data_Y5P
#

_chem_comp.id                                   Y5P
_chem_comp.name                                 "1-(5-O-phosphono-beta-D-ribofuranosyl)-1,4-dihydropyrimidine"
_chem_comp.type                                 "RNA LINKING"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C9 H15 N2 O7 P"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "PYRIMIDINE RIBOSIDE-5'-MONOPHOSPHATE"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2014-09-25
_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                       294.198
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    Y5P
_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       4V19
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 EBI
#   #
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
Y5P  OP3    OP3    O  0  1  N  Y  N  177.216  306.533  289.827  -3.556   1.650   1.238  OP3    Y5P   1  
Y5P  P      P      P  0  1  N  N  N  177.984  307.502  288.789  -3.811   0.681  -0.023  P      Y5P   2  
Y5P  "C5'"  "C5'"  C  0  1  N  N  N  180.527  306.953  288.331  -1.655  -0.860   0.320  "C5'"  Y5P   3  
Y5P  "O5'"  "O5'"  O  0  1  N  N  N  179.517  307.390  289.231  -2.413   0.036  -0.495  "O5'"  Y5P   4  
Y5P  "C4'"  "C4'"  C  0  1  N  N  R  181.189  305.683  288.811  -0.389  -1.282  -0.428  "C4'"  Y5P   5  
Y5P  "O4'"  "O4'"  O  0  1  N  N  N  180.162  304.710  289.162   0.480  -0.148  -0.595  "O4'"  Y5P   6  
Y5P  "C3'"  "C3'"  C  0  1  N  N  S  182.059  304.973  287.777   0.382  -2.331   0.397  "C3'"  Y5P   7  
Y5P  "O3'"  "O3'"  O  0  1  N  N  N  183.392  305.462  287.739   0.506  -3.551  -0.337  "O3'"  Y5P   8  
Y5P  "C2'"  "C2'"  C  0  1  N  N  R  181.940  303.505  288.172   1.773  -1.690   0.622  "C2'"  Y5P   9  
Y5P  "O2'"  "O2'"  O  0  1  N  N  N  182.790  303.190  289.268   2.812  -2.661   0.477  "O2'"  Y5P  10  
Y5P  "C1'"  "C1'"  C  0  1  N  N  R  180.491  303.442  288.643   1.835  -0.640  -0.517  "C1'"  Y5P  11  
Y5P  N1     N1     N  0  1  N  N  N  179.553  303.167  287.527   2.758   0.443  -0.170  N1     Y5P  12  
Y5P  C2     C2     C  0  1  N  N  N  179.678  302.017  286.765   2.532   1.215   0.939  C2     Y5P  13  
Y5P  N3     N3     N  0  1  N  N  N  178.739  301.902  285.769   3.108   2.355   1.086  N3     Y5P  14  
Y5P  C4     C4     C  0  1  N  N  N  177.711  302.767  285.449   4.024   2.909   0.096  C4     Y5P  15  
Y5P  C6     C6     C  0  1  N  N  N  178.547  304.065  287.251   3.875   0.694  -0.962  C6     Y5P  16  
Y5P  OP1    OP1    O  0  1  N  N  N  177.575  308.901  289.077  -4.746  -0.398   0.366  OP1    Y5P  17  
Y5P  OP2    OP2    O  0  1  N  N  N  177.794  306.975  287.410  -4.446   1.531  -1.234  OP2    Y5P  18  
Y5P  C5     C5     C  0  1  N  N  N  177.643  303.926  286.279   4.497   1.853  -0.862  C5     Y5P  19  
Y5P  HP3    HP3    H  0  1  N  N  N  176.667  307.054  290.401  -2.951   2.382   1.055  HP3    Y5P  20  
Y5P  HP2    HP2    H  0  1  N  N  N  177.411  307.650  286.862  -5.291   1.950  -1.020  HP2    Y5P  21  
Y5P  HA1    HA1    H  0  1  N  N  N  180.072  306.768  287.347  -1.380  -0.362   1.250  HA1    Y5P  22  
Y5P  HB2    HB2    H  0  1  N  N  N  181.289  307.741  288.241  -2.255  -1.742   0.544  HB2    Y5P  23  
Y5P  HA     HA     H  0  1  N  N  N  181.803  305.911  289.695  -0.653  -1.694  -1.402  HA     Y5P  24  
Y5P  HB     HB     H  0  1  N  N  N  181.591  305.101  286.790  -0.117  -2.509   1.350  HB     Y5P  25  
Y5P  HC     HC     H  0  1  N  N  N  180.393  302.664  289.414   2.128  -1.110  -1.456  HC     Y5P  26  
Y5P  "H2'"  "H2'"  H  0  1  N  N  N  182.104  302.847  287.305   1.827  -1.209   1.598  "H2'"  Y5P  27  
Y5P  HD     HD     H  0  1  N  N  N  182.694  302.271  289.490   2.761  -3.388   1.112  HD     Y5P  28  
Y5P  H2     H2     H  0  1  N  N  N  180.445  301.277  286.938   1.857   0.859   1.704  H2     Y5P  29  
Y5P  H6     H6     H  0  1  N  N  N  178.484  304.949  287.868   4.227  -0.054  -1.657  H6     Y5P  30  
Y5P  H4     H4     H  0  1  N  N  N  177.848  303.095  284.408   3.513   3.694  -0.462  H4     Y5P  31  
Y5P  H5     H5     H  0  1  N  N  N  176.878  304.673  286.124   5.364   2.044  -1.476  H5     Y5P  32  
Y5P  H4A    H4A    H  0  1  N  N  N  176.760  302.221  285.539   4.885   3.338   0.607  H4A    Y5P  33  
Y5P  "H3'"  "H3'"  H  0  1  N  N  N  183.886  304.987  287.081   0.983  -4.247   0.135  "H3'"  Y5P  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
Y5P  OP3    P      SING  N  N   1  
Y5P  P      "O5'"  SING  N  N   2  
Y5P  P      OP1    DOUB  N  N   3  
Y5P  P      OP2    SING  N  N   4  
Y5P  "C5'"  "O5'"  SING  N  N   5  
Y5P  "C5'"  "C4'"  SING  N  N   6  
Y5P  "C4'"  "O4'"  SING  N  N   7  
Y5P  "C4'"  "C3'"  SING  N  N   8  
Y5P  "O4'"  "C1'"  SING  N  N   9  
Y5P  "C3'"  "O3'"  SING  N  N  10  
Y5P  "C3'"  "C2'"  SING  N  N  11  
Y5P  "C2'"  "O2'"  SING  N  N  12  
Y5P  "C2'"  "C1'"  SING  N  N  13  
Y5P  "C1'"  N1     SING  N  N  14  
Y5P  N1     C2     SING  N  N  15  
Y5P  N1     C6     SING  N  N  16  
Y5P  C5     C6     DOUB  N  N  17  
Y5P  C2     N3     DOUB  N  N  18  
Y5P  N3     C4     SING  N  N  19  
Y5P  C4     C5     SING  N  N  20  
Y5P  OP3    HP3    SING  N  N  21  
Y5P  OP2    HP2    SING  N  N  22  
Y5P  "C5'"  HA1    SING  N  N  23  
Y5P  "C5'"  HB2    SING  N  N  24  
Y5P  "C4'"  HA     SING  N  N  25  
Y5P  "C3'"  HB     SING  N  N  26  
Y5P  "C1'"  HC     SING  N  N  27  
Y5P  "C2'"  "H2'"  SING  N  N  28  
Y5P  "O2'"  HD     SING  N  N  29  
Y5P  C2     H2     SING  N  N  30  
Y5P  C6     H6     SING  N  N  31  
Y5P  C4     H4     SING  N  N  32  
Y5P  "O3'"  "H3'"  SING  N  N  33  
Y5P  H5     C5     SING  N  N  34  
Y5P  C4     H4A    SING  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
Y5P  SMILES            ACDLabs               12.01  "O=P(O)(O)OCC2OC(N1C=NCC=C1)C(O)C2O"  
Y5P  InChI             InChI                 1.03   "InChI=1S/C9H15N2O7P/c12-7-6(4-17-19(14,15)16)18-9(8(7)13)11-3-1-2-10-5-11/h1,3,5-9,12-13H,2,4H2,(H2,14,15,16)/t6-,7-,8-,9-/m1/s1"  
Y5P  InChIKey          InChI                 1.03   ZGXCQKJYIKURPN-FNCVBFRFSA-N  
Y5P  SMILES_CANONICAL  CACTVS                3.385  "O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CCN=C2"  
Y5P  SMILES            CACTVS                3.385  "O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(O)=O)N2C=CCN=C2"  
Y5P  SMILES_CANONICAL  "OpenEye OEToolkits"  1.7.6  "C1C=CN(C=N1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O"  
Y5P  SMILES            "OpenEye OEToolkits"  1.7.6  "C1C=CN(C=N1)C2C(C(C(O2)COP(=O)(O)O)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
Y5P  "SYSTEMATIC NAME"  ACDLabs               12.01  "1-(5-O-phosphono-beta-D-ribofuranosyl)-1,4-dihydropyrimidine"  
Y5P  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.7.6  "[(2R,3S,4R,5R)-3,4-bis(oxidanyl)-5-(4H-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
Y5P  "Create component"  2014-09-25  EBI   
Y5P  "Initial release"   2014-10-08  RCSB  
Y5P  "Modify synonyms"   2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     Y5P
_pdbx_chem_comp_synonyms.name        "PYRIMIDINE RIBOSIDE-5'-MONOPHOSPHATE"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
