data_US2
#

_chem_comp.id                                   US2
_chem_comp.name                                 "2'-deoxy-5-(methylsulfanyl)uridine 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                        "5-SMe-deoxyuridine-5'-phosphate"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2009-06-10
_chem_comp.pdbx_modified_date                   2021-03-01
_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                    US2
_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       3HG8
_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
US2  P       P       P  0  1  N  N  N  33.997  25.600  7.412   4.704  -1.122  -0.312  P       US2   1  
US2  N1      N1      N  0  1  N  N  N  35.374  29.037  3.426  -1.798   0.379   0.133  N1      US2   2  
US2  C6      C6      C  0  1  N  N  N  34.359  28.242  3.435  -2.911   0.232  -0.657  C6      US2   3  
US2  C2      C2      C  0  1  N  N  N  35.145  29.960  2.478  -1.725  -0.193   1.346  C2      US2   4  
US2  O2      O2      O  0  1  N  N  N  35.956  30.884  2.240  -0.720  -0.039   2.014  O2      US2   5  
US2  N3      N3      N  0  1  N  N  N  33.982  29.880  1.757  -2.734  -0.931   1.841  N3      US2   6  
US2  C4      C4      C  0  1  N  N  N  33.013  28.922  1.947  -3.859  -1.117   1.119  C4      US2   7  
US2  O4      O4      O  0  1  N  N  N  32.030  28.900  1.177  -4.776  -1.785   1.562  O4      US2   8  
US2  C5      C5      C  0  1  N  N  N  33.218  27.949  2.932  -3.959  -0.497  -0.205  C5      US2   9  
US2  S5      S5      S  0  1  N  N  N  32.128  26.676  3.278  -5.405  -0.707  -1.191  S5      US2  10  
US2  C5A     C5A     C  0  1  N  N  N  30.932  27.525  4.249  -5.017   0.240  -2.689  C5A     US2  11  
US2  "C1'"   "C1'"   C  0  1  N  N  R  36.604  29.045  4.230  -0.666   1.168  -0.359  "C1'"   US2  12  
US2  "O4'"   "O4'"   O  0  1  N  N  N  36.826  27.771  4.843   0.553   0.398  -0.288  "O4'"   US2  13  
US2  "C4'"   "C4'"   C  0  1  N  N  R  36.915  27.938  6.256   1.620   1.371  -0.306  "C4'"   US2  14  
US2  "C3'"   "C3'"   C  0  1  N  N  S  36.148  29.209  6.522   1.120   2.521   0.596  "C3'"   US2  15  
US2  "O3'"   "O3'"   O  0  1  N  N  N  36.583  29.791  7.748   1.523   3.785   0.066  "O3'"   US2  16  
US2  "C2'"   "C2'"   C  0  1  N  N  N  36.485  30.081  5.337  -0.419   2.385   0.560  "C2'"   US2  17  
US2  "C5'"   "C5'"   C  0  1  N  N  N  36.319  26.751  6.984   2.903   0.765   0.266  "C5'"   US2  18  
US2  "O5'"   "O5'"   O  0  1  N  N  N  34.927  26.695  6.697   3.372  -0.267  -0.604  "O5'"   US2  19  
US2  O1P     O1P     O  0  1  N  N  N  32.564  25.846  7.066   4.610  -1.739   1.029  O1P     US2  20  
US2  O2P     O2P     O  0  1  N  N  N  34.515  25.387  9.038   4.855  -2.276  -1.425  O2P     US2  21  
US2  H6      H6      H  0  1  N  N  N  34.556  27.503  4.197  -2.951   0.696  -1.632  H6      US2  22  
US2  HN3     HN3     H  0  1  N  N  N  33.827  30.564  1.045  -2.652  -1.335   2.719  HN3     US2  23  
US2  H15A    H15A    H  0  0  N  N  N  31.336  27.702  5.257  -4.838   1.282  -2.424  H15A    US2  24  
US2  H25A    H25A    H  0  0  N  N  N  30.693  28.489  3.775  -4.125  -0.173  -3.159  H25A    US2  25  
US2  H35A    H35A    H  0  0  N  N  N  30.020  26.915  4.322  -5.855   0.181  -3.383  H35A    US2  26  
US2  "H1'"   "H1'"   H  0  1  N  N  N  37.442  29.281  3.558  -0.849   1.495  -1.383  "H1'"   US2  27  
US2  "H4'"   "H4'"   H  0  1  N  N  N  37.953  28.000  6.616   1.789   1.731  -1.321  "H4'"   US2  28  
US2  "H3'"   "H3'"   H  0  1  N  N  N  35.063  29.059  6.628   1.493   2.399   1.613  "H3'"   US2  29  
US2  "HO3'"  "HO3'"  H  0  0  N  Y  N  36.680  29.112  8.405   1.235   4.543   0.593  "HO3'"  US2  30  
US2  "H12'"  "H12'"  H  0  0  N  N  N  37.419  30.643  5.485  -0.872   3.282   0.138  "H12'"  US2  31  
US2  "H22'"  "H22'"  H  0  0  N  N  N  35.744  30.868  5.135  -0.809   2.193   1.560  "H22'"  US2  32  
US2  "H15'"  "H15'"  H  0  0  N  N  N  36.806  25.824  6.646   3.664   1.541   0.353  "H15'"  US2  33  
US2  "H25'"  "H25'"  H  0  0  N  N  N  36.475  26.858  8.068   2.699   0.345   1.251  "H25'"  US2  34  
US2  O3P     O3P     O  0  1  N  Y  N  33.342  24.356  8.403   5.988  -0.152  -0.368  O3P     US2  35  
US2  HO2P    HO2P    H  0  0  N  N  N  35.464  25.348  9.066   5.638  -2.832  -1.311  HO2P    US2  36  
US2  HO3P    HO3P    H  0  0  N  Y  N  33.221  23.569  7.885   6.112   0.287  -1.220  HO3P    US2  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
US2  P      O2P     SING  N  N   1  
US2  N1     C6      SING  N  N   2  
US2  N1     "C1'"   SING  N  N   3  
US2  C6     H6      SING  N  N   4  
US2  C2     N1      SING  N  N   5  
US2  O2     C2      DOUB  N  N   6  
US2  N3     C4      SING  N  N   7  
US2  N3     C2      SING  N  N   8  
US2  N3     HN3     SING  N  N   9  
US2  C4     C5      SING  N  N  10  
US2  O4     C4      DOUB  N  N  11  
US2  C5     S5      SING  N  N  12  
US2  C5     C6      DOUB  N  N  13  
US2  S5     C5A     SING  N  N  14  
US2  C5A    H15A    SING  N  N  15  
US2  C5A    H25A    SING  N  N  16  
US2  C5A    H35A    SING  N  N  17  
US2  "C1'"  "O4'"   SING  N  N  18  
US2  "C1'"  "C2'"   SING  N  N  19  
US2  "C1'"  "H1'"   SING  N  N  20  
US2  "O4'"  "C4'"   SING  N  N  21  
US2  "C4'"  "C3'"   SING  N  N  22  
US2  "C4'"  "C5'"   SING  N  N  23  
US2  "C4'"  "H4'"   SING  N  N  24  
US2  "C3'"  "O3'"   SING  N  N  25  
US2  "C3'"  "H3'"   SING  N  N  26  
US2  "O3'"  "HO3'"  SING  N  N  27  
US2  "C2'"  "C3'"   SING  N  N  28  
US2  "C2'"  "H12'"  SING  N  N  29  
US2  "C2'"  "H22'"  SING  N  N  30  
US2  "C5'"  "H15'"  SING  N  N  31  
US2  "C5'"  "H25'"  SING  N  N  32  
US2  "O5'"  "C5'"   SING  N  N  33  
US2  "O5'"  P       SING  N  N  34  
US2  O1P    P       DOUB  N  N  35  
US2  P      O3P     SING  N  N  36  
US2  O2P    HO2P    SING  N  N  37  
US2  O3P    HO3P    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
US2  SMILES            ACDLabs               10.04  "O=C1NC(=O)N(C=C1SC)C2OC(C(O)C2)COP(=O)(O)O"  
US2  SMILES_CANONICAL  CACTVS                3.341  "CSC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O"  
US2  SMILES            CACTVS                3.341  "CSC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O"  
US2  SMILES_CANONICAL  "OpenEye OEToolkits"  1.5.0  "CSC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O"  
US2  SMILES            "OpenEye OEToolkits"  1.5.0  "CSC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)O)O"  
US2  InChI             InChI                 1.03   "InChI=1S/C10H15N2O8PS/c1-22-7-3-12(10(15)11-9(7)14)8-2-5(13)6(20-8)4-19-21(16,17)18/h3,5-6,8,13H,2,4H2,1H3,(H,11,14,15)(H2,16,17,18)/t5-,6+,8+/m0/s1"  
US2  InChIKey          InChI                 1.03   BUQRVGJBJMBTPN-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
US2  "SYSTEMATIC NAME"  ACDLabs               10.04  "2'-deoxy-5-(methylsulfanyl)uridine 5'-(dihydrogen phosphate)"  
US2  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.5.0  "[(2R,3S,5R)-3-hydroxy-5-(5-methylsulfanyl-2,4-dioxo-pyrimidin-1-yl)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
US2  "Create component"   2009-06-10  RCSB  
US2  "Modify descriptor"  2011-06-04  RCSB  
US2  "Modify synonyms"    2021-03-01  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     US2
_pdbx_chem_comp_synonyms.name        "5-SMe-deoxyuridine-5'-phosphate"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
