data_1SC # _chem_comp.id 1SC _chem_comp.name "5'-O-THIOPHOSPHONOCYTIDINE" _chem_comp.type "RNA LINKING" _chem_comp.pdbx_type ATOMN _chem_comp.formula "C9 H14 N3 O7 P S" _chem_comp.mon_nstd_parent_comp_id C _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2006-10-19 _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 339.262 _chem_comp.one_letter_code C _chem_comp.three_letter_code 1SC _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 N _chem_comp.pdbx_model_coordinates_db_code 364D _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 1SC O3P O3P O 0 1 N Y N -13.520 -3.392 44.530 -4.754 1.370 -1.537 O3P 1SC 1 1SC P P P 0 1 N N S -13.737 -1.940 43.888 -3.950 0.625 -0.357 P 1SC 2 1SC O1P O1P O 0 1 N N N -12.539 -1.632 43.071 -4.794 -0.450 0.211 O1P 1SC 3 1SC "O5'" O5* O 0 1 N N N -14.980 -2.118 42.923 -2.596 -0.012 -0.950 "O5'" 1SC 4 1SC "C5'" C5* C 0 1 N N N -15.181 -3.345 42.257 -1.991 -0.755 0.111 "C5'" 1SC 5 1SC "C4'" C4* C 0 1 N N R -16.644 -3.669 42.226 -0.691 -1.390 -0.388 "C4'" 1SC 6 1SC "O4'" O4* O 0 1 N N N -17.076 -4.161 43.517 0.284 -0.368 -0.690 "O4'" 1SC 7 1SC "C3'" C3* C 0 1 N N S -17.525 -2.462 41.996 -0.041 -2.238 0.727 "C3'" 1SC 8 1SC "O3'" O3* O 0 1 N N N -17.572 -2.090 40.647 -0.361 -3.620 0.556 "O3'" 1SC 9 1SC "C2'" C2* C 0 1 N N R -18.858 -2.884 42.585 1.477 -2.005 0.541 "C2'" 1SC 10 1SC "O2'" O2* O 0 1 N N N -19.631 -3.678 41.720 2.140 -3.237 0.252 "O2'" 1SC 11 1SC "C1'" C1* C 0 1 N N R -18.398 -3.711 43.779 1.562 -1.041 -0.663 "C1'" 1SC 12 1SC N1 N1 N 0 1 N N N -18.393 -2.899 44.998 2.644 -0.073 -0.466 N1 1SC 13 1SC C2 C2 C 0 1 N N N -19.545 -2.883 45.777 2.584 0.799 0.557 C2 1SC 14 1SC O2 O2 O 0 1 N N N -20.517 -3.555 45.407 1.626 0.774 1.312 O2 1SC 15 1SC N3 N3 N 0 1 N N N -19.576 -2.141 46.903 3.554 1.689 0.760 N3 1SC 16 1SC C4 C4 C 0 1 N N N -18.514 -1.418 47.251 4.607 1.738 -0.046 C4 1SC 17 1SC N4 N4 N 0 1 N N N -18.598 -0.688 48.361 5.602 2.662 0.173 N4 1SC 18 1SC C5 C5 C 0 1 N N N -17.317 -1.411 46.474 4.697 0.842 -1.130 C5 1SC 19 1SC C6 C6 C 0 1 N N N -17.299 -2.163 45.365 3.706 -0.061 -1.319 C6 1SC 20 1SC S S S 0 1 N N N -14.270 -0.815 45.242 -3.469 2.023 1.162 S 1SC 21 1SC HO3P HO3P H 0 0 N N N -13.477 -4.041 43.838 -4.170 2.061 -1.879 HO3P 1SC 22 1SC "H5'1" 1H5* H 0 0 N N N -14.641 -4.142 42.789 -2.673 -1.537 0.442 "H5'1" 1SC 23 1SC "H5'2" 2H5* H 0 0 N N N -14.803 -3.267 41.227 -1.772 -0.087 0.944 "H5'2" 1SC 24 1SC "H4'" H4* H 0 1 N N N -16.746 -4.396 41.407 -0.883 -2.003 -1.269 "H4'" 1SC 25 1SC "H3'" H3* H 0 1 N N N -17.152 -1.545 42.475 -0.365 -1.891 1.708 "H3'" 1SC 26 1SC "HO3'" HO3* H 0 0 N N N -17.583 -1.142 40.580 0.069 -4.098 1.277 "HO3'" 1SC 27 1SC "H2'" H2* H 0 1 N N N -19.509 -2.027 42.812 1.904 -1.542 1.431 "H2'" 1SC 28 1SC "HO2'" HO2* H 0 0 N N N -19.805 -3.197 40.919 2.000 -3.816 1.013 "HO2'" 1SC 29 1SC "H1'" H1* H 0 1 N N N -19.084 -4.558 43.926 1.716 -1.599 -1.586 "H1'" 1SC 30 1SC HN41 1HN4 H 0 0 N N N -17.739 -0.197 48.507 5.535 3.280 0.918 HN41 1SC 31 1SC HN42 2HN4 H 0 0 N N N -19.399 -0.639 48.958 6.373 2.693 -0.415 HN42 1SC 32 1SC H5 H5 H 0 1 N N N -16.460 -0.823 46.768 5.548 0.869 -1.794 H5 1SC 33 1SC H6 H6 H 0 1 N N N -16.410 -2.189 44.753 3.755 -0.761 -2.140 H6 1SC 34 1SC HS HS H 0 1 N N N -14.396 -1.492 46.345 -4.705 2.424 1.511 HS 1SC 35 # 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 1SC O3P P SING N N 1 1SC O3P HO3P SING N N 2 1SC P O1P DOUB N N 3 1SC P "O5'" SING N N 4 1SC P S SING N N 5 1SC "O5'" "C5'" SING N N 6 1SC "C5'" "C4'" SING N N 7 1SC "C5'" "H5'1" SING N N 8 1SC "C5'" "H5'2" SING N N 9 1SC "C4'" "O4'" SING N N 10 1SC "C4'" "C3'" SING N N 11 1SC "C4'" "H4'" SING N N 12 1SC "O4'" "C1'" SING N N 13 1SC "C3'" "O3'" SING N N 14 1SC "C3'" "C2'" SING N N 15 1SC "C3'" "H3'" SING N N 16 1SC "O3'" "HO3'" SING N N 17 1SC "C2'" "O2'" SING N N 18 1SC "C2'" "C1'" SING N N 19 1SC "C2'" "H2'" SING N N 20 1SC "O2'" "HO2'" SING N N 21 1SC "C1'" N1 SING N N 22 1SC "C1'" "H1'" SING N N 23 1SC N1 C2 SING N N 24 1SC N1 C6 SING N N 25 1SC C2 O2 DOUB N N 26 1SC C2 N3 SING N N 27 1SC N3 C4 DOUB N N 28 1SC C4 N4 SING N N 29 1SC C4 C5 SING N N 30 1SC N4 HN41 SING N N 31 1SC N4 HN42 SING N N 32 1SC C5 C6 DOUB N N 33 1SC C5 H5 SING N N 34 1SC C6 H6 SING N N 35 1SC S HS SING N N 36 # 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 1SC SMILES ACDLabs 10.04 "O=P(O)(S)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2O" 1SC SMILES_CANONICAL CACTVS 3.341 "NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P@](O)(S)=O)[C@@H](O)[C@H]2O" 1SC SMILES CACTVS 3.341 "NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(S)=O)[CH](O)[CH]2O" 1SC SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@](=O)(O)S)O)O" 1SC SMILES "OpenEye OEToolkits" 1.5.0 "C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)S)O)O" 1SC InChI InChI 1.03 "InChI=1S/C9H14N3O7PS/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(19-8)3-18-20(16,17)21/h1-2,4,6-8,13-14H,3H2,(H2,10,11,15)(H2,16,17,21)/t4-,6-,7-,8-/m1/s1" 1SC InChIKey InChI 1.03 JOENGNVCVILJEG-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 1SC "SYSTEMATIC NAME" ACDLabs 10.04 "5'-O-thiophosphonocytidine" 1SC "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,4R,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-sulfanyl-phosphinic acid" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 1SC "Create component" 2006-10-19 RCSB 1SC "Modify descriptor" 2011-06-04 RCSB #