data_0U1 # _chem_comp.id 0U1 _chem_comp.name "2'-METHYLSELENYL-2'-DEOXY-L-URIDINE-5'-MONOPHOSPHATE" _chem_comp.type "L-RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H15 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 2014-10-23 _chem_comp.pdbx_modified_date 2015-04-24 _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 401.168 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 0U1 _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 4R8I _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 0U1 P P P 0 1 N N N 18.096 -44.446 -45.632 -4.820 0.193 -0.139 P 0U1 1 0U1 "O5'" "O5'" O 0 1 N N N 16.545 -44.715 -46.026 -3.359 -0.138 0.450 "O5'" 0U1 2 0U1 "C5'" "C5'" C 0 1 N N N 16.110 -45.539 -47.125 -2.380 -0.886 -0.273 "C5'" 0U1 3 0U1 "C4'" "C4'" C 0 1 N N S 14.616 -45.282 -47.388 -1.111 -1.016 0.572 "C4'" 0U1 4 0U1 "O4'" "O4'" O 0 1 N N N 14.444 -43.845 -47.555 -0.494 0.273 0.729 "O4'" 0U1 5 0U1 "C3'" "C3'" C 0 1 N N S 13.792 -45.641 -46.149 -0.095 -1.926 -0.144 "C3'" 0U1 6 0U1 "O3'" "O3'" O 0 1 N N N 13.314 -47.018 -46.185 0.210 -3.067 0.661 "O3'" 0U1 7 0U1 "C2'" "C2'" C 0 1 N N S 12.628 -44.617 -46.156 1.157 -1.033 -0.319 "C2'" 0U1 8 0U1 "C1'" "C1'" C 0 1 N N S 13.257 -43.375 -46.803 0.933 0.056 0.761 "C1'" 0U1 9 0U1 N1 N1 N 0 1 N N N 13.487 -42.304 -45.783 1.650 1.285 0.411 N1 0U1 10 0U1 C2 C2 C 0 1 N N N 12.515 -41.390 -45.525 0.957 2.408 0.149 C2 0U1 11 0U1 O2 O2 O 0 1 N N N 11.439 -41.423 -46.126 -0.257 2.391 0.205 O2 0U1 12 0U1 N3 N3 N 0 1 N N N 12.729 -40.384 -44.555 1.590 3.551 -0.175 N3 0U1 13 0U1 C4 C4 C 0 1 N N N 13.957 -40.310 -43.855 2.936 3.588 -0.241 C4 0U1 14 0U1 O4 O4 O 0 1 N N N 14.146 -39.432 -43.010 3.509 4.622 -0.534 O4 0U1 15 0U1 C5 C5 C 0 1 N N N 14.959 -41.250 -44.119 3.677 2.413 0.033 C5 0U1 16 0U1 C6 C6 C 0 1 N N N 14.718 -42.237 -45.080 3.017 1.281 0.360 C6 0U1 17 0U1 OP1 OP1 O 0 1 N N N 18.149 -43.941 -44.253 -5.489 -1.066 -0.537 OP1 0U1 18 0U1 OP2 OP2 O 0 1 N N N 18.934 -45.579 -46.045 -5.699 0.934 0.989 OP2 0U1 19 0U1 SE SE SE 0 0 N N N 10.998 -45.092 -47.200 2.796 -2.047 0.038 SE 0U1 20 0U1 CSE CSE C 0 1 N N N 11.515 -44.433 -48.987 2.691 -3.428 -1.349 CSE 0U1 21 0U1 "H5'" "H5'" H 0 1 N N N 16.262 -46.599 -46.873 -2.772 -1.878 -0.495 "H5'" 0U1 22 0U1 "H5''" "H5''" H 0 0 N N N 16.691 -45.289 -48.025 -2.144 -0.372 -1.205 "H5''" 0U1 23 0U1 "H4'" "H4'" H 0 1 N N N 14.270 -45.845 -48.268 -1.357 -1.433 1.549 "H4'" 0U1 24 0U1 "H3'" "H3'" H 0 1 N N N 14.404 -45.477 -45.250 -0.480 -2.237 -1.115 "H3'" 0U1 25 0U1 "HO3'" "HO3'" H 0 0 N Y N 12.809 -47.199 -45.401 -0.553 -3.630 0.849 "HO3'" 0U1 26 0U1 "H2'" "H2'" H 0 1 N N N 12.285 -44.403 -45.133 1.184 -0.592 -1.316 "H2'" 0U1 27 0U1 "H1'" "H1'" H 0 1 N N N 12.530 -42.988 -47.532 1.245 -0.306 1.741 "H1'" 0U1 28 0U1 H3 H3 H 0 1 N N N 12.007 -39.719 -44.362 1.075 4.352 -0.362 H3 0U1 29 0U1 H5 H5 H 0 1 N N N 15.900 -41.214 -43.591 4.756 2.423 -0.016 H5 0U1 30 0U1 H6 H6 H 0 1 N N N 15.487 -42.965 -45.292 3.566 0.377 0.577 H6 0U1 31 0U1 HOP2 HOP2 H 0 0 N N N 19.454 -45.874 -45.307 -6.593 1.164 0.702 HOP2 0U1 32 0U1 HC1 HC1 H 0 1 N N N 10.699 -44.625 -49.699 3.557 -4.085 -1.274 HC1 0U1 33 0U1 HC2 HC2 H 0 1 N N N 11.710 -43.352 -48.937 1.780 -4.011 -1.213 HC2 0U1 34 0U1 HC3 HC3 H 0 1 N N N 12.424 -44.955 -49.321 2.677 -2.956 -2.331 HC3 0U1 35 0U1 OP3 OP3 O 0 1 N Y N ? ? ? -4.676 1.153 -1.424 OP3 0U1 36 0U1 HOP3 HOP3 H 0 0 N Y N ? ? ? -4.246 1.999 -1.237 HOP3 0U1 37 # 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 0U1 CSE SE SING N N 1 0U1 "O4'" "C4'" SING N N 2 0U1 "O4'" "C1'" SING N N 3 0U1 "C4'" "C5'" SING N N 4 0U1 "C4'" "C3'" SING N N 5 0U1 SE "C2'" SING N N 6 0U1 "C5'" "O5'" SING N N 7 0U1 "C1'" "C2'" SING N N 8 0U1 "C1'" N1 SING N N 9 0U1 "O3'" "C3'" SING N N 10 0U1 "C2'" "C3'" SING N N 11 0U1 O2 C2 DOUB N N 12 0U1 OP2 P SING N N 13 0U1 "O5'" P SING N N 14 0U1 N1 C2 SING N N 15 0U1 N1 C6 SING N N 16 0U1 P OP1 DOUB N N 17 0U1 C2 N3 SING N N 18 0U1 C6 C5 DOUB N N 19 0U1 N3 C4 SING N N 20 0U1 C5 C4 SING N N 21 0U1 C4 O4 DOUB N N 22 0U1 "C5'" "H5'" SING N N 23 0U1 "C5'" "H5''" SING N N 24 0U1 "C4'" "H4'" SING N N 25 0U1 "C3'" "H3'" SING N N 26 0U1 "O3'" "HO3'" SING N N 27 0U1 "C2'" "H2'" SING N N 28 0U1 "C1'" "H1'" SING N N 29 0U1 N3 H3 SING N N 30 0U1 C5 H5 SING N N 31 0U1 C6 H6 SING N N 32 0U1 OP2 HOP2 SING N N 33 0U1 CSE HC1 SING N N 34 0U1 CSE HC2 SING N N 35 0U1 CSE HC3 SING N N 36 0U1 P OP3 SING N N 37 0U1 OP3 HOP3 SING N N 38 # 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 0U1 SMILES ACDLabs 12.01 "O=P(O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C([Se]C)C2O" 0U1 InChI InChI 1.03 "InChI=1S/C10H15N2O8PSe/c1-22-8-7(14)5(4-19-21(16,17)18)20-9(8)12-3-2-6(13)11-10(12)15/h2-3,5,7-9,14H,4H2,1H3,(H,11,13,15)(H2,16,17,18)/t5-,7-,8-,9-/m0/s1" 0U1 InChIKey InChI 1.03 PADIGPKUSVFCBC-ZITKLIBNSA-N 0U1 SMILES_CANONICAL CACTVS 3.385 "C[Se][C@H]1[C@@H](O)[C@H](CO[P](O)(O)=O)O[C@@H]1N2C=CC(=O)NC2=O" 0U1 SMILES CACTVS 3.385 "C[Se][CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=CC(=O)NC2=O" 0U1 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C[Se][C@H]1[C@H]([C@@H](O[C@@H]1N2C=CC(=O)NC2=O)COP(=O)(O)O)O" 0U1 SMILES "OpenEye OEToolkits" 1.7.6 "C[Se]C1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(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 0U1 "SYSTEMATIC NAME" ACDLabs 12.01 "1-(2-Se-methyl-5-O-phosphono-2-seleno-beta-L-ribofuranosyl)pyrimidine-2,4(1H,3H)-dione" 0U1 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2S,3S,4S,5S)-5-[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 0U1 "Create component" 2014-10-23 RCSB 0U1 "Initial release" 2015-04-29 RCSB #