 -0.803 -1.820 "H1'1" A1CY0 21 A1CY0 "H2'1" H2 H 0 0 N N N N N N 15.974 31.859 16.703 0.102 0.810 0.649 "H2'1" A1CY0 22 A1CY0 "H3'1" H3 H 0 0 N N N N N N 17.618 34.096 16.682 2.034 -0.539 -1.322 "H3'1" A1CY0 23 A1CY0 "H4'1" H4 H 0 0 N N N N N N 18.188 33.936 14.207 1.275 -1.926 1.243 "H4'1" A1CY0 24 A1CY0 "H5'3" H5 H 0 0 N N N N N N 16.703 35.826 13.854 2.870 -2.890 -0.408 "H5'3" A1CY0 25 A1CY0 "H5'1" H6 H 0 0 N N N N N N 15.783 35.400 15.337 1.426 -3.915 -0.230 "H5'1" A1CY0 26 A1CY0 "H5'2" H7 H 0 0 N N N N N N 17.496 35.926 15.462 1.596 -2.856 -1.650 "H5'2" A1CY0 27 A1CY0 H61 H8 H 0 1 N N N N N N 16.479 30.233 15.562 -2.874 -0.152 -2.236 H61 A1CY0 28 A1CY0 H72 H9 H 0 1 N N N N N N 15.442 26.749 14.721 -6.309 0.862 -1.194 H72 A1CY0 29 A1CY0 H71 H10 H 0 1 N N N N N N 16.953 27.720 14.690 -5.115 1.389 -2.404 H71 A1CY0 30 A1CY0 H73 H11 H 0 1 N N N N N N 15.957 27.655 16.184 -5.592 -0.324 -2.311 H73 A1CY0 31 A1CY0 H31 H12 H 0 1 N N N N N N 12.336 29.434 12.755 -3.659 0.321 2.460 H31 A1CY0 32 A1CY0 "H2'2" H13 H 0 0 N N N N N N 15.689 33.794 17.860 -0.428 1.930 -1.438 "H2'2" A1CY0 33 A1CY0 OP3 OP3 O 0 1 N Y N N N N 20.205 32.692 14.269 4.879 1.003 1.438 OP3 A1CY0 34 A1CY0 H1 H1 H 0 1 N N N N N N 20.594 33.818 17.284 3.440 2.602 -0.451 H1 A1CY0 35 A1CY0 H2 H2 H 0 1 N N N N N N 20.794 31.989 14.021 5.774 1.311 1.239 H2 A1CY0 36 # 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 A1CY0 P OP1 DOUB N N 1 A1CY0 "C3'" "O3'" SING N N 2 A1CY0 "C4'" "C3'" SING N N 3 A1CY0 "C5'" "C4'" SING N N 4 A1CY0 "O4'" "C4'" SING N N 5 A1CY0 "C1'" "O4'" SING N N 6 A1CY0 C2 N1 SING N N 7 A1CY0 C4 N3 SING N N 8 A1CY0 C7 C5 SING N N 9 A1CY0 C6 C5 DOUB N N 10 A1CY0 C5 C4 SING N N 11 A1CY0 O4 C4 DOUB N N 12 A1CY0 N3 C2 SING N N 13 A1CY0 O2 C2 DOUB N N 14 A1CY0 N1 "C1'" SING N N 15 A1CY0 "C2'" "C1'" SING N N 16 A1CY0 "O2'" "C2'" SING N N 17 A1CY0 "O3'" P SING N N 18 A1CY0 OP2 P SING N N 19 A1CY0 "C3'" "C2'" SING N N 20 A1CY0 N1 C6 SING N N 21 A1CY0 "C1'" "H1'1" SING N N 22 A1CY0 "C2'" "H2'1" SING N N 23 A1CY0 "C3'" "H3'1" SING N N 24 A1CY0 "C4'" "H4'1" SING N N 25 A1CY0 "C5'" "H5'3" SING N N 26 A1CY0 "C5'" "H5'1" SING N N 27 A1CY0 "C5'" "H5'2" SING N N 28 A1CY0 C6 H61 SING N N 29 A1CY0 C7 H72 SING N N 30 A1CY0 C7 H71 SING N N 31 A1CY0 C7 H73 SING N N 32 A1CY0 N3 H31 SING N N 33 A1CY0 "O2'" "H2'2" SING N N 34 A1CY0 P OP3 SING N N 35 A1CY0 OP2 H1 SING N N 36 A1CY0 OP3 H2 SING N N 37 # 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 A1CY0 SMILES ACDLabs 14.52 "O=P(O)(O)OC1C(C)OC(N2C=C(C)C(=O)NC2=O)C1O" A1CY0 InChI InChI 1.06 "InChI=1S/C10H15N2O8P/c1-4-3-12(10(15)11-8(4)14)9-6(13)7(5(2)19-9)20-21(16,17)18/h3,5-7,9,13H,1-2H3,(H,11,14,15)(H2,16,17,18)/t5-,6+,7-,9+/m0/s1" A1CY0 InChIKey InChI 1.06 HRWNUYQJWGICCU-VOQBNFLRSA-N A1CY0 SMILES_CANONICAL CACTVS 3.385 "C[C@@H]1O[C@H]([C@H](O)[C@H]1O[P](O)(O)=O)N2C=C(C)C(=O)NC2=O" A1CY0 SMILES CACTVS 3.385 "C[CH]1O[CH]([CH](O)[CH]1O[P](O)(O)=O)N2C=C(C)C(=O)NC2=O" A1CY0 SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "C[C@H]1[C@@H]([C@H]([C@@H](O1)N2C=C(C(=O)NC2=O)C)O)OP(=O)(O)O" A1CY0 SMILES "OpenEye OEToolkits" 3.1.0.0 "CC1C(C(C(O1)N2C=C(C(=O)NC2=O)C)O)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 A1CY0 "SYSTEMATIC NAME" ACDLabs 14.52 "1-(5-deoxy-3-O-phosphono-alpha-L-arabinofuranosyl)-5-methylpyrimidine-2,4(1H,3H)-dione" A1CY0 "SYSTEMATIC NAME" "OpenEye OEToolkits" 3.1.0.0 "[(2~{S},3~{R},4~{R},5~{R})-2-methyl-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-oxidanyl-oxolan-3-yl] dihydrogen 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 A1CY0 "Create component" 2025-10-20 RCSB A1CY0 "Initial release" 2026-10-21 RCSB #