data_SSU
#

_chem_comp.id                                   SSU
_chem_comp.name                                 "URIDINE-5'-PHOSPHOROTHIOATE"
_chem_comp.type                                 "RNA LINKING"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C9 H13 N2 O8 P S"
_chem_comp.mon_nstd_parent_comp_id              U
_chem_comp.pdbx_synonyms                        "SP-SULFUR-SUBSTITUTED URIDINE"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2003-04-09
_chem_comp.pdbx_modified_date                   2020-06-17
_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                       340.247
_chem_comp.one_letter_code                      U
_chem_comp.three_letter_code                    SSU
_chem_comp.pdbx_model_coordinates_details       ?
_chem_comp.pdbx_model_coordinates_missing_flag  Y
_chem_comp.pdbx_ideal_coordinates_details       ?
_chem_comp.pdbx_ideal_coordinates_missing_flag  N
_chem_comp.pdbx_model_coordinates_db_code       1NZ1
_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
SSU  "O2'"   O2*   O  0  1  N  N  N  -2.068  -3.875  -14.864   0.137  -0.058   2.041  "O2'"   SSU   1  
SSU  "C2'"   C2*   C  0  1  N  N  R  -2.623  -3.836  -13.545   0.748   0.163   0.786  "C2'"   SSU   2  
SSU  "C1'"   C1*   C  0  1  N  N  R  -2.568  -2.425  -12.958   1.373   1.543   0.675  "C1'"   SSU   3  
SSU  "O4'"   O4*   O  0  1  N  N  N  -3.898  -1.884  -13.034   2.470   1.422  -0.246  "O4'"   SSU   4  
SSU  "C4'"   C4*   C  0  1  N  N  R  -4.743  -2.785  -13.748   2.725   0.023  -0.498  "C4'"   SSU   5  
SSU  "C5'"   C5*   C  0  1  N  N  N  -6.170  -2.758  -13.209   2.282  -0.292  -1.921  "C5'"   SSU   6  
SSU  "O5'"   O5*   O  0  1  N  N  N  -6.201  -2.919  -11.788   3.063   0.476  -2.819  "O5'"   SSU   7  
SSU  P       P     P  0  1  N  N  N  -7.477  -2.424  -10.939   2.812   0.347  -4.417  P       SSU   8  
SSU  S1P     S1P   S  0  1  N  N  N  -9.119  -2.439  -12.265   1.133   1.036  -5.105  S1P     SSU   9  
SSU  OP2     O2P   O  0  1  N  N  N  -7.467  -3.134   -9.641   3.104  -1.222  -4.708  OP2     SSU  10  
SSU  OP3     O3P   O  0  1  N  Y  N       ?       ?        ?   4.136   1.046  -5.041  OP3     SSU  11  
SSU  "C3'"   C3*   C  0  1  N  N  S  -4.109  -4.150  -13.556   1.940  -0.742   0.560  "C3'"   SSU  12  
SSU  "O3'"   O3*   O  0  1  N  N  N  -4.392  -4.958  -14.704   2.742  -0.809   1.739  "O3'"   SSU  13  
SSU  N1      N1    N  0  1  N  N  N  -2.082  -2.466  -11.566   0.452   2.524   0.177  N1      SSU  14  
SSU  C6      C6    C  0  1  N  N  N  -2.941  -2.668  -10.520   0.308   2.664  -1.199  C6      SSU  15  
SSU  C5      C5    C  0  1  N  N  N  -2.491  -2.729   -9.242  -0.516   3.539  -1.779  C5      SSU  16  
SSU  C4      C4    C  0  1  N  N  N  -1.085  -2.578   -8.941  -1.338   4.427  -0.933  C4      SSU  17  
SSU  O4      O4    O  0  1  N  N  N  -0.591  -2.621   -7.817  -2.105   5.242  -1.435  O4      SSU  18  
SSU  N3      N3    N  0  1  N  N  N  -0.290  -2.378  -10.056  -1.161   4.252   0.431  N3      SSU  19  
SSU  C2      C2    C  0  1  N  N  N  -0.724  -2.312  -11.367  -0.301   3.338   1.055  C2      SSU  20  
SSU  O2      O2    O  0  1  N  N  N   0.055  -2.128  -12.299  -0.226   3.271   2.284  O2      SSU  21  
SSU  "HO2'"  2HO*  H  0  0  N  N  N  -1.583  -3.057  -14.993  -0.494   0.669   2.185  "HO2'"  SSU  22  
SSU  "H2'"   H2*   H  0  1  N  N  N  -2.106  -4.531  -12.884  -0.000   0.004  -0.000  "H2'"   SSU  23  
SSU  "H1'"   H1*   H  0  1  N  N  N  -1.895  -1.813  -13.557   1.754   1.910   1.633  "H1'"   SSU  24  
SSU  "H4'"   H4*   H  0  1  N  N  N  -4.742  -2.521  -14.804   3.804  -0.139  -0.410  "H4'"   SSU  25  
SSU  "H5'"   1H5*  H  0  1  N  N  N  -6.630  -1.805  -13.470   1.229  -0.035  -2.051  "H5'"   SSU  26  
SSU  "H5''"  2H5*  H  0  0  N  N  N  -6.738  -3.565  -13.671   2.428  -1.352  -2.133  "H5''"  SSU  27  
SSU  H2P     H2P   H  0  1  N  N  N  -8.219  -2.842   -9.140   3.952  -1.609  -4.402  H2P     SSU  28  
SSU  H3P     H3P   H  0  1  N  N  N  -0.752   0.292    0.500   4.167   1.222  -6.006  H3P     SSU  29  
SSU  "H3'"   H3*   H  0  1  N  N  N  -4.433  -4.622  -12.630   1.675  -1.764   0.277  "H3'"   SSU  30  
SSU  "HO3'"  H3T   H  0  0  N  Y  N  -5.321  -5.154  -14.710   3.447  -0.153   1.628  "HO3'"  SSU  31  
SSU  H6      6H    H  0  1  N  N  N  -4.006  -2.784  -10.719   0.921   2.002  -1.802  H6      SSU  32  
SSU  H5      5H    H  0  1  N  N  N  -3.199  -2.895   -8.430  -0.601   3.619  -2.856  H5      SSU  33  
SSU  H3      3H    H  0  1  N  N  N   0.701  -2.269   -9.897  -1.712   4.848   1.042  H3      SSU  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
SSU  "O2'"  "C2'"   SING  N  N   1  
SSU  "O2'"  "HO2'"  SING  N  N   2  
SSU  "C2'"  "C1'"   SING  N  N   3  
SSU  "C2'"  "C3'"   SING  N  N   4  
SSU  "C2'"  "H2'"   SING  N  N   5  
SSU  "C1'"  "O4'"   SING  N  N   6  
SSU  "C1'"  N1      SING  N  N   7  
SSU  "C1'"  "H1'"   SING  N  N   8  
SSU  "O4'"  "C4'"   SING  N  N   9  
SSU  "C4'"  "C5'"   SING  N  N  10  
SSU  "C4'"  "C3'"   SING  N  N  11  
SSU  "C4'"  "H4'"   SING  N  N  12  
SSU  "C5'"  "O5'"   SING  N  N  13  
SSU  "C5'"  "H5'"   SING  N  N  14  
SSU  "C5'"  "H5''"  SING  N  N  15  
SSU  "O5'"  P       SING  N  N  16  
SSU  P      S1P     DOUB  N  N  17  
SSU  P      OP2     SING  N  N  18  
SSU  P      OP3     SING  N  N  19  
SSU  OP2    H2P     SING  N  N  20  
SSU  OP3    H3P     SING  N  N  21  
SSU  "C3'"  "O3'"   SING  N  N  22  
SSU  "C3'"  "H3'"   SING  N  N  23  
SSU  "O3'"  "HO3'"  SING  N  N  24  
SSU  N1     C6      SING  N  N  25  
SSU  N1     C2      SING  N  N  26  
SSU  C6     C5      DOUB  N  N  27  
SSU  C6     H6      SING  N  N  28  
SSU  C5     C4      SING  N  N  29  
SSU  C5     H5      SING  N  N  30  
SSU  C4     O4      DOUB  N  N  31  
SSU  C4     N3      SING  N  N  32  
SSU  N3     C2      SING  N  N  33  
SSU  N3     H3      SING  N  N  34  
SSU  C2     O2      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
SSU  SMILES            ACDLabs               10.04  "O=C1NC(=O)N(C=C1)C2OC(C(O)C2O)COP(=S)(O)O"  
SSU  SMILES_CANONICAL  CACTVS                3.341  "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=S)N2C=CC(=O)NC2=O"  
SSU  SMILES            CACTVS                3.341  "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=S)N2C=CC(=O)NC2=O"  
SSU  SMILES_CANONICAL  "OpenEye OEToolkits"  1.5.0  "C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=S)(O)O)O)O"  
SSU  SMILES            "OpenEye OEToolkits"  1.5.0  "C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=S)(O)O)O)O"  
SSU  InChI             InChI                 1.03   "InChI=1S/C9H13N2O8PS/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(19-8)3-18-20(16,17)21/h1-2,4,6-8,13-14H,3H2,(H,10,12,15)(H2,16,17,21)/t4-,6-,7-,8-/m1/s1"  
SSU  InChIKey          InChI                 1.03   NSEBKRRODBXALJ-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
SSU  "SYSTEMATIC NAME"  ACDLabs               10.04  "5'-O-thiophosphonouridine"  
SSU  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.5.0  "1-[(2R,3R,4S,5R)-5-(dihydroxyphosphinothioyloxymethyl)-3,4-dihydroxy-oxolan-2-yl]pyrimidine-2,4-dione"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
SSU  "Create component"   2003-04-09  RCSB  
SSU  "Modify descriptor"  2011-06-04  RCSB  
SSU  "Modify synonyms"    2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     SSU
_pdbx_chem_comp_synonyms.name        "SP-SULFUR-SUBSTITUTED URIDINE"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
