data_UPS
# 
_chem_comp.id                                    UPS 
_chem_comp.name                                  "2'-deoxy-5'-O-thiophosphonouridine" 
_chem_comp.type                                  "DNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C9 H13 N2 O7 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                     2009-02-10 
_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                        324.247 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     UPS 
_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        3G3C 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBJ 
# 
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 
UPS OP3    O3P    O 0 1 N Y N 3.477  3.404  -32.752 3.365  -2.220 0.794  OP3    UPS 1  
UPS P      P      P 0 1 N N N 3.979  1.981  -33.280 3.769  -1.017 -0.197 P      UPS 2  
UPS S1P    S1P    S 0 1 N N N 4.054  2.071  -34.758 4.978  0.114  0.659  S1P    UPS 3  
UPS OP2    O2P    O 0 1 N N N 3.146  0.920  -32.675 4.448  -1.620 -1.526 OP2    UPS 4  
UPS "O5'"  "O5'"  O 0 1 N N N 5.450  1.878  -32.657 2.449  -0.186 -0.598 "O5'"  UPS 5  
UPS "C5'"  "C5'"  C 0 1 N N N 6.564  2.213  -33.457 1.800  0.722  0.294  "C5'"  UPS 6  
UPS "C4'"  "C4'"  C 0 1 N N R 7.829  2.058  -32.656 0.584  1.338  -0.400 "C4'"  UPS 7  
UPS "O4'"  "O4'"  O 0 1 N N N 7.595  2.620  -31.349 -0.448 0.344  -0.583 "O4'"  UPS 8  
UPS "C1'"  "C1'"  C 0 1 N N R 8.557  2.048  -30.496 -1.670 1.092  -0.764 "C1'"  UPS 9  
UPS N1     N1     N 0 1 N N N 8.188  2.333  -29.040 -2.832 0.249  -0.474 N1     UPS 10 
UPS C2     C2     C 0 1 N N N 9.148  2.884  -28.185 -2.911 -0.395 0.704  C2     UPS 11 
UPS O2     O2     O 0 1 N N N 10.293 3.143  -28.526 -2.015 -0.270 1.517  O2     UPS 12 
UPS N3     N3     N 0 1 N N N 8.728  3.127  -26.889 -3.968 -1.176 0.997  N3     UPS 13 
UPS C4     C4     C 0 1 N N N 7.458  2.875  -26.372 -4.970 -1.325 0.107  C4     UPS 14 
UPS O4     O4     O 0 1 N N N 7.226  3.135  -25.191 -5.926 -2.030 0.371  O4     UPS 15 
UPS C5     C5     C 0 1 N N N 6.511  2.300  -27.311 -4.899 -0.653 -1.137 C5     UPS 16 
UPS C6     C6     C 0 1 N N N 6.901  2.065  -28.578 -3.830 0.128  -1.402 C6     UPS 17 
UPS "C2'"  "C2'"  C 0 1 N N N 8.630  0.587  -30.941 -1.578 2.250  0.255  "C2'"  UPS 18 
UPS "C3'"  "C3'"  C 0 1 N N S 8.288  0.616  -32.438 -0.061 2.415  0.499  "C3'"  UPS 19 
UPS "O3'"  "O3'"  O 0 1 N N N 9.402  0.318  -33.334 0.370  3.720  0.106  "O3'"  UPS 20 
UPS HOP3   HO3P   H 0 0 N Y N 3.377  3.375  -31.808 2.737  -2.849 0.413  HOP3   UPS 21 
UPS HOP2   HO2P   H 0 0 N N N 2.967  0.249  -33.323 5.250  -2.134 -1.360 HOP2   UPS 22 
UPS "H5'"  "H5'"  H 0 1 N N N 6.601  1.545  -34.330 1.476  0.185  1.186  "H5'"  UPS 23 
UPS "H5'A" "H5'A" H 0 0 N N N 6.471  3.256  -33.793 2.495  1.512  0.578  "H5'A" UPS 24 
UPS "H4'"  "H4'"  H 0 1 N N N 8.616  2.563  -33.235 0.873  1.768  -1.360 "H4'"  UPS 25 
UPS "H1'"  "H1'"  H 0 1 N N N 9.572  2.468  -30.560 -1.729 1.482  -1.780 "H1'"  UPS 26 
UPS H5     H5     H 0 1 N N N 5.505  2.064  -26.996 -5.692 -0.760 -1.862 H5     UPS 27 
UPS H6     H6     H 0 1 N N N 6.182  1.649  -29.269 -3.761 0.652  -2.345 H6     UPS 28 
UPS "H2'"  "H2'"  H 0 1 N N N 9.635  0.172  -30.773 -1.999 3.163  -0.166 "H2'"  UPS 29 
UPS "H2'A" "H2'A" H 0 0 N N N 7.940  -0.054 -30.372 -2.090 1.986  1.180  "H2'A" UPS 30 
UPS "H3'"  "H3'"  H 0 1 N N N 7.547  -0.162 -32.674 0.179  2.232  1.547  "H3'"  UPS 31 
UPS "HO3'" "HO3'" H 0 0 N Y N 9.083  0.253  -34.226 -0.005 4.435  0.638  "HO3'" UPS 32 
UPS HN3    HN3    H 0 1 N N N 9.400  3.521  -26.263 -4.009 -1.633 1.852  HN3    UPS 33 
# 
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 
UPS P     OP3    SING N N 1  
UPS S1P   P      DOUB N N 2  
UPS P     OP2    SING N N 3  
UPS P     "O5'"  SING N N 4  
UPS OP3   HOP3   SING N N 5  
UPS OP2   HOP2   SING N N 6  
UPS "C5'" "O5'"  SING N N 7  
UPS "C5'" "C4'"  SING N N 8  
UPS "C5'" "H5'"  SING N N 9  
UPS "C5'" "H5'A" SING N N 10 
UPS "C4'" "C3'"  SING N N 11 
UPS "C4'" "O4'"  SING N N 12 
UPS "C4'" "H4'"  SING N N 13 
UPS "O4'" "C1'"  SING N N 14 
UPS "C2'" "C1'"  SING N N 15 
UPS "C1'" N1     SING N N 16 
UPS "C1'" "H1'"  SING N N 17 
UPS N1    C6     SING N N 18 
UPS N1    C2     SING N N 19 
UPS O2    C2     DOUB N N 20 
UPS C2    N3     SING N N 21 
UPS N3    C4     SING N N 22 
UPS C5    C4     SING N N 23 
UPS C4    O4     DOUB N N 24 
UPS C6    C5     DOUB N N 25 
UPS C5    H5     SING N N 26 
UPS C6    H6     SING N N 27 
UPS "C3'" "C2'"  SING N N 28 
UPS "C2'" "H2'"  SING N N 29 
UPS "C2'" "H2'A" SING N N 30 
UPS "O3'" "C3'"  SING N N 31 
UPS "C3'" "H3'"  SING N N 32 
UPS "O3'" "HO3'" SING N N 33 
UPS N3    HN3    SING N N 34 
# 
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 
UPS SMILES           ACDLabs              10.04 "O=C1NC(=O)N(C=C1)C2OC(C(O)C2)COP(=S)(O)O"                                                                                                     
UPS SMILES_CANONICAL CACTVS               3.341 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=S)N2C=CC(=O)NC2=O"                                                                                         
UPS SMILES           CACTVS               3.341 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=S)N2C=CC(=O)NC2=O"                                                                                              
UPS SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)COP(=S)(O)O)O"                                                                                          
UPS SMILES           "OpenEye OEToolkits" 1.5.0 "C1C(C(OC1N2C=CC(=O)NC2=O)COP(=S)(O)O)O"                                                                                                       
UPS InChI            InChI                1.03  "InChI=1S/C9H13N2O7PS/c12-5-3-8(11-2-1-7(13)10-9(11)14)18-6(5)4-17-19(15,16)20/h1-2,5-6,8,12H,3-4H2,(H,10,13,14)(H2,15,16,20)/t5-,6+,8+/m0/s1" 
UPS InChIKey         InChI                1.03  LGZBLTPUGKWVDT-SHYZEUOFSA-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 
UPS "SYSTEMATIC NAME" ACDLabs              10.04 "2'-deoxy-5'-O-thiophosphonouridine"                                                             
UPS "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "1-[(2R,4S,5R)-5-(dihydroxyphosphinothioyloxymethyl)-4-hydroxy-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 
UPS "Create component"  2009-02-10 PDBJ 
UPS "Modify descriptor" 2011-06-04 RCSB 
# 
