data_US5
#

_chem_comp.id                                   US5
_chem_comp.name                                 "1-(5-O-phosphono-beta-D-ribofuranosyl)-4-selanylpyrimidin-2(1H)-one"
_chem_comp.type                                 "RNA LINKING"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C9 H13 N2 O8 P Se"
_chem_comp.mon_nstd_parent_comp_id              U
_chem_comp.pdbx_synonyms                        "4-Se-ribouridine-5'-phosphate"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2009-07-17
_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                       387.142
_chem_comp.one_letter_code                      U
_chem_comp.three_letter_code                    US5
_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       3HGA
_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
US5  P       P     P   0  1  N  N  N  -11.885   5.934   9.253  -4.758   1.707  -0.059  P     US5   1  
US5  N1      N1    N   0  1  N  N  N   -8.790   2.586  11.674   1.251  -0.949  -0.501  N1    US5   2  
US5  C2      C2    C   0  1  N  N  N   -8.422   1.415  12.315   1.401  -0.021   0.463  C2    US5   3  
US5  O2      O2    O   0  1  N  N  N   -7.264   1.126  12.556   0.464   0.238   1.199  O2    US5   4  
US5  N3      N3    N   0  1  N  N  N   -9.468   0.592  12.678   2.561   0.620   0.624  N3    US5   5  
US5  C4      C4    C   0  1  N  N  N  -10.824   0.810  12.461   3.590   0.360  -0.157  C4    US5   6  
US5  SE4     SE4   SE  0  0  N  N  N  -11.651  -0.019  12.845   5.284   1.313   0.100  SE4   US5   7  
US5  C5      C5    C   0  1  N  N  N  -11.131   2.048  11.776   3.471  -0.597  -1.169  C5    US5   8  
US5  C6      C6    C   0  1  N  N  N  -10.126   2.864  11.420   2.287  -1.247  -1.328  C6    US5   9  
US5  "C1'"   C1*   C   0  1  N  N  R   -7.700   3.538  11.233  -0.030  -1.643  -0.654  C1*   US5  10  
US5  OP3     OP3   O   0  1  N  Y  N  -11.969   6.839   8.088  -4.048   2.652   1.035  OP3   US5  11  
US5  "C2'"   C2*   C   0  1  N  N  R   -7.035   3.086   9.935  -0.358  -2.470   0.615  C2*   US5  12  
US5  "O2'"   O2*   O   0  1  N  N  N   -5.686   3.509   9.871   0.241  -3.766   0.548  O2*   US5  13  
US5  O2P     O2P   O   0  1  N  N  N  -12.891   4.864   9.419  -5.170   2.589  -1.342  O2P   US5  14  
US5  "C3'"   C3*   C   0  1  N  N  S   -7.927   3.781   8.915  -1.901  -2.570   0.548  C3*   US5  15  
US5  "O3'"   O3*   O   0  1  N  N  N   -7.334   3.860   7.628  -2.297  -3.818  -0.023  O3*   US5  16  
US5  "C4'"   C4*   C   0  1  N  N  R   -8.066   5.148   9.564  -2.315  -1.402  -0.368  C4*   US5  17  
US5  "O4'"   O4*   O   0  1  N  N  N   -8.211   4.835  10.976  -1.116  -0.695  -0.732  O4*   US5  18  
US5  "C5'"   C5*   C   0  1  N  N  N   -9.252   5.968   9.096  -3.266  -0.466   0.380  C5*   US5  19  
US5  "O5'"   O5*   O   0  1  N  N  N  -10.455   5.226   9.267  -3.736   0.548  -0.511  O5*   US5  20  
US5  H5      H5    H   0  1  N  N  N  -12.155   2.312  11.554   4.308  -0.817  -1.815  H5    US5  21  
US5  H6      H6    H   0  1  N  N  N  -10.370   3.784  10.910   2.171  -1.991  -2.102  H6    US5  22  
US5  "H1'"   H1*   H   0  1  N  N  N   -6.977   3.550  12.062  -0.015  -2.283  -1.536  H1*   US5  23  
US5  HOP3    HOP3  H   0  0  N  Y  N  -12.026   6.325   7.291  -3.245   3.087   0.717  HOP3  US5  24  
US5  "H2'"   H2*   H   0  1  N  N  N   -6.965   1.997   9.795  -0.041  -1.944   1.515  H2*   US5  25  
US5  "HO2'"  HO2*  H   0  0  N  N  N   -5.300   3.214   9.055   0.064  -4.321   1.320  HO2*  US5  26  
US5  HO2P    HO2P  H   0  0  N  N  N  -12.467   4.017   9.349  -5.785   3.308  -1.144  HO2P  US5  27  
US5  "H3'"   H3*   H   0  1  N  N  N   -8.876   3.262   8.717  -2.335  -2.448   1.541  H3*   US5  28  
US5  "HO3'"  HO3*  H   0  0  N  N  N   -7.928   4.300   7.032  -2.011  -4.591   0.483  HO3*  US5  29  
US5  "H4'"   H4*   H   0  1  N  N  N   -7.201   5.776   9.306  -2.801  -1.788  -1.264  H4*   US5  30  
US5  "H5'"   H5*   H   0  1  N  N  N   -9.309   6.894   9.687  -4.114  -1.036   0.761  H5*   US5  31  
US5  "H5'A"  H5*A  H   0  0  N  N  N   -9.126   6.215   8.032  -2.738  -0.001   1.213  H5*A  US5  32  
US5  HSE4    HSE4  H   0  0  N  N  N  -10.962  -1.131  13.493   4.925   2.238   1.304  HSE4  US5  33  
US5  OP1     OP1   O   0  1  N  N  N  -11.885   4.464   9.253  -5.970   1.096   0.529  OP1   US5  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
US5  P      "O5'"   SING  N  N   1  
US5  P      O2P     SING  N  N   2  
US5  N1     C2      SING  N  N   3  
US5  C2     O2      DOUB  N  N   4  
US5  C2     N3      SING  N  N   5  
US5  C4     N3      DOUB  N  N   6  
US5  C4     SE4     SING  N  N   7  
US5  SE4    HSE4    SING  N  N   8  
US5  C5     C4      SING  N  N   9  
US5  C5     H5      SING  N  N  10  
US5  C6     N1      SING  N  N  11  
US5  C6     C5      DOUB  N  N  12  
US5  C6     H6      SING  N  N  13  
US5  "C1'"  N1      SING  N  N  14  
US5  "C1'"  "H1'"   SING  N  N  15  
US5  OP3    P       SING  N  N  16  
US5  OP3    HOP3    SING  N  N  17  
US5  "C2'"  "C1'"   SING  N  N  18  
US5  "C2'"  "H2'"   SING  N  N  19  
US5  "O2'"  "C2'"   SING  N  N  20  
US5  "O2'"  "HO2'"  SING  N  N  21  
US5  O2P    HO2P    SING  N  N  22  
US5  "C3'"  "C2'"   SING  N  N  23  
US5  "C3'"  "C4'"   SING  N  N  24  
US5  "C3'"  "H3'"   SING  N  N  25  
US5  "O3'"  "C3'"   SING  N  N  26  
US5  "O3'"  "HO3'"  SING  N  N  27  
US5  "C4'"  "O4'"   SING  N  N  28  
US5  "C4'"  "H4'"   SING  N  N  29  
US5  "O4'"  "C1'"   SING  N  N  30  
US5  "C5'"  "C4'"   SING  N  N  31  
US5  "C5'"  "O5'"   SING  N  N  32  
US5  "C5'"  "H5'"   SING  N  N  33  
US5  "C5'"  "H5'A"  SING  N  N  34  
US5  P      OP1     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
US5  SMILES            ACDLabs               11.02  "O=P(O)(O)OCC2OC(N1C(=O)N=C([SeH])C=C1)C(O)C2O"  
US5  SMILES_CANONICAL  CACTVS                3.352  "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CC(=NC2=O)[SeH]"  
US5  SMILES            CACTVS                3.352  "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C=CC(=NC2=O)[SeH]"  
US5  SMILES_CANONICAL  "OpenEye OEToolkits"  1.7.0  "C1=CN(C(=O)N=C1[SeH])[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O"  
US5  SMILES            "OpenEye OEToolkits"  1.7.0  "C1=CN(C(=O)N=C1[SeH])C2C(C(C(O2)COP(=O)(O)O)O)O"  
US5  InChI             InChI                 1.03   "InChI=1S/C9H13N2O8PSe/c12-6-4(3-18-20(15,16)17)19-8(7(6)13)11-2-1-5(21)10-9(11)14/h1-2,4,6-8,12-13H,3H2,(H,10,14,21)(H2,15,16,17)/t4-,6-,7-,8-/m1/s1"  
US5  InChIKey          InChI                 1.03   ZCQCFKOZDRTETH-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
US5  "SYSTEMATIC NAME"  ACDLabs               11.02  "1-(5-O-phosphono-beta-D-ribofuranosyl)-4-selanylpyrimidin-2(1H)-one"  
US5  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.6.1  "[(2R,3S,4R,5R)-3,4-dihydroxy-5-(2-oxo-4-selanyl-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
US5  "Create component"   2009-07-17  RCSB  
US5  "Modify descriptor"  2011-06-04  RCSB  
US5  "Modify synonyms"    2021-03-01  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     US5
_pdbx_chem_comp_synonyms.name        "4-Se-ribouridine-5'-phosphate"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
