data_T4S # _chem_comp.id T4S _chem_comp.name "1-(2-DEOXY-5-O-PHOSPHONO-BETA-D-ERYTHRO-PENTOFURANOSYL)-4-HYDROSELENO-5-METHYLPYRIMIDIN-2(1H)-ONE" _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H15 N2 O7 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 2006-11-06 _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 385.169 _chem_comp.one_letter_code T _chem_comp.three_letter_code T4S _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details ? _chem_comp.pdbx_ideal_coordinates_missing_flag Y _chem_comp.pdbx_model_coordinates_db_code 2NSK _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # # 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 T4S OP3 O3P O 0 1 N Y N 2.849 13.226 5.199 ? ? ? OP3 T4S 1 T4S P P P 0 1 N N N 4.155 12.556 4.527 ? ? ? P T4S 2 T4S OP1 O1P O 0 1 N N N 4.040 12.849 3.058 ? ? ? OP1 T4S 3 T4S OP2 O2P O 0 1 N N N 4.353 11.191 4.967 ? ? ? OP2 T4S 4 T4S "O5'" O5* O 0 1 N N N 5.361 13.407 5.139 ? ? ? "O5'" T4S 5 T4S N1 N1 N 0 1 N N N 7.627 13.865 8.359 ? ? ? N1 T4S 6 T4S C6 C6 C 0 1 N N N 6.641 12.986 7.988 ? ? ? C6 T4S 7 T4S C2 C2 C 0 1 N N N 8.486 13.591 9.413 ? ? ? C2 T4S 8 T4S O2 O2 O 0 1 N N N 9.392 14.343 9.740 ? ? ? O2 T4S 9 T4S N3 N3 N 0 1 N N N 8.263 12.381 10.058 ? ? ? N3 T4S 10 T4S C4 C4 C 0 1 N N N 7.305 11.426 9.735 ? ? ? C4 T4S 11 T4S SE SE SE 0 0 N N N 7.086 9.919 10.541 ? ? ? SE T4S 12 T4S C5 C5 C 0 1 N N N 6.436 11.774 8.602 ? ? ? C5 T4S 13 T4S C5A C5A C 0 1 N N N 5.380 10.806 8.173 ? ? ? C5A T4S 14 T4S "C2'" C2* C 0 1 N N N 8.789 14.856 6.477 ? ? ? "C2'" T4S 15 T4S "C5'" C5* C 0 1 N N N 5.363 14.821 5.029 ? ? ? "C5'" T4S 16 T4S "C4'" C4* C 0 1 N N R 6.625 15.411 5.614 ? ? ? "C4'" T4S 17 T4S "O4'" O4* O 0 1 N N N 6.543 15.365 7.062 ? ? ? "O4'" T4S 18 T4S "C1'" C1* C 0 1 N N R 7.849 15.152 7.620 ? ? ? "C1'" T4S 19 T4S "C3'" C3* C 0 1 N N S 7.887 14.635 5.274 ? ? ? "C3'" T4S 20 T4S "O3'" O3* O 0 1 N N N 8.530 15.121 4.123 ? ? ? "O3'" T4S 21 T4S HOP3 3HOP H 0 0 N N N 3.002 13.358 6.127 ? ? ? HOP3 T4S 22 T4S HOP2 2HOP H 0 0 N N N 4.396 10.617 4.211 ? ? ? HOP2 T4S 23 T4S H6 H6 H 0 1 N N N 5.992 13.261 7.170 ? ? ? H6 T4S 24 T4S HSE HSE H 0 1 N N N 7.022 8.814 9.528 ? ? ? HSE T4S 25 T4S H5A1 1H5A H 0 0 N N N 4.730 10.568 9.028 ? ? ? H5A1 T4S 26 T4S H5A2 2H5A H 0 0 N N N 4.778 11.253 7.369 ? ? ? H5A2 T4S 27 T4S H5A3 3H5A H 0 0 N N N 5.855 9.884 7.806 ? ? ? H5A3 T4S 28 T4S "H2'" 1H2* H 0 1 N N N 9.394 13.961 6.686 ? ? ? "H2'" T4S 29 T4S "H2''" 2H2* H 0 0 N N N 9.504 15.675 6.310 ? ? ? "H2''" T4S 30 T4S "H5'" 1H5* H 0 1 N N N 5.300 15.096 3.966 ? ? ? "H5'" T4S 31 T4S "H5''" 2H5* H 0 0 N N N 4.501 15.217 5.586 ? ? ? "H5''" T4S 32 T4S "H4'" H4* H 0 1 N N N 6.692 16.425 5.193 ? ? ? "H4'" T4S 33 T4S "H1'" H1* H 0 1 N N N 8.248 15.983 8.220 ? ? ? "H1'" T4S 34 T4S "H3'" H3* H 0 1 N N N 7.654 13.580 5.067 ? ? ? "H3'" T4S 35 T4S "HO3'" H3T H 0 0 N Y N 7.893 15.231 3.426 ? ? ? "HO3'" T4S 36 # # 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 T4S OP3 P SING N N 1 T4S OP3 HOP3 SING N N 2 T4S P OP1 DOUB N N 3 T4S P OP2 SING N N 4 T4S P "O5'" SING N N 5 T4S OP2 HOP2 SING N N 6 T4S "O5'" "C5'" SING N N 7 T4S N1 "C1'" SING N N 8 T4S N1 C6 SING N N 9 T4S N1 C2 SING N N 10 T4S C6 C5 DOUB N N 11 T4S C6 H6 SING N N 12 T4S C2 O2 DOUB N N 13 T4S C2 N3 SING N N 14 T4S N3 C4 DOUB N N 15 T4S C4 C5 SING N N 16 T4S C4 SE SING N N 17 T4S SE HSE SING N N 18 T4S C5 C5A SING N N 19 T4S C5A H5A1 SING N N 20 T4S C5A H5A2 SING N N 21 T4S C5A H5A3 SING N N 22 T4S "C2'" "C3'" SING N N 23 T4S "C2'" "C1'" SING N N 24 T4S "C2'" "H2'" SING N N 25 T4S "C2'" "H2''" SING N N 26 T4S "C5'" "C4'" SING N N 27 T4S "C5'" "H5'" SING N N 28 T4S "C5'" "H5''" SING N N 29 T4S "C4'" "C3'" SING N N 30 T4S "C4'" "O4'" SING N N 31 T4S "C4'" "H4'" SING N N 32 T4S "O4'" "C1'" SING N N 33 T4S "C1'" "H1'" SING N N 34 T4S "C3'" "O3'" SING N N 35 T4S "C3'" "H3'" SING N N 36 T4S "O3'" "HO3'" SING N N 37 # # 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 T4S SMILES ACDLabs 10.04 "O=C1N=C([SeH])C(=CN1C2OC(C(O)C2)COP(=O)(O)O)C" T4S SMILES_CANONICAL CACTVS 3.341 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)N=C1[SeH]" T4S SMILES CACTVS 3.341 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)N=C1[SeH]" T4S SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)N=C1[SeH])[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O" T4S SMILES "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)N=C1[SeH])C2CC(C(O2)COP(=O)(O)O)O" T4S InChI InChI 1.03 "InChI=1S/C10H15N2O7PSe/c1-5-3-12(10(14)11-9(5)21)8-2-6(13)7(19-8)4-18-20(15,16)17/h3,6-8,13H,2,4H2,1H3,(H,11,14,21)(H2,15,16,17)/t6-,7+,8+/m0/s1" T4S InChIKey InChI 1.03 HXENXQZDSWUILN-XLPZGREQSA-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 T4S "SYSTEMATIC NAME" ACDLabs 10.04 "1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-5-methyl-4-selanylpyrimidin-2(1H)-one" T4S "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2-oxo-4-selanyl-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 T4S "Create component" 2006-11-06 PDBJ T4S "Modify descriptor" 2011-06-04 RCSB ##