data_US5 # _chem_comp.id US5 _chem_comp.name "1-(5-O-phosphono-beta-D-ribofuranosyl)-4-selanylpyrimidin-2(1H)-one" _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C9 H13 N2 O8 P Se" _chem_comp.mon_nstd_parent_comp_id U _chem_comp.pdbx_synonyms "4-Se-ribouridine-5'-phosphate" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2009-07-17 _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 387.142 _chem_comp.one_letter_code U _chem_comp.three_letter_code US5 _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 3HGA _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 US5 P P P 0 1 N N N -11.885 5.934 9.253 -4.758 1.707 -0.059 P US5 1 US5 N1 N1 N 0 1 N N N -8.790 2.586 11.674 1.251 -0.949 -0.501 N1 US5 2 US5 C2 C2 C 0 1 N N N -8.422 1.415 12.315 1.401 -0.021 0.463 C2 US5 3 US5 O2 O2 O 0 1 N N N -7.264 1.126 12.556 0.464 0.238 1.199 O2 US5 4 US5 N3 N3 N 0 1 N N N -9.468 0.592 12.678 2.561 0.620 0.624 N3 US5 5 US5 C4 C4 C 0 1 N N N -10.824 0.810 12.461 3.590 0.360 -0.157 C4 US5 6 US5 SE4 SE4 SE 0 0 N N N -11.651 -0.019 12.845 5.284 1.313 0.100 SE4 US5 7 US5 C5 C5 C 0 1 N N N -11.131 2.048 11.776 3.471 -0.597 -1.169 C5 US5 8 US5 C6 C6 C 0 1 N N N -10.126 2.864 11.420 2.287 -1.247 -1.328 C6 US5 9 US5 "C1'" C1* C 0 1 N N R -7.700 3.538 11.233 -0.030 -1.643 -0.654 C1* US5 10 US5 OP3 OP3 O 0 1 N Y N -11.969 6.839 8.088 -4.048 2.652 1.035 OP3 US5 11 US5 "C2'" C2* C 0 1 N N R -7.035 3.086 9.935 -0.358 -2.470 0.615 C2* US5 12 US5 "O2'" O2* O 0 1 N N N -5.686 3.509 9.871 0.241 -3.766 0.548 O2* US5 13 US5 O2P O2P O 0 1 N N N -12.891 4.864 9.419 -5.170 2.589 -1.342 O2P US5 14 US5 "C3'" C3* C 0 1 N N S -7.927 3.781 8.915 -1.901 -2.570 0.548 C3* US5 15 US5 "O3'" O3* O 0 1 N N N -7.334 3.860 7.628 -2.297 -3.818 -0.023 O3* US5 16 US5 "C4'" C4* C 0 1 N N R -8.066 5.148 9.564 -2.315 -1.402 -0.368 C4* US5 17 US5 "O4'" O4* O 0 1 N N N -8.211 4.835 10.976 -1.116 -0.695 -0.732 O4* US5 18 US5 "C5'" C5* C 0 1 N N N -9.252 5.968 9.096 -3.266 -0.466 0.380 C5* US5 19 US5 "O5'" O5* O 0 1 N N N -10.455 5.226 9.267 -3.736 0.548 -0.511 O5* US5 20 US5 H5 H5 H 0 1 N N N -12.155 2.312 11.554 4.308 -0.817 -1.815 H5 US5 21 US5 H6 H6 H 0 1 N N N -10.370 3.784 10.910 2.171 -1.991 -2.102 H6 US5 22 US5 "H1'" H1* H 0 1 N N N -6.977 3.550 12.062 -0.015 -2.283 -1.536 H1* US5 23 US5 HOP3 HOP3 H 0 0 N Y N -12.026 6.325 7.291 -3.245 3.087 0.717 HOP3 US5 24 US5 "H2'" H2* H 0 1 N N N -6.965 1.997 9.795 -0.041 -1.944 1.515 H2* US5 25 US5 "HO2'" HO2* H 0 0 N N N -5.300 3.214 9.055 0.064 -4.321 1.320 HO2* US5 26 US5 HO2P HO2P H 0 0 N N N -12.467 4.017 9.349 -5.785 3.308 -1.144 HO2P US5 27 US5 "H3'" H3* H 0 1 N N N -8.876 3.262 8.717 -2.335 -2.448 1.541 H3* US5 28 US5 "HO3'" HO3* H 0 0 N N N -7.928 4.300 7.032 -2.011 -4.591 0.483 HO3* US5 29 US5 "H4'" H4* H 0 1 N N N -7.201 5.776 9.306 -2.801 -1.788 -1.264 H4* US5 30 US5 "H5'" H5* H 0 1 N N N -9.309 6.894 9.687 -4.114 -1.036 0.761 H5* US5 31 US5 "H5'A" H5*A H 0 0 N N N -9.126 6.215 8.032 -2.738 -0.001 1.213 H5*A US5 32 US5 HSE4 HSE4 H 0 0 N N N -10.962 -1.131 13.493 4.925 2.238 1.304 HSE4 US5 33 US5 OP1 OP1 O 0 1 N N N -11.885 4.464 9.253 -5.970 1.096 0.529 OP1 US5 34 # # 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 US5 P "O5'" SING N N 1 US5 P O2P SING N N 2 US5 N1 C2 SING N N 3 US5 C2 O2 DOUB N N 4 US5 C2 N3 SING N N 5 US5 C4 N3 DOUB N N 6 US5 C4 SE4 SING N N 7 US5 SE4 HSE4 SING N N 8 US5 C5 C4 SING N N 9 US5 C5 H5 SING N N 10 US5 C6 N1 SING N N 11 US5 C6 C5 DOUB N N 12 US5 C6 H6 SING N N 13 US5 "C1'" N1 SING N N 14 US5 "C1'" "H1'" SING N N 15 US5 OP3 P SING N N 16 US5 OP3 HOP3 SING N N 17 US5 "C2'" "C1'" SING N N 18 US5 "C2'" "H2'" SING N N 19 US5 "O2'" "C2'" SING N N 20 US5 "O2'" "HO2'" SING N N 21 US5 O2P HO2P SING N N 22 US5 "C3'" "C2'" SING N N 23 US5 "C3'" "C4'" SING N N 24 US5 "C3'" "H3'" SING N N 25 US5 "O3'" "C3'" SING N N 26 US5 "O3'" "HO3'" SING N N 27 US5 "C4'" "O4'" SING N N 28 US5 "C4'" "H4'" SING N N 29 US5 "O4'" "C1'" SING N N 30 US5 "C5'" "C4'" SING N N 31 US5 "C5'" "O5'" SING N N 32 US5 "C5'" "H5'" SING N N 33 US5 "C5'" "H5'A" SING N N 34 US5 P OP1 DOUB N N 35 # # 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 US5 SMILES ACDLabs 11.02 "O=P(O)(O)OCC2OC(N1C(=O)N=C([SeH])C=C1)C(O)C2O" US5 SMILES_CANONICAL CACTVS 3.352 "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=NC2=O)[SeH]" US5 SMILES CACTVS 3.352 "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=NC2=O)[SeH]" US5 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.0 "C1=CN(C(=O)N=C1[SeH])[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O" US5 SMILES "OpenEye OEToolkits" 1.7.0 "C1=CN(C(=O)N=C1[SeH])C2C(C(C(O2)COP(=O)(O)O)O)O" US5 InChI InChI 1.03 "InChI=1S/C9H13N2O8PSe/c12-6-4(3-18-20(15,16)17)19-8(7(6)13)11-2-1-5(21)10-9(11)14/h1-2,4,6-8,12-13H,3H2,(H,10,14,21)(H2,15,16,17)/t4-,6-,7-,8-/m1/s1" US5 InChIKey InChI 1.03 ZCQCFKOZDRTETH-XVFCMESISA-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 US5 "SYSTEMATIC NAME" ACDLabs 11.02 "1-(5-O-phosphono-beta-D-ribofuranosyl)-4-selanylpyrimidin-2(1H)-one" US5 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.6.1 "[(2R,3S,4R,5R)-3,4-dihydroxy-5-(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 US5 "Create component" 2009-07-17 RCSB US5 "Modify descriptor" 2011-06-04 RCSB US5 "Modify synonyms" 2021-03-01 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id US5 _pdbx_chem_comp_synonyms.name "4-Se-ribouridine-5'-phosphate" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##