data_T5S # _chem_comp.id T5S _chem_comp.name ; 2'-deoxy-5-(methylselanyl)uridine 5'-phosphate ; _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H15 N2 O8 P Se" _chem_comp.mon_nstd_parent_comp_id DT _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2007-12-27 _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 401.168 _chem_comp.one_letter_code T _chem_comp.three_letter_code T5S _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 3BM0 _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 T5S OP3 OP3 O 0 1 N Y N 34.237 18.207 11.038 -5.438 2.545 -1.291 OP3 T5S 1 T5S P P P 0 1 N N N 33.712 16.885 10.297 -5.374 1.298 -0.274 P T5S 2 T5S OP1 OP1 O 0 1 N N N 34.179 17.003 8.883 -5.276 1.799 1.115 OP1 T5S 3 T5S OP2 OP2 O 0 1 N N N 32.288 16.654 10.574 -6.707 0.409 -0.431 OP2 T5S 4 T5S "O5'" "O5'" O 0 1 N N N 34.517 15.736 11.042 -4.085 0.395 -0.612 "O5'" T5S 5 T5S N1 N1 N 0 1 N N N 34.928 13.162 14.236 1.025 -0.597 0.160 N1 T5S 6 T5S C6 C6 C 0 1 N N N 34.010 14.180 14.023 2.181 -0.499 -0.566 C6 T5S 7 T5S C2 C2 C 0 1 N N N 34.791 12.282 15.304 0.944 -0.067 1.394 C2 T5S 8 T5S O2 O2 O 0 1 N N N 35.604 11.416 15.548 -0.093 -0.166 2.022 O2 T5S 9 T5S N3 N3 N 0 1 N N N 33.654 12.457 16.082 1.994 0.570 1.944 N3 T5S 10 T5S C4 C4 C 0 1 N N N 32.654 13.415 15.915 3.151 0.688 1.261 C4 T5S 11 T5S O4 O4 O 0 1 N N N 31.672 13.451 16.662 4.102 1.265 1.757 O4 T5S 12 T5S C5 C5 C 0 1 N N N 32.867 14.348 14.796 3.250 0.134 -0.039 C5 T5S 13 T5S SE SE SE 0 0 N N N 31.533 15.697 14.482 4.917 0.287 -1.059 SE T5S 14 T5S CH3 CH3 C 0 1 N N N 31.105 15.706 13.079 6.041 1.276 0.207 CH3 T5S 15 T5S "C2'" "C2'" C 0 1 N N N 35.373 12.278 12.088 -0.471 -2.550 0.398 "C2'" T5S 16 T5S "C5'" "C5'" C 0 1 N N N 35.935 15.719 11.031 -3.692 -0.728 0.179 "C5'" T5S 17 T5S "C4'" "C4'" C 0 1 N N R 36.432 14.356 11.445 -2.432 -1.357 -0.417 "C4'" T5S 18 T5S "O4'" "O4'" O 0 1 N N N 36.351 14.271 12.891 -1.314 -0.450 -0.302 "O4'" T5S 19 T5S "C1'" "C1'" C 0 1 N N R 36.059 12.926 13.276 -0.137 -1.280 -0.415 "C1'" T5S 20 T5S "C3'" "C3'" C 0 1 N N S 35.522 13.243 10.927 -2.015 -2.602 0.396 "C3'" T5S 21 T5S "O3'" "O3'" O 0 1 N N N 36.048 12.474 9.867 -2.475 -3.795 -0.243 "O3'" T5S 22 T5S HOP3 HOP3 H 0 0 N N N 34.341 18.031 11.966 -6.191 3.133 -1.146 HOP3 T5S 23 T5S HOP2 HOP2 H 0 0 N N N 32.152 16.604 11.513 -6.837 0.047 -1.318 HOP2 T5S 24 T5S H6 H6 H 0 1 N N N 34.192 14.876 13.217 2.238 -0.928 -1.556 H6 T5S 25 T5S HN3 HN3 H 0 1 N N N 33.539 11.825 16.848 1.919 0.946 2.834 HN3 T5S 26 T5S HH3 HH3 H 0 1 N N N 30.006 15.708 13.030 7.025 1.440 -0.232 HH3 T5S 27 T5S HH3A HH3A H 0 0 N N N 31.496 16.606 12.582 5.577 2.237 0.430 HH3A T5S 28 T5S HH3B HH3B H 0 0 N N N 31.492 14.810 12.572 6.144 0.701 1.127 HH3B T5S 29 T5S "H2'" "H2'" H 0 1 N N N 34.310 12.100 12.307 -0.058 -3.434 -0.088 "H2'" T5S 30 T5S "H2'A" "H2'A" H 0 0 N N N 35.823 11.302 11.853 -0.091 -2.463 1.416 "H2'A" T5S 31 T5S "H5'" "H5'" H 0 1 N N N 36.295 15.946 10.017 -3.487 -0.401 1.199 "H5'" T5S 32 T5S "H5'A" "H5'A" H 0 0 N N N 36.313 16.474 11.736 -4.496 -1.464 0.189 "H5'A" T5S 33 T5S "H4'" "H4'" H 0 1 N N N 37.450 14.235 11.047 -2.599 -1.622 -1.461 "H4'" T5S 34 T5S "H1'" "H1'" H 0 1 N N N 36.923 12.346 13.633 0.049 -1.534 -1.458 "H1'" T5S 35 T5S "H3'" "H3'" H 0 1 N N N 34.604 13.721 10.554 -2.400 -2.540 1.414 "H3'" T5S 36 T5S "HO3'" "HO3'" H 0 0 N Y N 36.166 13.026 9.103 -2.190 -4.610 0.194 "HO3'" T5S 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 T5S P OP3 SING N N 1 T5S OP3 HOP3 SING N N 2 T5S OP1 P DOUB N N 3 T5S P OP2 SING N N 4 T5S P "O5'" SING N N 5 T5S OP2 HOP2 SING N N 6 T5S "C5'" "O5'" SING N N 7 T5S "C1'" N1 SING N N 8 T5S C6 N1 SING N N 9 T5S N1 C2 SING N N 10 T5S C6 C5 DOUB N N 11 T5S C6 H6 SING N N 12 T5S C2 O2 DOUB N N 13 T5S C2 N3 SING N N 14 T5S C4 N3 SING N N 15 T5S N3 HN3 SING N N 16 T5S C5 C4 SING N N 17 T5S C4 O4 DOUB N N 18 T5S SE C5 SING N N 19 T5S CH3 SE SING N N 20 T5S CH3 HH3 SING N N 21 T5S CH3 HH3A SING N N 22 T5S CH3 HH3B SING N N 23 T5S "C3'" "C2'" SING N N 24 T5S "C2'" "C1'" SING N N 25 T5S "C2'" "H2'" SING N N 26 T5S "C2'" "H2'A" SING N N 27 T5S "C5'" "C4'" SING N N 28 T5S "C5'" "H5'" SING N N 29 T5S "C5'" "H5'A" SING N N 30 T5S "C3'" "C4'" SING N N 31 T5S "C4'" "O4'" SING N N 32 T5S "C4'" "H4'" SING N N 33 T5S "O4'" "C1'" SING N N 34 T5S "C1'" "H1'" SING N N 35 T5S "O3'" "C3'" SING N N 36 T5S "C3'" "H3'" SING N N 37 T5S "O3'" "HO3'" 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 T5S SMILES ACDLabs 10.04 "O=P(O)(O)OCC2OC(N1C(=O)NC(=O)C([Se]C)=C1)CC2O" T5S SMILES_CANONICAL CACTVS 3.341 "C[Se]C1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O" T5S SMILES CACTVS 3.341 "C[Se]C1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O" T5S SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C[Se]C1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O" T5S SMILES "OpenEye OEToolkits" 1.5.0 "C[Se]C1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)O)O" T5S InChI InChI 1.03 "InChI=1S/C10H15N2O8PSe/c1-22-7-3-12(10(15)11-9(7)14)8-2-5(13)6(20-8)4-19-21(16,17)18/h3,5-6,8,13H,2,4H2,1H3,(H,11,14,15)(H2,16,17,18)/t5-,6+,8+/m0/s1" T5S InChIKey InChI 1.03 KJNLUXBKSKRISX-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 T5S "SYSTEMATIC NAME" ACDLabs 10.04 "2'-deoxy-5-(methylselanyl)uridine 5'-(dihydrogen phosphate)" T5S "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-3-hydroxy-5-(5-methylselanyl-2,4-dioxo-pyrimidin-1-yl)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 T5S "Create component" 2007-12-27 RCSB T5S "Modify descriptor" 2011-06-04 RCSB ##