data_U48
#

_chem_comp.id                                   U48
_chem_comp.name                                 "5-METHYL-2'-DEOXY-N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE"
_chem_comp.type                                 "DNA linking"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C10 H17 N3 O7 P"
_chem_comp.mon_nstd_parent_comp_id              DC
_chem_comp.pdbx_synonyms                        "[(2~{R},3~{S},5~{R})-5-(4-azanyl-5-methyl-2-oxidanylidene-pyrimidin-3-ium-1-yl)-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate"
_chem_comp.pdbx_formal_charge                   1
_chem_comp.pdbx_initial_date                    2021-01-20
_chem_comp.pdbx_modified_date                   2021-11-05
_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                       322.232
_chem_comp.one_letter_code                      C
_chem_comp.three_letter_code                    U48
_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       7BL0
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 PDBE
#   #
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
U48  C2      C1   C  0  1  N  N  N  39.054  32.744  39.371  -2.279   0.146  -0.839  C2      U48   1  
U48  O2      O1   O  0  1  N  N  N  38.761  32.016  38.437  -1.328  -0.090  -1.565  O2      U48   2  
U48  C4      C2   C  0  1  N  N  N  40.570  34.448  40.264  -4.339   1.147  -0.534  C4      U48   3  
U48  C5      C3   C  0  1  N  N  N  39.864  34.534  41.524  -4.373   0.667   0.792  C5      U48   4  
U48  C6      C4   C  0  1  N  N  N  38.717  33.667  41.613  -3.336  -0.074   1.248  C6      U48   5  
U48  OP1     O2   O  0  1  N  N  N  32.317  32.109  44.323   5.278   0.111  -0.449  OP1     U48   6  
U48  P       P1   P  0  1  N  N  N  32.814  33.439  43.834   4.246   1.020   0.097  P       U48   7  
U48  OP2     O3   O  0  1  N  N  N  32.268  34.597  44.612   3.817   2.085  -1.033  OP2     U48   8  
U48  "O5'"   O4   O  0  1  N  N  N  34.453  33.466  43.747   2.957   0.164   0.543  "O5'"   U48   9  
U48  "C5'"   C5   C  0  1  N  N  N  35.188  32.232  43.611   2.267  -0.721  -0.341  "C5'"   U48  10  
U48  "C4'"   C6   C  0  1  N  N  R  35.207  31.760  42.135   1.097  -1.372   0.400  "C4'"   U48  11  
U48  "O4'"   O5   O  0  1  N  N  N  36.053  32.677  41.391   0.076  -0.394   0.696  "O4'"   U48  12  
U48  "C3'"   C7   C  0  1  N  N  S  35.866  30.367  41.966   0.371  -2.392  -0.514  "C3'"   U48  13  
U48  "O3'"   O6   O  0  1  N  N  N  35.192  29.613  40.956   0.999  -3.674  -0.446  "O3'"   U48  14  
U48  "C2'"   C8   C  0  1  N  N  N  37.291  30.687  41.500  -1.045  -2.436   0.110  "C2'"   U48  15  
U48  "C1'"   C9   C  0  1  N  N  R  37.102  31.979  40.696  -1.148  -1.117   0.907  "C1'"   U48  16  
U48  N1      N1   N  0  1  N  N  N  38.313  32.817  40.552  -2.283  -0.327   0.421  N1      U48  17  
U48  C5M     C10  C  0  1  N  N  N  40.279  35.462  42.651  -5.546   0.974   1.686  C5M     U48  18  
U48  N4      N2   N  0  1  N  N  N  41.650  35.224  39.978  -5.379   1.902  -1.023  N4      U48  19  
U48  N3      N3   N  1  1  N  N  N  40.159  33.573  39.280  -3.295   0.871  -1.304  N3      U48  20  
U48  O1      O7   O  0  1  N  Y  N  32.483  33.616  42.242   4.839   1.801   1.373  O1      U48  21  
U48  H6      H2   H  0  1  N  N  N  38.140  33.664  42.526  -3.339  -0.453   2.260  H1      U48  22  
U48  H2      H3   H  0  1  N  N  N  31.690  34.276  45.294   3.142   2.714  -0.744  H2      U48  23  
U48  "H5'"   H4   H  0  1  N  N  N  34.711  31.458  44.230   1.889  -0.160  -1.195  "H5'"   U48  24  
U48  "H5''"  H5   H  0  0  N  N  N  36.222  32.389  43.952   2.952  -1.495  -0.688  "H5''"  U48  25  
U48  "H4'"   H6   H  0  1  N  N  N  34.183  31.743  41.733   1.443  -1.854   1.314  "H4'"   U48  26  
U48  "H3'"   H7   H  0  1  N  N  N  35.887  29.838  42.930   0.333  -2.034  -1.543  "H3'"   U48  27  
U48  H3T     H8   H  0  1  N  N  N  34.309  29.415  41.245   0.581  -4.346  -1.001  H3T     U48  28  
U48  "H2'"   H9   H  0  1  N  N  N  37.691  29.881  40.867  -1.805  -2.472  -0.671  "H2'"   U48  29  
U48  "H2''"  H10  H  0  0  N  N  N  37.962  30.848  42.357  -1.143  -3.293   0.775  "H2''"  U48  30  
U48  "H1'"   H11  H  0  1  N  N  N  36.747  31.703  39.692  -1.273  -1.335   1.967  "H1'"   U48  31  
U48  H53     H12  H  0  1  N  N  N  39.587  35.343  43.498  -6.272   1.577   1.140  H53     U48  32  
U48  H51     H13  H  0  1  N  N  N  41.300  35.212  42.974  -6.015   0.042   2.004  H51     U48  33  
U48  H52     H14  H  0  1  N  N  N  40.250  36.503  42.298  -5.202   1.524   2.562  H52     U48  34  
U48  H41     H15  H  0  1  N  N  N  41.983  35.884  40.651  -6.139   2.106  -0.456  H41     U48  35  
U48  H42     H16  H  0  1  N  N  N  42.111  35.134  39.095  -5.352   2.231  -1.935  H42     U48  36  
U48  H3      H17  H  0  1  N  N  N  40.699  33.535  38.439  -3.270   1.201  -2.216  H3      U48  37  
U48  H4      H18  H  0  1  N  N  N  32.036  32.841  41.923   5.619   2.339   1.177  H4      U48  38  
#   #
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
U48  O2     C2      DOUB  N  N   1  
U48  N3     C2      SING  N  N   2  
U48  N3     C4      DOUB  N  N   3  
U48  C2     N1      SING  N  N   4  
U48  N4     C4      SING  N  N   5  
U48  C4     C5      SING  N  N   6  
U48  N1     "C1'"   SING  N  N   7  
U48  N1     C6      SING  N  N   8  
U48  "C1'"  "O4'"   SING  N  N   9  
U48  "C1'"  "C2'"   SING  N  N  10  
U48  "O3'"  "C3'"   SING  N  N  11  
U48  "O4'"  "C4'"   SING  N  N  12  
U48  "C2'"  "C3'"   SING  N  N  13  
U48  C5     C6      DOUB  N  N  14  
U48  C5     C5M     SING  N  N  15  
U48  "C3'"  "C4'"   SING  N  N  16  
U48  "C4'"  "C5'"   SING  N  N  17  
U48  "C5'"  "O5'"   SING  N  N  18  
U48  "O5'"  P       SING  N  N  19  
U48  P      OP1     DOUB  N  N  20  
U48  P      OP2     SING  N  N  21  
U48  P      O1      SING  N  N  22  
U48  C6     H6      SING  N  N  23  
U48  OP2    H2      SING  N  N  24  
U48  "C5'"  "H5'"   SING  N  N  25  
U48  "C5'"  "H5''"  SING  N  N  26  
U48  "C4'"  "H4'"   SING  N  N  27  
U48  "C3'"  "H3'"   SING  N  N  28  
U48  "O3'"  H3T     SING  N  N  29  
U48  "C2'"  "H2'"   SING  N  N  30  
U48  "C2'"  "H2''"  SING  N  N  31  
U48  "C1'"  "H1'"   SING  N  N  32  
U48  C5M    H53     SING  N  N  33  
U48  C5M    H51     SING  N  N  34  
U48  C5M    H52     SING  N  N  35  
U48  N4     H41     SING  N  N  36  
U48  N4     H42     SING  N  N  37  
U48  N3     H3      SING  N  N  38  
U48  O1     H4      SING  N  N  39  
#   #
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
U48  InChI             InChI                 1.03   "InChI=1S/C10H16N3O7P/c1-5-3-13(10(15)12-9(5)11)8-2-6(14)7(20-8)4-19-21(16,17)18/h3,6-8,14H,2,4H2,1H3,(H2,11,12,15)(H2,16,17,18)/p+1/t6-,7+,8+/m0/s1"  
U48  InChIKey          InChI                 1.03   RGDVNLHBCKWZDA-XLPZGREQSA-O  
U48  SMILES_CANONICAL  CACTVS                3.385  "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)[NH+]=C1N"  
U48  SMILES            CACTVS                3.385  "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)[NH+]=C1N"  
U48  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "CC1=CN(C(=O)[NH+]=C1N)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O"  
U48  SMILES            "OpenEye OEToolkits"  2.0.7  "CC1=CN(C(=O)[NH+]=C1N)C2CC(C(O2)COP(=O)(O)O)O"  
#
_pdbx_chem_comp_identifier.comp_id          U48
_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-(4-azanyl-5-methyl-2-oxidanylidene-pyrimidin-3-ium-1-yl)-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate"
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     U48
_pdbx_chem_comp_synonyms.name        "[(2~{R},3~{S},5~{R})-5-(4-azanyl-5-methyl-2-oxidanylidene-pyrimidin-3-ium-1-yl)-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate"
_pdbx_chem_comp_synonyms.provenance  PDB
_pdbx_chem_comp_synonyms.type        ?
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
U48  "Create component"  2021-01-20  PDBE  
U48  "Modify atom id"    2021-01-21  PDBE  
U48  "Modify synonyms"   2021-03-13  RCSB  
U48  "Initial release"   2021-11-10  RCSB  
##
