data_5SE # _chem_comp.id 5SE _chem_comp.name ;2'-deoxy-5-(methylselanyl)cytidine 5'-(dihydrogen phosphate) ; _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H16 N3 O7 P Se" _chem_comp.mon_nstd_parent_comp_id DU _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2009-08-07 _chem_comp.pdbx_modified_date 2011-06-04 _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 400.184 _chem_comp.one_letter_code U _chem_comp.three_letter_code 5SE _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 3IJN _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 5SE P P P 0 1 N N N 12.611 26.315 -1.037 5.320 -1.337 -0.051 P 5SE 1 5SE N1 N1 N 0 1 N N N 9.764 26.760 3.384 -1.062 0.712 -0.050 N1 5SE 2 5SE C2 C2 C 0 1 N N N 8.708 27.066 4.229 -0.928 0.617 1.286 C2 5SE 3 5SE O2 O2 O 0 1 N N N 8.535 26.355 5.208 0.137 0.910 1.804 O2 5SE 4 5SE N3 N3 N 0 1 N N N 7.880 28.103 3.983 -1.938 0.208 2.051 N3 5SE 5 5SE C4 C4 C 0 1 N N N 8.097 28.828 2.921 -3.107 -0.117 1.513 C4 5SE 6 5SE N4 N4 N 0 1 N N N 7.259 29.832 2.723 -4.143 -0.537 2.314 N4 5SE 7 5SE C5 C5 C 0 1 N N N 9.188 28.535 2.056 -3.280 -0.028 0.117 C5 5SE 8 5SE C6 C6 C 0 1 N N N 10.000 27.508 2.299 -2.245 0.395 -0.647 C6 5SE 9 5SE "C1'" C1* C 0 1 N N R 10.641 25.694 3.754 0.068 1.165 -0.865 C1* 5SE 10 5SE OP3 OP3 O 0 1 N Y N 13.343 25.208 -1.665 4.940 -2.017 1.359 OP3 5SE 11 5SE "C2'" C2* C 0 1 N N N 10.150 24.292 3.532 0.413 2.626 -0.517 C2* 5SE 12 5SE OP2 OP2 O 0 1 N N N 11.496 26.977 -1.691 5.687 -2.484 -1.118 OP2 5SE 13 5SE "C3'" C3* C 0 1 N N S 10.738 24.156 2.156 1.890 2.568 -0.058 C3* 5SE 14 5SE "O3'" O3* O 0 1 N N N 10.683 22.800 1.748 2.628 3.679 -0.571 O3* 5SE 15 5SE "C4'" C4* C 0 1 N N R 12.150 24.651 2.366 2.376 1.241 -0.695 C4* 5SE 16 5SE "O4'" O4* O 0 1 N N N 11.807 25.902 2.987 1.229 0.368 -0.578 O4* 5SE 17 5SE "C5'" C5* C 0 1 N N N 12.962 24.929 1.113 3.566 0.674 0.083 C5* 5SE 18 5SE "O5'" O5* O 0 1 N N N 12.157 25.777 0.370 4.066 -0.483 -0.590 O5* 5SE 19 5SE CA5 CA5 C 0 1 N N N 8.095 29.110 -0.855 -4.784 -2.439 -0.920 CA5 5SE 20 5SE SE5 SE5 SE 0 0 N N N 9.463 29.597 0.481 -4.995 -0.502 -0.705 SE5 5SE 21 5SE HN4 HN4 H 0 1 N N N 6.514 29.997 3.370 -3.997 -0.678 3.262 HN4 5SE 22 5SE HN4A HN4A H 0 0 N N N 7.370 30.427 1.927 -5.021 -0.692 1.930 HN4A 5SE 23 5SE H6 H6 H 0 1 N N N 10.826 27.285 1.639 -2.353 0.471 -1.719 H6 5SE 24 5SE "H1'" H1* H 0 1 N N N 10.772 25.740 4.845 -0.184 1.086 -1.923 H1* 5SE 25 5SE HOP3 HOP3 H 0 0 N Y N 13.862 25.541 -2.388 4.184 -2.618 1.314 HOP3 5SE 26 5SE "H2'" H2* H 0 1 N N N 10.521 23.557 4.262 0.311 3.262 -1.396 H2* 5SE 27 5SE "H2'A" H2*A H 0 0 N N N 9.057 24.179 3.574 -0.226 2.987 0.289 H2*A 5SE 28 5SE HOP2 HOP2 H 0 0 N N N 11.825 27.559 -2.366 6.436 -3.039 -0.858 HOP2 5SE 29 5SE "H3'" H3* H 0 1 N N N 10.217 24.713 1.363 1.958 2.526 1.029 H3* 5SE 30 5SE "HO3'" HO3* H 0 0 N N N 11.055 22.715 0.878 2.302 4.539 -0.271 HO3* 5SE 31 5SE "H4'" H4* H 0 1 N N N 12.787 23.928 2.897 2.636 1.390 -1.742 H4* 5SE 32 5SE "H5'" H5* H 0 1 N N N 13.924 25.403 1.357 4.351 1.427 0.144 H5* 5SE 33 5SE "H5'A" H5*A H 0 0 N N N 13.179 24.001 0.564 3.246 0.400 1.088 H5*A 5SE 34 5SE HA5 HA5 H 0 1 N N N 8.240 29.711 -1.765 -3.875 -2.645 -1.485 HA5 5SE 35 5SE HA5A HA5A H 0 0 N N N 8.188 28.042 -1.103 -4.716 -2.908 0.061 HA5A 5SE 36 5SE HA5B HA5B H 0 0 N N N 7.094 29.305 -0.442 -5.644 -2.841 -1.456 HA5B 5SE 37 5SE OP1 OP1 O 0 1 N N N 13.363 27.318 -2.215 6.485 -0.442 0.132 OP1 5SE 38 # 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 5SE P "O5'" SING N N 1 5SE N1 "C1'" SING N N 2 5SE N1 C2 SING N N 3 5SE C2 O2 DOUB N N 4 5SE N3 C2 SING N N 5 5SE C4 N3 DOUB N N 6 5SE N4 C4 SING N N 7 5SE N4 HN4 SING N N 8 5SE N4 HN4A SING N N 9 5SE C5 C4 SING N N 10 5SE C5 C6 DOUB N N 11 5SE C6 N1 SING N N 12 5SE C6 H6 SING N N 13 5SE "C1'" "H1'" SING N N 14 5SE OP3 P SING N N 15 5SE OP3 HOP3 SING N N 16 5SE "C2'" "C1'" SING N N 17 5SE "C2'" "H2'" SING N N 18 5SE "C2'" "H2'A" SING N N 19 5SE OP2 P SING N N 20 5SE OP2 HOP2 SING N N 21 5SE "C3'" "C2'" SING N N 22 5SE "C3'" "C4'" SING N N 23 5SE "C3'" "H3'" SING N N 24 5SE "O3'" "C3'" SING N N 25 5SE "O3'" "HO3'" SING N N 26 5SE "C4'" "O4'" SING N N 27 5SE "C4'" "H4'" SING N N 28 5SE "O4'" "C1'" SING N N 29 5SE "C5'" "C4'" SING N N 30 5SE "C5'" "H5'" SING N N 31 5SE "C5'" "H5'A" SING N N 32 5SE "O5'" "C5'" SING N N 33 5SE CA5 SE5 SING N N 34 5SE CA5 HA5 SING N N 35 5SE CA5 HA5A SING N N 36 5SE CA5 HA5B SING N N 37 5SE SE5 C5 SING N N 38 5SE P OP1 DOUB N N 39 # 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 5SE SMILES ACDLabs 11.02 "O=P(O)(O)OCC2OC(N1C(=O)N=C(N)C([Se]C)=C1)CC2O" 5SE SMILES_CANONICAL CACTVS 3.352 "C[Se]C1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)N=C1N" 5SE SMILES CACTVS 3.352 "C[Se]C1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)N=C1N" 5SE SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "C[Se]C1=CN(C(=O)N=C1N)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O" 5SE SMILES "OpenEye OEToolkits" 1.7.0 "C[Se]C1=CN(C(=O)N=C1N)C2CC(C(O2)COP(=O)(O)O)O" 5SE InChI InChI 1.03 "InChI=1S/C10H16N3O7PSe/c1-22-7-3-13(10(15)12-9(7)11)8-2-5(14)6(20-8)4-19-21(16,17)18/h3,5-6,8,14H,2,4H2,1H3,(H2,11,12,15)(H2,16,17,18)/t5-,6+,8+/m0/s1" 5SE InChIKey InChI 1.03 NLUQHLNACKOXLS-SHYZEUOFSA-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 5SE "SYSTEMATIC NAME" ACDLabs 11.02 ;2'-deoxy-5-(methylselanyl)cytidine 5'-(dihydrogen phosphate) ; 5SE "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.6.1 "[(2R,3S,5R)-5-(4-azanyl-5-methylselanyl-2-oxo-pyrimidin-1-yl)-3-hydroxy-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 5SE "Create component" 2009-08-07 RCSB 5SE "Modify descriptor" 2011-06-04 RCSB #