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                    2009-01-07 
_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 InChI            InChI                1.02b "InChI=1/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/f/h16,21H,10H2" 
1SC InChIKey         InChI                1.02b JOENGNVCVILJEG-MCSDBIMBDE                                                                                                                                           
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"                                                                                                                       
# 
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" 
# 
