data_A1CNT # _chem_comp.id A1CNT _chem_comp.name "[(3R,4R,5R)-4-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)oxolan-3-yl]methyl dihydrogen phosphate" _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 2025-08-19 _chem_comp.pdbx_modified_date 2025-10-31 _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 A1CNT _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 9Q3C _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 A1CNT O4 O1 O 0 1 N N N N N N 22.299 27.733 57.909 3.722 -2.913 -0.824 O4 A1CNT 1 A1CNT C6 C1 C 0 1 N N N N N N 21.474 31.185 57.792 2.052 -0.510 1.083 C6 A1CNT 2 A1CNT "C1'" C2 C 0 1 N N R N N N 22.536 33.047 56.540 1.625 1.855 0.601 "C1'" A1CNT 3 A1CNT C2 C3 C 0 1 N N N N N N 23.329 30.745 56.331 2.843 0.418 -0.935 C2 A1CNT 4 A1CNT "C2'" C4 C 0 1 N N R N N N 21.222 33.684 56.079 0.448 2.212 -0.333 "C2'" A1CNT 5 A1CNT "C3'" C5 C 0 1 N N R N N N 21.204 35.072 56.757 -0.802 1.732 0.437 "C3'" A1CNT 6 A1CNT C4 C6 C 0 1 N N N N N N 22.292 28.937 57.640 3.247 -1.841 -0.494 C4 A1CNT 7 A1CNT "C4'" C7 C 0 1 N N N N N N 22.562 35.128 57.455 -0.232 1.141 1.746 "C4'" A1CNT 8 A1CNT C5 C8 C 0 1 N N N N N N 21.369 29.905 58.191 2.569 -1.709 0.741 C5 A1CNT 9 A1CNT "C5'" C9 C 0 1 N N N N N N 20.065 35.275 57.737 -1.542 0.655 -0.360 "C5'" A1CNT 10 A1CNT C7 C10 C 0 1 N N N N N N 20.324 29.433 59.153 2.426 -2.892 1.664 C7 A1CNT 11 A1CNT N1 N1 N 0 1 N N N N N N 22.423 31.620 56.895 2.191 0.554 0.234 N1 A1CNT 12 A1CNT N3 N2 N 0 1 N N N N N N 23.205 29.445 56.740 3.373 -0.765 -1.298 N3 A1CNT 13 A1CNT O2 O2 O 0 1 N N N N N N 24.172 31.088 55.518 2.964 1.379 -1.670 O2 A1CNT 14 A1CNT "O2'" O3 O 0 1 N N N N N N 21.213 33.834 54.668 0.391 3.624 -0.549 "O2'" A1CNT 15 A1CNT "O4'" O4 O 0 1 N N N N N N 22.934 33.763 57.697 1.043 1.795 1.921 "O4'" A1CNT 16 A1CNT "O5'" O5 O 0 1 N N N N N N 19.931 34.099 58.544 -2.755 0.314 0.313 "O5'" A1CNT 17 A1CNT OP1 O6 O 0 1 N N N N N N 17.703 34.986 59.341 -3.073 -2.068 -0.461 OP1 A1CNT 18 A1CNT OP2 O7 O 0 1 N N N N N N 18.343 32.527 59.648 -4.968 -1.009 0.827 OP2 A1CNT 19 A1CNT P P1 P 0 1 N N N N N N 18.927 34.026 59.810 -3.787 -0.789 -0.244 P A1CNT 20 A1CNT H6 H1 H 0 1 N N N N N N 20.780 31.907 58.195 1.528 -0.391 2.019 H6 A1CNT 21 A1CNT "H1'" H2 H 0 1 N N N N N N 23.284 33.167 55.743 2.392 2.629 0.559 "H1'" A1CNT 22 A1CNT "H2'" H3 H 0 1 N N N N N N 20.369 33.085 56.430 0.539 1.683 -1.282 "H2'" A1CNT 23 A1CNT "H3'" H4 H 0 1 N N N N N N 21.162 35.850 55.981 -1.464 2.571 0.653 "H3'" A1CNT 24 A1CNT "H4'" H5 H 0 1 N N N N N N 23.305 35.619 56.809 -0.893 1.366 2.583 "H4'" A1CNT 25 A1CNT "H4''" H6 H 0 0 N N N N N N 22.482 35.677 58.405 -0.096 0.064 1.648 "H4''" A1CNT 26 A1CNT "H5'" H7 H 0 1 N N N N N N 20.281 36.141 58.380 -1.773 1.035 -1.355 "H5'" A1CNT 27 A1CNT "H5''" H8 H 0 0 N N N N N N 19.130 35.452 57.185 -0.912 -0.230 -0.446 "H5''" A1CNT 28 A1CNT H73 H9 H 0 1 N N N N N N 19.709 30.286 59.475 2.906 -3.763 1.215 H73 A1CNT 29 A1CNT H71 H10 H 0 1 N N N N N N 19.684 28.685 58.662 2.901 -2.668 2.619 H71 A1CNT 30 A1CNT H72 H11 H 0 1 N N N N N N 20.810 28.980 60.030 1.369 -3.103 1.824 H72 A1CNT 31 A1CNT H3 H12 H 0 1 N N N N N N 23.848 28.791 56.342 3.847 -0.845 -2.141 H3 A1CNT 32 A1CNT H1 H13 H 0 1 N N N N N N 20.393 34.230 54.396 1.179 3.988 -0.976 H1 A1CNT 33 A1CNT HP H14 H 0 1 N N N N N N 17.450 32.568 59.327 -5.628 -1.662 0.556 HP A1CNT 34 A1CNT OP3 OP3 O 0 1 N Y N N N N 19.612 34.446 61.143 -4.413 -0.282 -1.638 OP3 A1CNT 35 A1CNT H2 H15 H 0 1 N Y N N N N 19.190 35.226 61.484 -4.897 0.553 -1.571 H2 A1CNT 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 A1CNT C4 C5 SING N N 1 A1CNT C5 C6 DOUB N N 2 A1CNT C6 N1 SING N N 3 A1CNT N1 C2 SING N N 4 A1CNT C4 N3 SING N N 5 A1CNT C2 N3 SING N N 6 A1CNT C2 O2 DOUB N N 7 A1CNT N1 "C1'" SING N N 8 A1CNT "C1'" "C2'" SING N N 9 A1CNT "C2'" "C3'" SING N N 10 A1CNT "C3'" "C4'" SING N N 11 A1CNT "C1'" "O4'" SING N N 12 A1CNT "C4'" "O4'" SING N N 13 A1CNT "C3'" "C5'" SING N N 14 A1CNT "C5'" "O5'" SING N N 15 A1CNT "O5'" P SING N N 16 A1CNT P OP2 SING N N 17 A1CNT P OP1 DOUB N N 18 A1CNT "C2'" "O2'" SING N N 19 A1CNT C5 C7 SING N N 20 A1CNT C4 O4 DOUB N N 21 A1CNT C6 H6 SING N N 22 A1CNT "C1'" "H1'" SING N N 23 A1CNT "C2'" "H2'" SING N N 24 A1CNT "C3'" "H3'" SING N N 25 A1CNT "C4'" "H4'" SING N N 26 A1CNT "C4'" "H4''" SING N N 27 A1CNT "C5'" "H5'" SING N N 28 A1CNT "C5'" "H5''" SING N N 29 A1CNT C7 H73 SING N N 30 A1CNT C7 H71 SING N N 31 A1CNT C7 H72 SING N N 32 A1CNT N3 H3 SING N N 33 A1CNT "O2'" H1 SING N N 34 A1CNT OP2 HP SING N N 35 A1CNT P OP3 SING N N 36 A1CNT 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 A1CNT SMILES ACDLabs 14.52 "O=P(O)(O)OCC1COC(N2C=C(C)C(=O)NC2=O)C1O" A1CNT InChI InChI 1.06 "InChI=1S/C10H15N2O8P/c1-5-2-12(10(15)11-8(5)14)9-7(13)6(3-19-9)4-20-21(16,17)18/h2,6-7,9,13H,3-4H2,1H3,(H,11,14,15)(H2,16,17,18)/t6-,7-,9-/m1/s1" A1CNT InChIKey InChI 1.06 CLFGYSCORDJBPE-ZXFLCMHBSA-N A1CNT SMILES_CANONICAL CACTVS 3.385 "CC1=CN([C@@H]2OC[C@H](CO[P](O)(O)=O)[C@H]2O)C(=O)NC1=O" A1CNT SMILES CACTVS 3.385 "CC1=CN([CH]2OC[CH](CO[P](O)(O)=O)[CH]2O)C(=O)NC1=O" A1CNT SMILES_CANONICAL "OpenEye OEToolkits" 3.1.0.0 "CC1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@H](CO2)COP(=O)(O)O)O" A1CNT SMILES "OpenEye OEToolkits" 3.1.0.0 "CC1=CN(C(=O)NC1=O)C2C(C(CO2)COP(=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 A1CNT "SYSTEMATIC NAME" ACDLabs 14.52 "[(3R,4R,5R)-4-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)oxolan-3-yl]methyl dihydrogen phosphate" A1CNT "SYSTEMATIC NAME" "OpenEye OEToolkits" 3.1.0.0 "[(3~{R},4~{R},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-oxidanyl-oxolan-3-yl]methyl 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 A1CNT "Create component" 2025-08-19 RCSB A1CNT "Modify descriptor" 2025-10-30 RCSB A1CNT "Initial release" 2025-11-05 RCSB #