data_TYU # _chem_comp.id TYU _chem_comp.name TETRAHYDROURIDINE _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C9 H16 N2 O6" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "1-(3,4-DIHYDROXY-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-2-YL)-4- HYDROXY-TETRAHYDRO-PYRIMIDIN-2-ONE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2004-11-11 _chem_comp.pdbx_modified_date 2021-03-13 _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 248.233 _chem_comp.one_letter_code N _chem_comp.three_letter_code TYU _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 EBI # # 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 TYU "O5'" O5* O 0 1 N N N 14.672 1.254 63.361 3.110 2.840 0.578 "O5'" TYU 1 TYU "C5'" C5* C 0 1 N N N 13.627 0.506 63.985 3.112 1.711 -0.298 "C5'" TYU 2 TYU "C4'" C4* C 0 1 N N R 13.742 0.612 65.487 2.526 0.500 0.431 "C4'" TYU 3 TYU "O4'" O4* O 0 1 N N N 14.816 -0.265 65.930 1.131 0.720 0.701 "O4'" TYU 4 TYU "C1'" C1* C 0 1 N N R 15.741 0.473 66.700 0.475 -0.562 0.602 "C1'" TYU 5 TYU N1 N1 N 0 1 N N N 17.076 -0.120 66.525 -0.959 -0.390 0.361 N1 TYU 6 TYU C6 C6 C 0 1 N N N 17.520 -0.597 65.301 -1.920 -1.051 1.246 C6 TYU 7 TYU C2 C2 C 0 1 N N N 17.804 -0.367 67.655 -1.366 0.374 -0.664 C2 TYU 8 TYU O2 O2 O 0 1 N N N 17.378 -0.189 68.781 -0.527 0.891 -1.375 O2 TYU 9 TYU N3 N3 N 0 1 N N N 19.063 -0.828 67.408 -2.662 0.581 -0.941 N3 TYU 10 TYU C4 C4 C 0 1 N N R 19.631 -1.011 66.165 -3.720 -0.024 -0.131 C4 TYU 11 TYU O4 O4 O 0 1 N N N 20.955 -0.300 66.228 -4.862 0.836 -0.114 O4 TYU 12 TYU C5 C5 C 0 1 N N N 18.844 -0.325 65.155 -3.207 -0.222 1.300 C5 TYU 13 TYU "C2'" C2* C 0 1 N N R 15.609 1.907 66.194 1.162 -1.226 -0.618 "C2'" TYU 14 TYU "O2'" O2* O 0 1 N N N 16.124 2.831 67.128 1.078 -2.650 -0.539 "O2'" TYU 15 TYU "C3'" C3* C 0 1 N N S 14.099 2.006 66.000 2.631 -0.750 -0.464 "C3'" TYU 16 TYU "O3'" O3* O 0 1 N N N 13.432 2.283 67.233 3.420 -1.760 0.168 "O3'" TYU 17 TYU "H5'" H5* H 0 1 N N N 14.445 1.420 62.454 3.486 3.580 0.082 "H5'" TYU 18 TYU "H5'1" 1H5* H 0 0 N N N 13.713 -0.550 63.690 2.508 1.933 -1.177 "H5'1" TYU 19 TYU "H5''" 2H5* H 0 0 N N N 12.653 0.906 63.666 4.134 1.491 -0.605 "H5''" TYU 20 TYU "H4'" H4* H 0 1 N N N 12.750 0.346 65.880 3.063 0.334 1.365 "H4'" TYU 21 TYU "H1'" H1* H 0 1 N N N 15.560 0.458 67.785 0.644 -1.150 1.504 "H1'" TYU 22 TYU H61 1H6 H 0 1 N N N 16.957 -0.107 64.493 -2.144 -2.047 0.863 H61 TYU 23 TYU H62 2H6 H 0 1 N N N 17.364 -1.685 65.255 -1.496 -1.132 2.247 H62 TYU 24 TYU HN3 HN3 H 0 1 N N N 19.627 -1.054 68.202 -2.903 1.145 -1.692 HN3 TYU 25 TYU H4 H4 H 0 1 N N N 19.704 -2.081 65.919 -3.997 -0.989 -0.555 H4 TYU 26 TYU HO4 HO4 H 0 1 N N N 21.277 -0.150 65.347 -5.152 0.933 -1.032 HO4 TYU 27 TYU H51 1H5 H 0 1 N N N 18.995 0.759 65.269 -3.958 -0.749 1.888 H51 TYU 28 TYU H52 2H5 H 0 1 N N N 19.170 -0.660 64.159 -2.999 0.749 1.751 H52 TYU 29 TYU "H2'" H2* H 0 1 N N N 16.177 2.139 65.281 0.731 -0.864 -1.552 "H2'" TYU 30 TYU H1 H1 H 0 1 N N N 16.240 2.402 67.968 1.521 -3.001 -1.323 H1 TYU 31 TYU "H3'" H3* H 0 1 N N N 13.799 2.818 65.322 3.052 -0.490 -1.435 "H3'" TYU 32 TYU H2 H2 H 0 1 N N N 14.072 2.344 67.933 4.319 -1.410 0.237 H2 TYU 33 # # 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 TYU "O5'" "C5'" SING N N 1 TYU "O5'" "H5'" SING N N 2 TYU "C5'" "C4'" SING N N 3 TYU "C5'" "H5'1" SING N N 4 TYU "C5'" "H5''" SING N N 5 TYU "C4'" "O4'" SING N N 6 TYU "C4'" "C3'" SING N N 7 TYU "C4'" "H4'" SING N N 8 TYU "O4'" "C1'" SING N N 9 TYU "C1'" N1 SING N N 10 TYU "C1'" "C2'" SING N N 11 TYU "C1'" "H1'" SING N N 12 TYU N1 C6 SING N N 13 TYU N1 C2 SING N N 14 TYU C6 C5 SING N N 15 TYU C6 H61 SING N N 16 TYU C6 H62 SING N N 17 TYU C2 O2 DOUB N N 18 TYU C2 N3 SING N N 19 TYU N3 C4 SING N N 20 TYU N3 HN3 SING N N 21 TYU C4 O4 SING N N 22 TYU C4 C5 SING N N 23 TYU C4 H4 SING N N 24 TYU O4 HO4 SING N N 25 TYU C5 H51 SING N N 26 TYU C5 H52 SING N N 27 TYU "C2'" "O2'" SING N N 28 TYU "C2'" "C3'" SING N N 29 TYU "C2'" "H2'" SING N N 30 TYU "O2'" H1 SING N N 31 TYU "C3'" "O3'" SING N N 32 TYU "C3'" "H3'" SING N N 33 TYU "O3'" H2 SING N N 34 # # 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 TYU SMILES ACDLabs 10.04 "O=C1N(CCC(O)N1)C2OC(C(O)C2O)CO" TYU SMILES_CANONICAL CACTVS 3.341 "OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2CC[C@@H](O)NC2=O" TYU SMILES CACTVS 3.341 "OC[CH]1O[CH]([CH](O)[CH]1O)N2CC[CH](O)NC2=O" TYU SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1CN(C(=O)N[C@@H]1O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO)O)O" TYU SMILES "OpenEye OEToolkits" 1.5.0 "C1CN(C(=O)NC1O)C2C(C(C(O2)CO)O)O" TYU InChI InChI 1.03 "InChI=1S/C9H16N2O6/c12-3-4-6(14)7(15)8(17-4)11-2-1-5(13)10-9(11)16/h4-8,12-15H,1-3H2,(H,10,16)/t4-,5-,6-,7-,8-/m1/s1" TYU InChIKey InChI 1.03 UCKYOOZPSJFJIZ-FMDGEEDCSA-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 TYU "SYSTEMATIC NAME" ACDLabs 10.04 "(4R)-4-hydroxy-1-beta-D-ribofuranosyltetrahydropyrimidin-2(1H)-one" TYU "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(4R)-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-4-hydroxy-1,3-diazinan-2-one" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site TYU "Create component" 2004-11-11 EBI TYU "Modify descriptor" 2011-06-04 RCSB TYU "Modify synonyms" 2021-03-13 RCSB # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id TYU _pdbx_chem_comp_synonyms.name "1-(3,4-DIHYDROXY-5-HYDROXYMETHYL-TETRAHYDRO-FURAN-2-YL)-4- HYDROXY-TETRAHYDRO-PYRIMIDIN-2-ONE" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? ##