data_USM # _chem_comp.id USM _chem_comp.name ;2'-S-methyl-2'-thiouridine 5'-(dihydrogen phosphate) ; _chem_comp.type "DNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C10 H15 N2 O8 P S" _chem_comp.mon_nstd_parent_comp_id DU _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2008-10-29 _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 354.273 _chem_comp.one_letter_code U _chem_comp.three_letter_code USM _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 3EY1 _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 USM OP2 OP2 O 0 1 N N N 8.073 -11.502 -1.566 -5.009 1.996 -1.129 OP2 USM 1 USM P P P 0 1 N N N 8.795 -12.112 -2.850 -4.543 0.925 -0.021 P USM 2 USM OP1 OP1 O 0 1 N N N 8.542 -11.213 -3.994 -4.451 1.590 1.299 OP1 USM 3 USM OP3 OP3 O 0 1 N Y N 10.193 -12.462 -2.497 -5.618 -0.271 0.055 OP3 USM 4 USM "O5'" "O5'" O 0 1 N N N 7.960 -13.474 -3.037 -3.103 0.329 -0.423 "O5'" USM 5 USM N1 N1 N 0 1 N N N 3.208 -11.796 -2.184 2.139 0.696 -0.157 N1 USM 6 USM C6 C6 C 0 1 N N N 3.995 -10.878 -2.818 2.039 1.334 1.049 C6 USM 7 USM C2 C2 C 0 1 N N N 1.913 -11.607 -1.817 3.150 0.978 -0.999 C2 USM 8 USM O2 O2 O 0 1 N N N 1.197 -12.407 -1.245 3.222 0.397 -2.065 O2 USM 9 USM N3 N3 N 0 1 N N N 1.431 -10.345 -2.145 4.081 1.896 -0.680 N3 USM 10 USM C4 C4 C 0 1 N N N 2.158 -9.359 -2.784 4.015 2.549 0.498 C4 USM 11 USM O4 O4 O 0 1 N N N 1.614 -8.284 -3.026 4.858 3.379 0.788 O4 USM 12 USM C5 C5 C 0 1 N N N 3.529 -9.660 -3.140 2.963 2.255 1.398 C5 USM 13 USM "C2'" "C2'" C 0 1 N N R 3.274 -14.506 -2.503 1.212 -1.521 0.421 "C2'" USM 14 USM "S2'" "S2'" S 0 1 N N N 3.344 -15.737 -1.177 2.173 -2.864 -0.329 "S2'" USM 15 USM C2A C2A C 0 1 N N N 1.983 -15.236 -0.123 2.256 -4.097 0.998 C2A USM 16 USM "C5'" "C5'" C 0 1 N N N 6.660 -13.421 -3.643 -2.371 -0.569 0.414 "C5'" USM 17 USM "C4'" "C4'" C 0 1 N N R 5.603 -14.021 -2.756 -1.051 -0.938 -0.266 "C4'" USM 18 USM "O4'" "O4'" O 0 1 N N N 5.040 -13.036 -1.863 -0.193 0.220 -0.359 "O4'" USM 19 USM "C1'" "C1'" C 0 1 N N R 3.628 -13.224 -1.755 1.141 -0.308 -0.533 "C1'" USM 20 USM "C3'" "C3'" C 0 1 N N R 4.391 -14.570 -3.509 -0.263 -1.945 0.601 "C3'" USM 21 USM "O3'" "O3'" O 0 1 N N N 4.642 -15.914 -4.028 -0.462 -3.278 0.126 "O3'" USM 22 USM HOP2 HOP2 H 0 0 N N N 8.710 -11.381 -0.872 -5.871 2.397 -0.951 HOP2 USM 23 USM HOP3 HOP3 H 0 0 N Y N 10.711 -12.537 -3.290 -5.730 -0.752 -0.777 HOP3 USM 24 USM H6 H6 H 0 1 N N N 5.014 -11.137 -3.066 1.224 1.102 1.719 H6 USM 25 USM H5 H5 H 0 1 N N N 4.151 -8.935 -3.644 2.895 2.766 2.347 H5 USM 26 USM "H2'" "H2'" H 0 1 N N N 2.314 -14.618 -3.028 1.647 -1.229 1.377 "H2'" USM 27 USM H2A H2A H 0 1 N N N 2.339 -15.133 0.913 1.247 -4.406 1.271 H2A USM 28 USM H2AA H2AA H 0 0 N N N 1.586 -14.271 -0.471 2.820 -4.964 0.654 H2AA USM 29 USM H2AB H2AB H 0 0 N N N 1.189 -15.996 -0.164 2.750 -3.663 1.867 H2AB USM 30 USM "H5'" "H5'" H 0 1 N N N 6.403 -12.369 -3.835 -2.165 -0.088 1.370 "H5'" USM 31 USM "H5'A" "H5'A" H 0 0 N N N 6.694 -14.002 -4.577 -2.959 -1.472 0.580 "H5'A" USM 32 USM "H4'" "H4'" H 0 1 N N N 6.140 -14.829 -2.237 -1.238 -1.352 -1.257 "H4'" USM 33 USM "H1'" "H1'" H 0 1 N N N 3.092 -13.460 -0.824 1.293 -0.627 -1.564 "H1'" USM 34 USM "H3'" "H3'" H 0 1 N N N 4.143 -13.991 -4.411 -0.559 -1.862 1.646 "H3'" USM 35 USM "HO3'" "HO3'" H 0 0 N Y N 4.696 -15.883 -4.976 -1.371 -3.595 0.215 "HO3'" USM 36 USM HN3 HN3 H 0 1 N N N 0.485 -10.134 -1.899 4.803 2.087 -1.298 HN3 USM 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 USM P OP2 SING N N 1 USM OP2 HOP2 SING N N 2 USM OP1 P DOUB N N 3 USM "O5'" P SING N N 4 USM P OP3 SING N N 5 USM OP3 HOP3 SING N N 6 USM "C5'" "O5'" SING N N 7 USM C6 N1 SING N N 8 USM N1 C2 SING N N 9 USM N1 "C1'" SING N N 10 USM C5 C6 DOUB N N 11 USM C6 H6 SING N N 12 USM N3 C2 SING N N 13 USM C2 O2 DOUB N N 14 USM C4 N3 SING N N 15 USM C5 C4 SING N N 16 USM O4 C4 DOUB N N 17 USM C5 H5 SING N N 18 USM "C3'" "C2'" SING N N 19 USM "C2'" "C1'" SING N N 20 USM "C2'" "S2'" SING N N 21 USM "C2'" "H2'" SING N N 22 USM "S2'" C2A SING N N 23 USM C2A H2A SING N N 24 USM C2A H2AA SING N N 25 USM C2A H2AB SING N N 26 USM "C5'" "C4'" SING N N 27 USM "C5'" "H5'" SING N N 28 USM "C5'" "H5'A" SING N N 29 USM "C3'" "C4'" SING N N 30 USM "C4'" "O4'" SING N N 31 USM "C4'" "H4'" SING N N 32 USM "O4'" "C1'" SING N N 33 USM "C1'" "H1'" SING N N 34 USM "O3'" "C3'" SING N N 35 USM "C3'" "H3'" SING N N 36 USM "O3'" "HO3'" SING N N 37 USM N3 HN3 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 USM SMILES ACDLabs 10.04 "O=C1NC(=O)N(C=C1)C2OC(C(O)C2SC)COP(=O)(O)O" USM SMILES_CANONICAL CACTVS 3.341 "CS[C@@H]1[C@H](O)[C@@H](CO[P](O)(O)=O)O[C@H]1N2C=CC(=O)NC2=O" USM SMILES CACTVS 3.341 "CS[CH]1[CH](O)[CH](CO[P](O)(O)=O)O[CH]1N2C=CC(=O)NC2=O" USM SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CS[C@@H]1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)COP(=O)(O)O)O" USM SMILES "OpenEye OEToolkits" 1.5.0 "CSC1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(O)O)O" USM InChI InChI 1.03 "InChI=1S/C10H15N2O8PS/c1-22-8-7(14)5(4-19-21(16,17)18)20-9(8)12-3-2-6(13)11-10(12)15/h2-3,5,7-9,14H,4H2,1H3,(H,11,13,15)(H2,16,17,18)/t5-,7-,8-,9-/m1/s1" USM InChIKey InChI 1.03 NZYFPIYZUCYZKH-ZOQUXTDFSA-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 USM "SYSTEMATIC NAME" ACDLabs 10.04 ;2'-S-methyl-2'-thiouridine 5'-(dihydrogen phosphate) ; USM "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3R,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3-hydroxy-4-methylsulfanyl-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 USM "Create component" 2008-10-29 RCSB USM "Modify descriptor" 2011-06-04 RCSB #