data_URD # _chem_comp.id URD _chem_comp.name "1-((2R,3R,4S,5R)-TETRAHYDRO-3,4-DIHYDROXY-5-(HYDROXYMETHYL)FURAN-2-YL)PYRIDINE-2,4(1H,3H)-DIONE" _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H13 N O6" _chem_comp.mon_nstd_parent_comp_id U _chem_comp.pdbx_synonyms 3-DEAZAURIDINE _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2005-04-08 _chem_comp.pdbx_modified_date 2021-03-01 _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 243.213 _chem_comp.one_letter_code U _chem_comp.three_letter_code URD _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code ? _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # # 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.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 URD "O5'" O5* O 0 1 N N N 14.592 1.028 63.327 3.373 2.694 0.738 "O5'" URD 1 URD "C5'" C5* C 0 1 N N N 13.418 0.500 63.932 3.273 1.671 -0.256 "C5'" URD 2 URD "C4'" C4* C 0 1 N N R 13.506 0.624 65.434 2.570 0.450 0.339 "C4'" URD 3 URD "O4'" O4* O 0 1 N N N 14.431 -0.377 65.943 1.201 0.771 0.637 "O4'" URD 4 URD "C1'" C1* C 0 1 N N R 15.462 0.252 66.679 0.426 -0.425 0.402 "C1'" URD 5 URD N1 N1 N 0 1 N N N 16.705 -0.507 66.474 -0.984 -0.092 0.186 N1 URD 6 URD C6 C6 C 0 1 N N N 17.032 -1.029 65.244 -1.301 0.824 -0.768 C6 URD 7 URD C2 C2 C 0 1 N N N 17.538 -0.693 67.568 -1.917 -0.709 0.937 C2 URD 8 URD O2 O2 O 0 1 N N N 17.297 -0.230 68.670 -1.600 -1.522 1.778 O2 URD 9 URD C3 C3 C 0 1 N N N 18.664 -1.441 67.320 -3.373 -0.354 0.709 C3 URD 10 URD C4 C4 C 0 1 N N N 19.044 -2.006 66.118 -3.660 0.674 -0.369 C4 URD 11 URD O4 O4 O 0 1 N N N 19.929 -2.869 66.122 -4.795 1.020 -0.626 O4 URD 12 URD C5 C5 C 0 1 N N N 18.140 -1.749 65.034 -2.555 1.212 -1.059 C5 URD 13 URD "C2'" C2* C 0 1 N N R 15.512 1.676 66.141 1.055 -1.015 -0.886 "C2'" URD 14 URD "O2'" O2* O 0 1 N N N 16.190 2.544 67.028 0.835 -2.425 -0.962 "O2'" URD 15 URD "C3'" C3* C 0 1 N N S 14.024 1.960 65.946 2.561 -0.701 -0.687 "C3'" URD 16 URD "O3'" O3* O 0 1 N N N 13.379 2.273 67.173 3.246 -1.844 -0.172 "O3'" URD 17 URD "HO5'" *HO5 H 0 0 N Y N 14.444 1.146 62.396 3.821 3.443 0.323 "HO5'" URD 18 URD "H5'" 1H5* H 0 1 N N N 13.322 -0.562 63.664 2.699 2.044 -1.104 "H5'" URD 19 URD "H5''" 2H5* H 0 0 N N N 12.542 1.060 63.573 4.272 1.389 -0.589 "H5''" URD 20 URD "H4'" H4* H 0 1 N N N 12.470 0.502 65.782 3.082 0.132 1.247 "H4'" URD 21 URD "H1'" H1* H 0 1 N N N 15.302 0.280 67.767 0.532 -1.121 1.234 "H1'" URD 22 URD H6 H6 H 0 1 N N N 16.366 -0.850 64.413 -0.492 1.270 -1.329 H6 URD 23 URD H31 1H3 H 0 1 N N N 18.411 -2.352 67.882 -3.783 0.017 1.648 H31 URD 24 URD H32 2H3 H 0 1 N N N 19.493 -0.762 67.567 -3.904 -1.271 0.452 H32 URD 25 URD H5 H5 H 0 1 N N N 18.354 -2.137 64.049 -2.718 1.946 -1.833 H5 URD 26 URD "H2'" H2* H 0 1 N N N 16.086 1.823 65.214 0.666 -0.514 -1.773 "H2'" URD 27 URD "HO2'" *HO2 H 0 0 N N N 16.342 2.099 67.853 1.248 -2.729 -1.781 "HO2'" URD 28 URD "H3'" H3* H 0 1 N N N 13.841 2.817 65.281 3.011 -0.378 -1.625 "H3'" URD 29 URD "HO3'" *HO3 H 0 0 N Y N 14.028 2.343 67.863 4.174 -1.591 -0.069 "HO3'" URD 30 # # 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 URD "O5'" "C5'" SING N N 1 URD "O5'" "HO5'" SING N N 2 URD "C5'" "C4'" SING N N 3 URD "C5'" "H5'" SING N N 4 URD "C5'" "H5''" SING N N 5 URD "C4'" "O4'" SING N N 6 URD "C4'" "C3'" SING N N 7 URD "C4'" "H4'" SING N N 8 URD "O4'" "C1'" SING N N 9 URD "C1'" N1 SING N N 10 URD "C1'" "C2'" SING N N 11 URD "C1'" "H1'" SING N N 12 URD N1 C6 SING N N 13 URD N1 C2 SING N N 14 URD C6 C5 DOUB N N 15 URD C6 H6 SING N N 16 URD C2 O2 DOUB N N 17 URD C2 C3 SING N N 18 URD C3 C4 SING N N 19 URD C3 H31 SING N N 20 URD C3 H32 SING N N 21 URD C4 O4 DOUB N N 22 URD C4 C5 SING N N 23 URD C5 H5 SING N N 24 URD "C2'" "O2'" SING N N 25 URD "C2'" "C3'" SING N N 26 URD "C2'" "H2'" SING N N 27 URD "O2'" "HO2'" SING N N 28 URD "C3'" "O3'" SING N N 29 URD "C3'" "H3'" SING N N 30 URD "O3'" "HO3'" SING N N 31 # # 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 URD SMILES ACDLabs 10.04 "O=C1C=CN(C(=O)C1)C2OC(C(O)C2O)CO" URD SMILES_CANONICAL CACTVS 3.341 "OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2C=CC(=O)CC2=O" URD SMILES CACTVS 3.341 "OC[CH]1O[CH]([CH](O)[CH]1O)N2C=CC(=O)CC2=O" URD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1C(=O)C=CN(C1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO)O)O" URD SMILES "OpenEye OEToolkits" 1.5.0 "C1C(=O)C=CN(C1=O)C2C(C(C(O2)CO)O)O" URD InChI InChI 1.03 "InChI=1S/C10H13NO6/c12-4-6-8(15)9(16)10(17-6)11-2-1-5(13)3-7(11)14/h1-2,6,8-10,12,15-16H,3-4H2/t6-,8-,9-,10-/m1/s1" URD InChIKey InChI 1.03 WIRVQQCUKDPURA-PEBGCTIMSA-N # # 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 URD "SYSTEMATIC NAME" ACDLabs 10.04 "1-beta-D-ribofuranosylpyridine-2,4(1H,3H)-dione" URD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]pyridine-2,4-dione" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site URD "Create component" 2005-04-08 RCSB URD "Modify descriptor" 2011-06-04 RCSB URD "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id URD _pdbx_chem_comp_synonyms.name 3-DEAZAURIDINE _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##