data_8YN
#

_chem_comp.id                                   8YN
_chem_comp.name                                 Pseudoisocytidine
_chem_comp.type                                 "DNA linking"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C9 H14 N3 O7 P"
_chem_comp.mon_nstd_parent_comp_id              DC
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2017-03-27
_chem_comp.pdbx_modified_date                   2019-05-07
_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                       307.197
_chem_comp.one_letter_code                      C
_chem_comp.three_letter_code                    8YN
_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       5NIP
_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
8YN  P       P1   P  0  1  N  N  N  26.249  26.755  11.852  -3.932   1.021  -0.110  P       8YN   1  
8YN  C1      C1   C  0  1  N  N  N  20.568  24.914  11.401   2.516  -0.359  -0.375  C1      8YN   2  
8YN  C2      C2   C  0  1  N  N  N  19.967  23.661  11.714   2.484   0.606   0.646  C2      8YN   3  
8YN  C4      C3   C  0  1  N  N  N  18.991  24.540  13.674   4.585   1.353  -0.078  C4      8YN   4  
8YN  C6      C4   C  0  1  N  N  N  20.338  25.986  12.308   3.602  -0.410  -1.201  C6      8YN   5  
8YN  O1P     O1   O  0  1  N  N  N  27.687  26.416  11.788  -4.469   1.803  -1.411  O1P     8YN   6  
8YN  O2P     O2   O  0  1  N  N  N  25.834  28.155  12.065  -5.019   0.184   0.446  O2P     8YN   7  
8YN  "O5'"   O3   O  0  1  N  N  N  25.620  26.227  10.460  -2.690   0.084  -0.522  "O5'"   8YN   8  
8YN  "C5'"   C5   C  0  1  N  N  N  24.494  26.866   9.861  -2.058  -0.817   0.390  "C5'"   8YN   9  
8YN  "C4'"   C6   C  0  1  N  N  R  23.448  25.851   9.387  -0.919  -1.549  -0.322  "C4'"   8YN  10  
8YN  "O4'"   O4   O  0  1  N  N  N  22.776  25.296  10.517   0.121  -0.618  -0.665  "O4'"   8YN  11  
8YN  "C1'"   C7   C  0  1  N  N  R  21.425  25.101  10.159   1.374  -1.327  -0.552  "C1'"   8YN  12  
8YN  O2      O5   O  0  1  N  N  N  20.135  22.719  10.939   1.529   0.679   1.403  O2      8YN  13  
8YN  N3      N1   N  0  1  N  N  N  19.233  23.487  12.855   3.529   1.450   0.775  N3      8YN  14  
8YN  N4      N2   N  0  1  N  N  N  18.179  24.330  14.668   5.641   2.213   0.059  N4      8YN  15  
8YN  N5      N3   N  0  1  N  N  N  19.521  25.780  13.423   4.608   0.445  -1.033  N5      8YN  16  
8YN  "C2'"   C8   C  0  1  N  N  N  21.142  26.391   9.390   1.188  -2.190   0.722  "C2'"   8YN  17  
8YN  "C3'"   C9   C  0  1  N  N  S  22.366  26.472   8.490  -0.302  -2.600   0.621  "C3'"   8YN  18  
8YN  "O3'"   O6   O  0  1  N  N  N  22.215  25.665   7.331  -0.423  -3.908   0.060  "O3'"   8YN  19  
8YN  H6      H1   H  0  1  N  N  N  20.791  26.951  12.136   3.644  -1.144  -1.991  H6      8YN  20  
8YN  H1      H2   H  0  1  N  N  N  28.204  27.205  11.901  -5.219   2.388  -1.237  H1      8YN  21  
8YN  "H52'"  H4   H  0  0  N  N  N  24.837  27.454   8.997  -1.658  -0.257   1.235  "H52'"  8YN  22  
8YN  "H51'"  H5   H  0  0  N  N  N  24.030  27.536  10.600  -2.789  -1.542   0.749  "H51'"  8YN  23  
8YN  "H4'"   H6   H  0  1  N  N  N  23.959  25.057   8.823  -1.296  -2.033  -1.223  "H4'"   8YN  24  
8YN  "H1'"   H7   H  0  1  N  N  N  21.307  24.236   9.490   1.539  -1.958  -1.426  "H1'"   8YN  25  
8YN  H3      H8   H  0  1  N  N  N  18.875  22.582  13.085   3.528   2.124   1.473  H3      8YN  26  
8YN  H41     H9   H  0  1  N  N  N  17.925  25.084  15.274   5.633   2.884   0.759  H41     8YN  27  
8YN  H42     H10  H  0  1  N  N  N  17.808  23.415  14.826   6.398   2.151  -0.545  H42     8YN  28  
8YN  "H22'"  H11  H  0  0  N  N  N  21.080  27.257  10.065   1.835  -3.066   0.696  "H22'"  8YN  29  
8YN  "H21'"  H12  H  0  0  N  N  N  20.214  26.316   8.803   1.370  -1.601   1.621  "H21'"  8YN  30  
8YN  "H3'"   H13  H  0  1  N  N  N  22.610  27.517   8.249  -0.776  -2.559   1.601  "H3'"   8YN  31  
8YN  H4      H14  H  0  1  N  N  N  21.548  26.040   6.768  -0.051  -4.609   0.612  H4      8YN  32  
8YN  O3P     O3P  O  0  1  N  Y  N  25.580  25.829  12.976  -3.456   2.088   0.998  O3P     8YN  33  
8YN  H2      H15  H  0  1  N  Y  N  25.050  26.365  13.555  -2.744   2.671   0.702  H2      8YN  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
8YN  "O3'"  "C3'"   SING  N  N   1  
8YN  "C3'"  "C4'"   SING  N  N   2  
8YN  "C3'"  "C2'"   SING  N  N   3  
8YN  "C4'"  "C5'"   SING  N  N   4  
8YN  "C4'"  "O4'"   SING  N  N   5  
8YN  "C2'"  "C1'"   SING  N  N   6  
8YN  "C5'"  "O5'"   SING  N  N   7  
8YN  "C1'"  "O4'"   SING  N  N   8  
8YN  "C1'"  C1      SING  N  N   9  
8YN  "O5'"  P       SING  N  N  10  
8YN  O2     C2      DOUB  N  N  11  
8YN  C1     C2      SING  N  N  12  
8YN  C1     C6      DOUB  N  N  13  
8YN  C2     N3      SING  N  N  14  
8YN  O1P    P       SING  N  N  15  
8YN  P      O2P     DOUB  N  N  16  
8YN  C6     N5      SING  N  N  17  
8YN  N3     C4      SING  N  N  18  
8YN  N5     C4      DOUB  N  N  19  
8YN  C4     N4      SING  N  N  20  
8YN  C6     H6      SING  N  N  21  
8YN  O1P    H1      SING  N  N  22  
8YN  "C5'"  "H52'"  SING  N  N  23  
8YN  "C5'"  "H51'"  SING  N  N  24  
8YN  "C4'"  "H4'"   SING  N  N  25  
8YN  "C1'"  "H1'"   SING  N  N  26  
8YN  N3     H3      SING  N  N  27  
8YN  N4     H41     SING  N  N  28  
8YN  N4     H42     SING  N  N  29  
8YN  "C2'"  "H22'"  SING  N  N  30  
8YN  "C2'"  "H21'"  SING  N  N  31  
8YN  "C3'"  "H3'"   SING  N  N  32  
8YN  "O3'"  H4      SING  N  N  33  
8YN  P      O3P     SING  N  N  34  
8YN  O3P    H2      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
8YN  InChI             InChI                 1.03   "InChI=1S/C9H14N3O7P/c10-9-11-2-4(8(14)12-9)6-1-5(13)7(19-6)3-18-20(15,16)17/h2,5-7,13H,1,3H2,(H2,15,16,17)(H3,10,11,12,14)/t5-,6+,7+/m0/s1"  
8YN  InChIKey          InChI                 1.03   LMPCXRMBUOVHQD-RRKCRQDMSA-N  
8YN  SMILES_CANONICAL  CACTVS                3.385  "NC1=NC=C([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)N1"  
8YN  SMILES            CACTVS                3.385  "NC1=NC=C([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)N1"  
8YN  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "C1[C@@H]([C@H](O[C@H]1C2=CN=C(NC2=O)N)COP(=O)(O)O)O"  
8YN  SMILES            "OpenEye OEToolkits"  2.0.7  "C1C(C(OC1C2=CN=C(NC2=O)N)COP(=O)(O)O)O"  
#
_pdbx_chem_comp_identifier.comp_id          8YN
_pdbx_chem_comp_identifier.type             "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program          "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version  2.0.7
_pdbx_chem_comp_identifier.identifier       "[(2~{R},3~{S},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-pyrimidin-5-yl)-3-oxidanyl-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
8YN  "Create component"    2017-03-27  EBI   
8YN  "Initial release"     2017-06-28  RCSB  
8YN  "Other modification"  2019-05-07  EBI   
##
