data_US3 # _chem_comp.id US3 _chem_comp.name "1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-5-methyl-2-selanylpyrimidin-4(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 "2-Se-Thymidine-5'-phosphate" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2009-06-15 _chem_comp.pdbx_modified_date 2021-03-01 _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 US3 _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 3HGD _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 US3 P P P 0 1 N N N -9.241 9.704 8.212 -4.390 1.051 -0.368 P US3 1 US3 N1 N1 N 0 1 N N N -12.913 11.821 4.626 2.187 -0.310 -0.734 N1 US3 2 US3 C2 C2 C 0 1 N N N -13.627 12.622 3.666 2.282 0.282 0.471 C2 US3 3 US3 SE2 SE2 SE 0 0 N N N -14.700 12.254 2.742 0.835 0.042 1.771 SE2 US3 4 US3 N3 N3 N 0 1 N N N -12.953 13.831 3.819 3.316 1.011 0.793 N3 US3 5 US3 C4 C4 C 0 1 N N N -11.910 14.290 4.665 4.325 1.196 -0.076 C4 US3 6 US3 O4 O4 O 0 1 N N N -11.418 15.480 4.750 5.289 1.879 0.234 O4 US3 7 US3 C5 C5 C 0 1 N N N -11.272 13.348 5.525 4.259 0.588 -1.354 C5 US3 8 US3 C6 C6 C 0 1 N N N -11.882 12.121 5.454 3.178 -0.167 -1.657 C6 US3 9 US3 "C1'" "C1'" C 0 1 N N R -13.339 10.442 4.759 1.010 -1.121 -1.053 "C1'" US3 10 US3 OP3 OP3 O 0 1 N Y N -8.272 10.798 7.787 -4.757 2.121 -1.513 OP3 US3 11 US3 "C2'" "C2'" C 0 1 N N N -12.641 9.686 3.694 0.903 -2.319 -0.085 "C2'" US3 12 US3 OP2 OP2 O 0 1 N N N -8.703 8.310 8.457 -5.628 0.041 -0.160 OP2 US3 13 US3 "C3'" "C3'" C 0 1 N N S -11.559 8.970 4.559 -0.615 -2.470 0.161 "C3'" US3 14 US3 "O3'" "O3'" O 0 1 N N N -10.990 7.775 4.012 -1.069 -3.749 -0.285 "O3'" US3 15 US3 "C4'" "C4'" C 0 1 N N R -12.249 8.751 5.885 -1.246 -1.345 -0.689 "C4'" US3 16 US3 "O4'" "O4'" O 0 1 N N N -12.987 9.939 6.060 -0.199 -0.361 -0.834 "O4'" US3 17 US3 "C5'" "C5'" C 0 1 N N N -11.302 8.490 7.048 -2.448 -0.739 0.038 "C5'" US3 18 US3 "O5'" "O5'" O 0 1 N N N -10.394 9.591 7.103 -3.086 0.216 -0.811 "O5'" US3 19 US3 C5A C5A C 0 1 N N N -10.091 13.696 6.378 5.373 0.774 -2.352 C5A US3 20 US3 H6 H6 H 0 1 N N N -11.515 11.340 6.103 3.101 -0.647 -2.622 H6 US3 21 US3 "H1'" "H1'" H 0 1 N N N -14.430 10.343 4.658 1.058 -1.468 -2.086 "H1'" US3 22 US3 HOP3 HOP3 H 0 0 N Y N -7.380 10.494 7.905 -5.535 2.660 -1.313 HOP3 US3 23 US3 "H2'" "H2'" H 0 1 N N N -13.300 8.984 3.163 1.307 -3.221 -0.546 "H2'" US3 24 US3 "H2'A" "H2'A" H 0 0 N N N -12.210 10.336 2.918 1.422 -2.103 0.849 "H2'A" US3 25 US3 HOP2 HOP2 H 0 0 N N N -7.753 8.331 8.453 -5.865 -0.459 -0.953 HOP2 US3 26 US3 "H3'" "H3'" H 0 1 N N N -10.656 9.594 4.630 -0.847 -2.328 1.216 "H3'" US3 27 US3 "HO3'" "HO3'" H 0 0 N N N -10.347 7.424 4.617 -0.659 -4.495 0.174 "HO3'" US3 28 US3 "H4'" "H4'" H 0 1 N N N -12.868 7.841 5.873 -1.545 -1.728 -1.664 "H4'" US3 29 US3 "H5'" "H5'" H 0 1 N N N -11.866 8.413 7.989 -3.155 -1.529 0.292 "H5'" US3 30 US3 "H5'A" "H5'A" H 0 0 N N N -10.753 7.550 6.889 -2.111 -0.247 0.951 "H5'A" US3 31 US3 H5A H5A H 0 1 N N N -9.777 12.810 6.950 6.148 1.406 -1.919 H5A US3 32 US3 H5AA H5AA H 0 0 N N N -9.262 14.031 5.737 5.797 -0.197 -2.608 H5AA US3 33 US3 H5AB H5AB H 0 0 N N N -10.366 14.503 7.073 4.979 1.247 -3.252 H5AB US3 34 US3 HSE2 HSE2 H 0 0 N N N -15.035 13.401 1.902 1.372 0.882 2.971 HSE2 US3 35 US3 OP1 OP1 O 0 1 N N N -7.411 9.704 8.212 -4.114 1.760 0.901 OP1 US3 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 US3 P OP2 SING N N 1 US3 N1 "C1'" SING N N 2 US3 N1 C6 SING N N 3 US3 C2 N1 SING N N 4 US3 C2 N3 DOUB N N 5 US3 SE2 C2 SING N N 6 US3 SE2 HSE2 SING N N 7 US3 N3 C4 SING N N 8 US3 C4 O4 DOUB N N 9 US3 C4 C5 SING N N 10 US3 C5 C5A SING N N 11 US3 C6 C5 DOUB N N 12 US3 C6 H6 SING N N 13 US3 "C1'" "O4'" SING N N 14 US3 "C1'" "H1'" SING N N 15 US3 OP3 P SING N N 16 US3 OP3 HOP3 SING N N 17 US3 "C2'" "C1'" SING N N 18 US3 "C2'" "C3'" SING N N 19 US3 "C2'" "H2'" SING N N 20 US3 "C2'" "H2'A" SING N N 21 US3 OP2 HOP2 SING N N 22 US3 "C3'" "C4'" SING N N 23 US3 "C3'" "H3'" SING N N 24 US3 "O3'" "C3'" SING N N 25 US3 "O3'" "HO3'" SING N N 26 US3 "C4'" "O4'" SING N N 27 US3 "C4'" "C5'" SING N N 28 US3 "C4'" "H4'" SING N N 29 US3 "C5'" "O5'" SING N N 30 US3 "C5'" "H5'" SING N N 31 US3 "C5'" "H5'A" SING N N 32 US3 "O5'" P SING N N 33 US3 C5A H5A SING N N 34 US3 C5A H5AA SING N N 35 US3 C5A H5AB SING N N 36 US3 P OP1 DOUB 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 US3 SMILES ACDLabs 11.02 "O=P(O)(O)OCC2OC(N1C(=NC(=O)C(=C1)C)[SeH])CC2O" US3 SMILES_CANONICAL CACTVS 3.352 "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=NC1=O)[SeH]" US3 SMILES CACTVS 3.352 "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=NC1=O)[SeH]" US3 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "CC1=CN(C(=NC1=O)[SeH])[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O" US3 SMILES "OpenEye OEToolkits" 1.7.0 "CC1=CN(C(=NC1=O)[SeH])C2CC(C(O2)COP(=O)(O)O)O" US3 InChI InChI 1.03 "InChI=1S/C10H15N2O7PSe/c1-5-3-12(10(21)11-9(5)14)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" US3 InChIKey InChI 1.03 NJOAZAGHIQNDNL-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 US3 "SYSTEMATIC NAME" ACDLabs 11.02 "1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-5-methyl-2-selanylpyrimidin-4(1H)-one" US3 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.6.1 "[(2R,3S,5R)-3-hydroxy-5-(5-methyl-4-oxo-2-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 US3 "Create component" 2009-06-15 RCSB US3 "Modify descriptor" 2011-06-04 RCSB US3 "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id US3 _pdbx_chem_comp_synonyms.name "2-Se-Thymidine-5'-phosphate" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##