data_U4P # _chem_comp.id U4P _chem_comp.name "5'-deoxyuridine" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C9 H12 N2 O5" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-04-16 _chem_comp.pdbx_modified_date 2021-04-16 _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 228.202 _chem_comp.one_letter_code ? _chem_comp.three_letter_code U4P _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 6WKB _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 U4P OAC O1 O 0 1 N N N 2.750 -56.622 25.466 0.331 1.364 0.871 OAC U4P 1 U4P CAM C1 C 0 1 N N N 2.726 -57.284 24.229 1.198 0.659 0.393 CAM U4P 2 U4P NAI N1 N 0 1 N N N 1.868 -58.447 24.080 2.487 0.888 0.706 NAI U4P 3 U4P CAL C2 C 0 1 N N N 1.812 -59.128 22.900 3.461 0.115 0.184 CAL U4P 4 U4P OAB O2 O 0 1 N N N 0.986 -60.255 22.753 4.627 0.321 0.467 OAB U4P 5 U4P CAK C3 C 0 1 N N N 2.602 -58.691 21.786 3.115 -0.940 -0.695 CAK U4P 6 U4P CAG C4 C 0 1 N N N 3.433 -57.566 21.916 1.814 -1.147 -0.992 CAG U4P 7 U4P NAR N2 N 0 1 N N N 3.499 -56.853 23.135 0.856 -0.343 -0.437 NAR U4P 8 U4P "C1'" C5 C 0 1 N N R 4.360 -55.734 23.182 -0.555 -0.569 -0.759 "C1'" U4P 9 U4P "O4'" O3 O 0 1 N N N 5.616 -56.025 24.071 -1.153 0.655 -1.219 "O4'" U4P 10 U4P "C4'" C6 C 0 1 N N R 5.688 -54.662 24.813 -2.523 0.653 -0.762 "C4'" U4P 11 U4P "C5'" C7 C 0 1 N N N 6.285 -54.823 26.162 -3.080 2.077 -0.724 "C5'" U4P 12 U4P "C3'" C8 C 0 1 N N S 4.305 -54.199 24.936 -2.425 0.066 0.669 "C3'" U4P 13 U4P "O3'" O4 O 0 1 N N N 4.239 -52.746 25.175 -3.662 -0.534 1.060 "O3'" U4P 14 U4P "C2'" C9 C 0 1 N N R 3.714 -54.516 23.684 -1.319 -1.004 0.507 "C2'" U4P 15 U4P "O2'" O5 O 0 1 N N N 3.996 -53.405 22.734 -1.897 -2.297 0.322 "O2'" U4P 16 U4P H1 H1 H 0 1 N N N 1.311 -58.752 24.853 2.716 1.612 1.309 H1 U4P 17 U4P H2 H2 H 0 1 N N N 2.558 -59.226 20.849 3.882 -1.567 -1.125 H2 U4P 18 U4P H3 H3 H 0 1 N N N 4.028 -57.242 21.075 1.531 -1.947 -1.660 H3 U4P 19 U4P H4 H4 H 0 1 N N N 4.729 -55.529 22.166 -0.642 -1.338 -1.527 H4 U4P 20 U4P H5 H5 H 0 1 N N N 6.281 -53.953 24.216 -3.138 0.015 -1.397 H5 U4P 21 U4P H6 H6 H 0 1 N N N 6.324 -53.846 26.665 -3.067 2.499 -1.729 H6 U4P 22 U4P H7 H7 H 0 1 N N N 5.670 -55.516 26.755 -4.105 2.056 -0.352 H7 U4P 23 U4P H8 H8 H 0 1 N N N 7.304 -55.227 26.066 -2.467 2.690 -0.064 H8 U4P 24 U4P H9 H9 H 0 1 N N N 3.799 -54.736 25.752 -2.124 0.832 1.384 H9 U4P 25 U4P H10 H10 H 0 1 N N N 4.636 -52.544 26.014 -4.407 0.082 1.088 H10 U4P 26 U4P H11 H11 H 0 1 N N N 2.629 -54.667 23.782 -0.655 -1.002 1.372 H11 U4P 27 U4P H12 H12 H 0 1 N N N 3.583 -52.608 23.046 -2.390 -2.621 1.089 H12 U4P 28 # # 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 U4P CAK CAG DOUB N N 1 U4P CAK CAL SING N N 2 U4P CAG NAR SING N N 3 U4P "O2'" "C2'" SING N N 4 U4P OAB CAL DOUB N N 5 U4P CAL NAI SING N N 6 U4P NAR "C1'" SING N N 7 U4P NAR CAM SING N N 8 U4P "C1'" "C2'" SING N N 9 U4P "C1'" "O4'" SING N N 10 U4P "C2'" "C3'" SING N N 11 U4P "O4'" "C4'" SING N N 12 U4P NAI CAM SING N N 13 U4P CAM OAC DOUB N N 14 U4P "C4'" "C3'" SING N N 15 U4P "C4'" "C5'" SING N N 16 U4P "C3'" "O3'" SING N N 17 U4P NAI H1 SING N N 18 U4P CAK H2 SING N N 19 U4P CAG H3 SING N N 20 U4P "C1'" H4 SING N N 21 U4P "C4'" H5 SING N N 22 U4P "C5'" H6 SING N N 23 U4P "C5'" H7 SING N N 24 U4P "C5'" H8 SING N N 25 U4P "C3'" H9 SING N N 26 U4P "O3'" H10 SING N N 27 U4P "C2'" H11 SING N N 28 U4P "O2'" H12 SING N N 29 # # 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 U4P SMILES ACDLabs 12.01 "O=C1NC(=O)C=CN1C2C(C(C(O2)C)O)O" U4P InChI InChI 1.03 "InChI=1S/C9H12N2O5/c1-4-6(13)7(14)8(16-4)11-3-2-5(12)10-9(11)15/h2-4,6-8,13-14H,1H3,(H,10,12,15)/t4-,6-,7-,8-/m1/s1" U4P InChIKey InChI 1.03 WUBAOANSQGKRHF-XVFCMESISA-N U4P SMILES_CANONICAL CACTVS 3.385 "C[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2C=CC(=O)NC2=O" U4P SMILES CACTVS 3.385 "C[CH]1O[CH]([CH](O)[CH]1O)N2C=CC(=O)NC2=O" U4P SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@@H]1[C@H]([C@H]([C@@H](O1)N2C=CC(=O)NC2=O)O)O" U4P SMILES "OpenEye OEToolkits" 2.0.7 "CC1C(C(C(O1)N2C=CC(=O)NC2=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 U4P "SYSTEMATIC NAME" ACDLabs 12.01 "5'-deoxyuridine" U4P "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "1-[(2~{R},3~{R},4~{S},5~{R})-5-methyl-3,4-bis(oxidanyl)oxolan-2-yl]pyrimidine-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 U4P "Create component" 2020-04-16 RCSB U4P "Initial release" 2021-04-21 RCSB ##