data_A1L4U # _chem_comp.id A1L4U _chem_comp.name "methyl 2-[1-[(2~{R},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-4-oxidanylidene-pyrimidin-5-yl]ethanoate" _chem_comp.type "RNA linking" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C12 H17 N2 O10 P" _chem_comp.mon_nstd_parent_comp_id U _chem_comp.pdbx_synonyms 5-methoxycarbonylmethyl-2-deoxouridine _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2024-10-09 _chem_comp.pdbx_modified_date 2026-03-06 _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 380.245 _chem_comp.one_letter_code U _chem_comp.three_letter_code A1L4U _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 9JPO _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ _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 A1L4U C6 C1 C 0 1 N N N N N N 174.301 187.739 265.981 2.440 0.845 0.203 C6 A1L4U 1 A1L4U C8 C2 C 0 1 N N N N N N 172.493 187.285 263.491 5.157 -0.971 0.723 C8 A1L4U 2 A1L4U O4 O1 O 0 1 N N N N N N 176.530 187.362 263.314 4.114 -0.688 -2.455 O4 A1L4U 3 A1L4U "C1'" C3 C 0 1 N N R N N N 174.718 187.684 268.466 0.061 1.361 0.434 "C1'" A1L4U 4 A1L4U C2 C4 C 0 1 N N N N N N 176.498 187.388 266.770 0.970 0.283 -1.546 C2 A1L4U 5 A1L4U "C2'" C5 C 0 1 N N R N N N 175.408 188.798 269.250 -0.538 2.595 -0.287 "C2'" A1L4U 6 A1L4U "C3'" C6 C 0 1 N N S N N N 174.331 189.866 269.282 -1.987 2.617 0.256 "C3'" A1L4U 7 A1L4U C4 C7 C 0 1 N N N N N N 176.116 187.435 264.457 3.207 -0.217 -1.786 C4 A1L4U 8 A1L4U "C4'" C8 C 0 1 N N R N N N 173.070 189.041 269.367 -2.225 1.178 0.755 "C4'" A1L4U 9 A1L4U C5 C9 C 0 1 N N N N N N 174.724 187.659 264.689 3.471 0.333 -0.508 C5 A1L4U 10 A1L4U "C5'" C10 C 0 1 N N N N N N 171.801 189.728 268.955 -3.422 0.566 0.024 "C5'" A1L4U 11 A1L4U C5M C11 C 0 1 N N N N N N 173.914 187.806 263.433 4.871 0.347 0.049 C5M A1L4U 12 A1L4U C9 C12 C 0 1 N N N N N N 171.630 188.347 261.534 6.557 -2.479 1.925 C9 A1L4U 13 A1L4U N1 N1 N 0 1 N N N N N N 175.166 187.611 267.064 1.186 0.813 -0.328 N1 A1L4U 14 A1L4U N3 N2 N 0 1 N N N N N N 176.992 187.304 265.567 1.946 -0.214 -2.256 N3 A1L4U 15 A1L4U "O2'" O2 O 0 1 N N N N N N 175.648 188.315 270.559 0.162 3.787 0.078 "O2'" A1L4U 16 A1L4U "O3'" O3 O 0 1 N N N N N N 174.466 190.761 270.365 -2.103 3.546 1.336 "O3'" A1L4U 17 A1L4U "O4'" O4 O 0 1 N N N N N N 173.338 187.942 268.479 -1.037 0.423 0.465 "O4'" A1L4U 18 A1L4U "O5'" O5 O 0 1 N N N N N N 171.957 190.372 267.710 -3.707 -0.722 0.573 "O5'" A1L4U 19 A1L4U O8 O6 O 0 1 N N N N N N 172.209 186.242 264.034 4.310 -1.833 0.748 O8 A1L4U 20 A1L4U O9 O7 O 0 1 N N N N N N 171.465 188.008 262.901 6.352 -1.187 1.294 O9 A1L4U 21 A1L4U OP1 O8 O 0 1 N N N N N N 170.279 189.203 266.309 -6.180 -0.902 0.100 OP1 A1L4U 22 A1L4U OP2 O9 O 0 1 N N N N N N 169.748 191.460 267.462 -4.612 -2.096 -1.477 OP2 A1L4U 23 A1L4U P P1 P 0 1 N N N N N N 170.717 190.570 266.749 -4.907 -1.655 0.043 P A1L4U 24 A1L4U OP3 O10 O 0 1 N N N N N N 171.333 191.360 265.500 -5.017 -2.967 0.970 OP3 A1L4U 25 A1L4U H6 H1 H 0 1 N N N N N N 173.252 187.909 266.173 2.609 1.271 1.181 H6 A1L4U 26 A1L4U "H1'" H2 H 0 1 N N N N N N 174.929 186.726 268.963 0.372 1.620 1.446 "H1'" A1L4U 27 A1L4U H2 H3 H 0 1 N N N N N N 177.181 187.275 267.599 -0.033 0.273 -1.947 H2 A1L4U 28 A1L4U "H2'" H4 H 0 1 N N N N N N 176.317 189.150 268.740 -0.529 2.456 -1.368 "H2'" A1L4U 29 A1L4U "H3'" H5 H 0 1 N N N N N N 174.340 190.413 268.327 -2.689 2.866 -0.539 "H3'" A1L4U 30 A1L4U "H4'" H6 H 0 1 N N N N N N 172.957 188.670 270.396 -2.408 1.184 1.829 "H4'" A1L4U 31 A1L4U "H5''" H7 H 0 0 N N N N N N 170.997 188.981 268.876 -4.291 1.213 0.144 "H5''" A1L4U 32 A1L4U "H5'" H8 H 0 1 N N N N N N 171.533 190.476 269.716 -3.188 0.465 -1.036 "H5'" A1L4U 33 A1L4U H71 H9 H 0 1 N N N N N N 173.869 188.877 263.185 4.965 1.154 0.775 H71 A1L4U 34 A1L4U H72 H10 H 0 1 N N N N N N 174.437 187.266 262.630 5.583 0.502 -0.762 H72 A1L4U 35 A1L4U H92 H11 H 0 1 N N N N N N 170.754 188.915 261.188 7.561 -2.522 2.346 H92 A1L4U 36 A1L4U H91 H12 H 0 1 N N N N N N 172.535 188.961 261.415 5.823 -2.617 2.719 H91 A1L4U 37 A1L4U H93 H13 H 0 1 N N N N N N 171.730 187.428 260.938 6.440 -3.268 1.182 H93 A1L4U 38 A1L4U "HO2'" H14 H 0 0 N N N N N N 176.078 188.989 271.072 -0.176 4.587 -0.348 "HO2'" A1L4U 39 A1L4U "HO3'" H15 H 0 0 N N N N N N 173.768 191.404 270.334 -1.906 4.460 1.091 "HO3'" A1L4U 40 A1L4U H1 H16 H 0 1 N N N N N N 171.300 190.808 264.728 -5.721 -3.576 0.708 H1 A1L4U 41 A1L4U H3 H17 H 0 1 N N N N N N 168.915 191.013 267.553 -3.792 -2.595 -1.590 H3 A1L4U 42 # 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 A1L4U N1 C2 SING N N 1 A1L4U N1 C6 SING N N 2 A1L4U N1 "C1'" SING N N 3 A1L4U C2 N3 DOUB N N 4 A1L4U N3 C4 SING N N 5 A1L4U C4 C5 SING N N 6 A1L4U C4 O4 DOUB N N 7 A1L4U C5 C5M SING N N 8 A1L4U C5 C6 DOUB N N 9 A1L4U C5M C8 SING N N 10 A1L4U C8 O9 SING N N 11 A1L4U C8 O8 DOUB N N 12 A1L4U O9 C9 SING N N 13 A1L4U "C1'" "C2'" SING N N 14 A1L4U "C1'" "O4'" SING N N 15 A1L4U "O2'" "C2'" SING N N 16 A1L4U "C2'" "C3'" SING N N 17 A1L4U "O3'" "C3'" SING N N 18 A1L4U "C3'" "C4'" SING N N 19 A1L4U "C4'" "O4'" SING N N 20 A1L4U "C4'" "C5'" SING N N 21 A1L4U "C5'" "O5'" SING N N 22 A1L4U "O5'" P SING N N 23 A1L4U P OP2 SING N N 24 A1L4U P OP3 SING N N 25 A1L4U P OP1 DOUB N N 26 A1L4U C6 H6 SING N N 27 A1L4U "C1'" "H1'" SING N N 28 A1L4U C2 H2 SING N N 29 A1L4U "C2'" "H2'" SING N N 30 A1L4U "C3'" "H3'" SING N N 31 A1L4U "C4'" "H4'" SING N N 32 A1L4U "C5'" "H5''" SING N N 33 A1L4U "C5'" "H5'" SING N N 34 A1L4U C5M H71 SING N N 35 A1L4U C5M H72 SING N N 36 A1L4U C9 H92 SING N N 37 A1L4U C9 H91 SING N N 38 A1L4U C9 H93 SING N N 39 A1L4U "O2'" "HO2'" SING N N 40 A1L4U "O3'" "HO3'" SING N N 41 A1L4U OP3 H1 SING N N 42 A1L4U OP2 H3 SING N N 43 # 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 A1L4U InChI InChI 1.06 "InChI=1S/C12H17N2O10P/c1-22-8(15)2-6-3-14(5-13-11(6)18)12-10(17)9(16)7(24-12)4-23-25(19,20)21/h3,5,7,9-10,12,16-17H,2,4H2,1H3,(H2,19,20,21)" A1L4U InChIKey InChI 1.06 FCZFXJJAOVKHCD-UHFFFAOYSA-N A1L4U SMILES_CANONICAL CACTVS 3.385 "COC(=O)CC1=CN(C=NC1=O)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O" A1L4U SMILES CACTVS 3.385 "COC(=O)CC1=CN(C=NC1=O)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O" A1L4U SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "COC(=O)CC1=CN(C=NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O" A1L4U SMILES "OpenEye OEToolkits" 2.0.7 "COC(=O)CC1=CN(C=NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)O" # _pdbx_chem_comp_identifier.comp_id A1L4U _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "methyl 2-[1-[(2~{R},3~{R},4~{S},5~{R})-3,4-bis(oxidanyl)-5-(phosphonooxymethyl)oxolan-2-yl]-4-oxidanylidene-pyrimidin-5-yl]ethanoate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site A1L4U "Create component" 2024-10-09 PDBJ A1L4U "Modify synonyms" 2024-10-30 PDBJ A1L4U "Initial release" 2026-03-11 RCSB # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id A1L4U _pdbx_chem_comp_synonyms.name 5-methoxycarbonylmethyl-2-deoxouridine _pdbx_chem_comp_synonyms.provenance AUTHOR _pdbx_chem_comp_synonyms.type ? #