data_UWJ # _chem_comp.id UWJ _chem_comp.name "5-methyl-1-(2-Se-methyl-5-O-phosphono-2-seleno-beta-D-arabinofuranosyl)pyrimidine-2,4(1H,3H)-dione" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C11 H17 N2 O8 P Se" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2020-06-02 _chem_comp.pdbx_modified_date 2021-05-28 _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 415.195 _chem_comp.one_letter_code ? _chem_comp.three_letter_code UWJ _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 6X5D _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 UWJ C2 C1 C 0 1 N N N 12.212 22.933 13.065 -1.644 -0.880 0.697 C2 UWJ 1 UWJ C6 C2 C 0 1 N N N 12.258 25.223 12.366 -2.576 -1.479 -1.383 C6 UWJ 2 UWJ OP2 O1 O 0 1 N N N 7.706 28.644 9.167 4.666 -1.295 1.617 OP2 UWJ 3 UWJ P P1 P 0 1 N N N 9.074 28.331 9.610 4.952 -0.881 0.225 P UWJ 4 UWJ OP1 O2 O 0 1 N N N 9.953 29.290 10.229 5.593 -2.118 -0.582 OP1 UWJ 5 UWJ "O5'" O3 O 0 1 N N N 8.842 26.982 10.534 3.584 -0.424 -0.491 "O5'" UWJ 6 UWJ "C5'" C3 C 0 1 N N N 8.134 25.800 10.072 2.724 0.582 0.046 "C5'" UWJ 7 UWJ "C4'" C4 C 0 1 N N R 8.360 24.618 11.039 1.519 0.770 -0.879 "C4'" UWJ 8 UWJ "O4'" O4 O 0 1 N N N 9.812 24.532 11.176 0.694 -0.415 -0.885 "O4'" UWJ 9 UWJ "C3'" C5 C 0 1 N N R 7.799 24.821 12.464 0.573 1.867 -0.329 "C3'" UWJ 10 UWJ "O3'" O5 O 0 1 N N N 6.930 23.735 12.675 0.986 3.163 -0.767 "O3'" UWJ 11 UWJ "C2'" C6 C 0 1 N N S 9.130 24.787 13.406 -0.783 1.475 -0.964 "C2'" UWJ 12 UWJ SE2 SE1 SE 0 0 N N N 9.774 26.423 14.008 -2.238 1.705 0.329 SE2 UWJ 13 UWJ "CA'" C7 C 0 1 N N N 8.183 26.744 15.121 -2.125 3.630 0.681 "CA'" UWJ 14 UWJ "C1'" C8 C 0 1 N N R 10.080 24.015 12.532 -0.614 -0.013 -1.327 "C1'" UWJ 15 UWJ N1 N1 N 0 1 N N N 11.547 24.104 12.704 -1.637 -0.811 -0.646 N1 UWJ 16 UWJ O2 O6 O 0 1 N N N 11.601 21.921 13.423 -0.802 -0.274 1.333 O2 UWJ 17 UWJ C5 C9 C 0 1 N N N 13.598 25.258 12.423 -3.520 -2.214 -0.756 C5 UWJ 18 UWJ C7 C10 C 0 1 N N N 14.367 26.447 12.086 -4.563 -2.956 -1.551 C7 UWJ 19 UWJ C4 C11 C 0 1 N N N 14.294 24.073 12.727 -3.512 -2.282 0.658 C4 UWJ 20 UWJ N3 N2 N 0 1 N N N 13.557 22.954 13.077 -2.572 -1.605 1.348 N3 UWJ 21 UWJ O4 O7 O 0 1 N N N 15.513 23.923 12.693 -4.352 -2.939 1.246 O4 UWJ 22 UWJ O1 O8 O 0 1 N Y N 9.828 27.736 8.309 5.990 0.350 0.234 O1 UWJ 23 UWJ H6 H1 H 0 1 N N N 11.724 26.105 12.044 -2.567 -1.415 -2.461 H6 UWJ 24 UWJ H1 H2 H 0 1 N N N 9.510 30.128 10.298 6.422 -2.446 -0.206 H1 UWJ 25 UWJ "H5'1" H3 H 0 0 N N N 7.058 26.022 10.017 2.379 0.278 1.034 "H5'1" UWJ 26 UWJ "H5'2" H4 H 0 0 N N N 8.503 25.525 9.073 3.270 1.522 0.125 "H5'2" UWJ 27 UWJ "H4'" H5 H 0 1 N N N 7.949 23.695 10.604 1.847 1.014 -1.890 "H4'" UWJ 28 UWJ "H3'" H6 H 0 1 N N N 7.301 25.798 12.556 0.521 1.825 0.759 "H3'" UWJ 29 UWJ "HO3'" H7 H 0 0 N N N 6.547 23.799 13.542 1.870 3.416 -0.468 "HO3'" UWJ 30 UWJ "H2'" H8 H 0 1 N N N 8.897 24.204 14.309 -0.971 2.069 -1.858 "H2'" UWJ 31 UWJ "HA'1" H9 H 0 0 N N N 8.285 27.710 15.638 -2.893 3.913 1.401 "HA'1" UWJ 32 UWJ "HA'3" H10 H 0 0 N N N 7.287 26.762 14.483 -1.142 3.868 1.086 "HA'3" UWJ 33 UWJ "HA'2" H11 H 0 0 N N N 8.087 25.939 15.865 -2.278 4.179 -0.249 "HA'2" UWJ 34 UWJ "H1'" H12 H 0 1 N N N 9.790 22.954 12.565 -0.697 -0.146 -2.405 "H1'" UWJ 35 UWJ H72 H13 H 0 1 N N N 15.440 26.237 12.207 -4.199 -3.958 -1.781 H72 UWJ 36 UWJ H2 H14 H 0 1 N N N 14.164 26.731 11.043 -5.481 -3.029 -0.967 H2 UWJ 37 UWJ H71 H15 H 0 1 N N N 14.078 27.272 12.753 -4.763 -2.420 -2.478 H71 UWJ 38 UWJ H3 H16 H 0 1 N N N 14.046 22.126 13.351 -2.565 -1.641 2.318 H3 UWJ 39 UWJ H4 H17 H 0 1 N N N 9.228 27.725 7.572 6.223 0.674 -0.647 H4 UWJ 40 # # 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 UWJ OP2 P DOUB N N 1 UWJ P OP1 SING N N 2 UWJ P "O5'" SING N N 3 UWJ "C5'" "O5'" SING N N 4 UWJ "C5'" "C4'" SING N N 5 UWJ "C4'" "O4'" SING N N 6 UWJ "C4'" "C3'" SING N N 7 UWJ "O4'" "C1'" SING N N 8 UWJ C7 C5 SING N N 9 UWJ C6 C5 DOUB N N 10 UWJ C6 N1 SING N N 11 UWJ C5 C4 SING N N 12 UWJ "C3'" "O3'" SING N N 13 UWJ "C3'" "C2'" SING N N 14 UWJ "C1'" N1 SING N N 15 UWJ "C1'" "C2'" SING N N 16 UWJ O4 C4 DOUB N N 17 UWJ N1 C2 SING N N 18 UWJ C4 N3 SING N N 19 UWJ C2 N3 SING N N 20 UWJ C2 O2 DOUB N N 21 UWJ "C2'" SE2 SING N N 22 UWJ SE2 "CA'" SING N N 23 UWJ P O1 SING N N 24 UWJ C6 H6 SING N N 25 UWJ OP1 H1 SING N N 26 UWJ "C5'" "H5'1" SING N N 27 UWJ "C5'" "H5'2" SING N N 28 UWJ "C4'" "H4'" SING N N 29 UWJ "C3'" "H3'" SING N N 30 UWJ "O3'" "HO3'" SING N N 31 UWJ "C2'" "H2'" SING N N 32 UWJ "CA'" "HA'1" SING N N 33 UWJ "CA'" "HA'3" SING N N 34 UWJ "CA'" "HA'2" SING N N 35 UWJ "C1'" "H1'" SING N N 36 UWJ C7 H72 SING N N 37 UWJ C7 H2 SING N N 38 UWJ C7 H71 SING N N 39 UWJ N3 H3 SING N N 40 UWJ O1 H4 SING N N 41 # # 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 UWJ SMILES ACDLabs 12.01 "C1(NC(C(=CN1C2OC(COP(=O)(O)O)C(O)C2[Se]C)C)=O)=O" UWJ InChI InChI 1.03 "InChI=1S/C11H17N2O8PSe/c1-5-3-13(11(16)12-9(5)15)10-8(23-2)7(14)6(21-10)4-20-22(17,18)19/h3,6-8,10,14H,4H2,1-2H3,(H,12,15,16)(H2,17,18,19)/t6-,7-,8+,10-/m1/s1" UWJ InChIKey InChI 1.03 KLYIIOBIPBBIGV-BDNRQGISSA-N UWJ SMILES_CANONICAL CACTVS 3.385 "C[Se][C@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=C(C)C(=O)NC2=O" UWJ SMILES CACTVS 3.385 "C[Se][CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=C(C)C(=O)NC2=O" UWJ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)[C@H]2[C@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)[Se]C" UWJ SMILES "OpenEye OEToolkits" 2.0.7 "CC1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)O)O)[Se]C" # # 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 UWJ "SYSTEMATIC NAME" ACDLabs 12.01 "5-methyl-1-(2-Se-methyl-5-O-phosphono-2-seleno-beta-D-arabinofuranosyl)pyrimidine-2,4(1H,3H)-dione" UWJ "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "[(2~{R},3~{R},4~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-4-methylselanyl-3-oxidanyl-oxolan-2-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 UWJ "Create component" 2020-06-02 RCSB UWJ "Initial release" 2021-06-02 RCSB ##