data_523
#

_chem_comp.id                                   523
_chem_comp.name                                 "2'-DEOXY-5-METHYLCYTIDINE 5'-(TETRAHYDROGEN TRIPHOSPHATE)"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C10 H19 N3 O13 P3"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "5-METHYL-2'-DEOXY-CYTIDINE-5'-TRIPHOSPHATE"
_chem_comp.pdbx_formal_charge                   1
_chem_comp.pdbx_initial_date                    2007-01-22
_chem_comp.pdbx_modified_date                   2021-03-01
_chem_comp.pdbx_ambiguous_flag                  ?
_chem_comp.pdbx_release_status                  REL
_chem_comp.pdbx_replaced_by                     ?
_chem_comp.pdbx_replaces                        ?
_chem_comp.formula_weight                       482.191
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    523
_chem_comp.pdbx_model_coordinates_details       ?
_chem_comp.pdbx_model_coordinates_missing_flag  N
_chem_comp.pdbx_ideal_coordinates_details       "OpenEye/OEToolkits V1.4.2"
_chem_comp.pdbx_ideal_coordinates_missing_flag  N
_chem_comp.pdbx_model_coordinates_db_code       ?
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 PDBJ
#   #
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
523  N1      N1    N  1  1  Y  N  N  58.736  126.724  57.584   0.359  -3.142  -1.011  N1      523   1  
523  C2      C2    C  0  1  Y  N  N  57.897  125.955  58.405  -0.661  -3.970  -0.129  C2      523   2  
523  N3      N3    N  0  1  Y  N  N  57.901  124.621  58.318  -0.352  -5.286   0.121  N3      523   3  
523  C4      C4    C  0  1  Y  N  N  58.661  123.967  57.439   0.787  -5.920  -0.349  C4      523   4  
523  C5      C5    C  0  1  Y  N  N  59.523  124.687  56.568   1.668  -5.221  -1.105  C5      523   5  
523  C5A     C5A   C  0  1  N  N  N  60.366  123.973  55.584   2.947  -5.736  -1.697  C5A     523   6  
523  C6      C6    C  0  1  Y  N  N  59.544  126.055  56.646   1.394  -3.790  -1.414  C6      523   7  
523  O2      O2    O  0  1  N  N  N  57.166  126.462  59.235  -1.648  -3.363   0.260  O2      523   8  
523  N4      N4    N  0  1  N  N  N  58.620  122.598  57.386   0.961  -7.239  -0.017  N4      523   9  
523  "C1'"   C1*   C  0  1  N  N  R  58.792  128.238  57.641   0.046  -1.732  -1.290  "C1'"   523  10  
523  "C2'"   C2*   C  0  1  N  N  N  58.475  128.759  59.051   0.643  -0.870  -0.188  "C2'"   523  11  
523  "C3'"   C3*   C  0  1  N  N  S  59.770  129.466  59.524   1.945  -0.412  -0.806  "C3'"   523  12  
523  "C4'"   C4*   C  0  1  N  N  R  60.530  129.787  58.174   1.533  -0.203  -2.253  "C4'"   523  13  
523  "O4'"   O4*   O  0  1  N  N  N  60.121  128.665  57.323   0.546  -1.210  -2.535  "O4'"   523  14  
523  "O3'"   O3*   O  0  1  N  N  N  59.408  130.698  60.197   2.411   0.778  -0.203  "O3'"   523  15  
523  "C5'"   C5*   C  0  1  N  N  N  62.082  129.648  58.184   2.685  -0.334  -3.233  "C5'"   523  16  
523  "O5'"   O5*   O  0  1  N  N  N  62.498  130.927  57.649   2.197  -0.134  -4.549  "O5'"   523  17  
523  PA      PA    P  0  1  N  N  R  64.116  131.145  57.412   2.346  -1.308  -5.653  PA      523  18  
523  O1A     O1A   O  0  1  N  N  N  64.710  129.949  56.792   1.535  -0.755  -6.939  O1A     523  19  
523  O2A     O2A   O  0  1  N  N  N  64.454  132.465  56.543   3.759  -1.725  -5.943  O2A     523  20  
523  O3A     O3A   O  0  1  N  N  N  64.718  131.360  58.866   1.403  -2.500  -5.106  O3A     523  21  
523  PB      PB    P  0  1  N  N  S  66.345  131.195  59.003   0.974  -3.910  -5.767  PB      523  22  
523  O1B     O1B   O  0  1  N  N  N  66.954  131.021  60.349   0.053  -3.493  -7.028  O1B     523  23  
523  O2B     O2B   O  0  1  N  N  N  66.800  129.941  58.166   2.102  -4.844  -6.092  O2B     523  24  
523  O3B     O3B   O  0  1  N  N  N  66.907  132.430  58.172  -0.085  -4.469  -4.682  O3B     523  25  
523  PG      PG    P  0  1  N  N  N  68.145  132.020  57.236  -1.043  -5.770  -4.684  PG      523  26  
523  O1G     O1G   O  0  1  N  N  N  67.932  132.459  55.801  -2.033  -5.817  -5.810  O1G     523  27  
523  O2G     O2G   O  0  1  N  N  N  69.435  132.711  57.935  -1.684  -5.771  -3.200  O2G     523  28  
523  O3G     O3G   O  0  1  N  N  N  68.324  130.444  57.279   0.007  -6.998  -4.641  O3G     523  29  
523  HN3     HN3   H  0  1  N  N  N  57.314  124.095  58.933  -0.999  -5.828   0.686  HN3     523  30  
523  H5A1    1H5A  H  0  0  N  N  N  59.788  123.796  54.665   3.288  -5.053  -2.471  H5A1    523  31  
523  H5A2    2H5A  H  0  0  N  N  N  61.251  124.583  55.348   2.777  -6.720  -2.128  H5A2    523  32  
523  H5A3    3H5A  H  0  0  N  N  N  60.686  123.009  56.007   3.702  -5.813  -0.918  H5A3    523  33  
523  H6      H6    H  0  1  N  N  N  60.183  126.622  55.985   2.134  -3.256  -2.033  H6      523  34  
523  HN41    1HN4  H  0  0  N  N  N  58.610  122.301  56.431   0.311  -7.902  -0.370  HN41    523  35  
523  HN42    2HN4  H  0  0  N  N  N  59.426  122.223  57.843   1.730  -7.480   0.563  HN42    523  36  
523  "H1'"   H1*   H  0  1  N  N  N  58.051  128.629  56.929  -1.046  -1.665  -1.298  "H1'"   523  37  
523  "H2'1"  1H2*  H  0  0  N  N  N  57.629  129.462  59.029   0.781  -1.372   0.777  "H2'1"  523  38  
523  "H2'2"  2H2*  H  0  0  N  N  N  58.181  127.946  59.731   0.000   0.000  -0.001  "H2'2"  523  39  
523  "H3'"   H3*   H  0  1  N  N  N  60.377  128.868  60.220   2.712  -1.189  -0.710  "H3'"   523  40  
523  "H4'"   H4*   H  0  1  N  N  N  60.297  130.826  57.899   1.064   0.778  -2.394  "H4'"   523  41  
523  "HO3'"  HO3*  H  0  0  N  N  N  59.329  130.538  61.130   3.312   0.919  -0.531  "HO3'"  523  42  
523  "H5'1"  1H5*  H  0  0  N  N  N  62.426  128.808  57.563   3.132  -1.330  -3.171  "H5'1"  523  43  
523  "H5'2"  2H5*  H  0  0  N  N  N  62.500  129.427  59.177   3.454   0.417  -3.025  "H5'2"  523  44  
523  HO1A    HO1A  H  0  0  N  N  N  64.838  130.104  55.863   1.971  -0.107  -7.532  HO1A    523  45  
523  HO1B    HO1B  H  0  0  N  N  N  67.900  130.984  60.267  -0.283  -4.197  -7.624  HO1B    523  46  
523  HO2G    HO2G  H  0  0  N  N  N  70.114  132.846  57.284  -2.374  -6.433  -2.981  HO2G    523  47  
523  HO3G    HO3G  H  0  0  N  N  N  68.360  130.105  56.392  -0.330  -7.915  -4.726  HO3G    523  48  
#   #
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
523  N1     C6      DOUB  Y  N   1  
523  N1     "C1'"   SING  N  N   2  
523  N1     C2      SING  Y  N   3  
523  C2     N3      SING  Y  N   4  
523  C2     O2      DOUB  N  N   5  
523  N3     C4      SING  Y  N   6  
523  N3     HN3     SING  N  N   7  
523  C4     C5      DOUB  Y  N   8  
523  C4     N4      SING  N  N   9  
523  C5     C5A     SING  N  N  10  
523  C5     C6      SING  Y  N  11  
523  C5A    H5A1    SING  N  N  12  
523  C5A    H5A2    SING  N  N  13  
523  C5A    H5A3    SING  N  N  14  
523  C6     H6      SING  N  N  15  
523  N4     HN41    SING  N  N  16  
523  N4     HN42    SING  N  N  17  
523  "C1'"  "O4'"   SING  N  N  18  
523  "C1'"  "C2'"   SING  N  N  19  
523  "C1'"  "H1'"   SING  N  N  20  
523  "C2'"  "C3'"   SING  N  N  21  
523  "C2'"  "H2'1"  SING  N  N  22  
523  "C2'"  "H2'2"  SING  N  N  23  
523  "C3'"  "C4'"   SING  N  N  24  
523  "C3'"  "O3'"   SING  N  N  25  
523  "C3'"  "H3'"   SING  N  N  26  
523  "C4'"  "O4'"   SING  N  N  27  
523  "C4'"  "C5'"   SING  N  N  28  
523  "C4'"  "H4'"   SING  N  N  29  
523  "O3'"  "HO3'"  SING  N  N  30  
523  "C5'"  "O5'"   SING  N  N  31  
523  "C5'"  "H5'1"  SING  N  N  32  
523  "C5'"  "H5'2"  SING  N  N  33  
523  "O5'"  PA      SING  N  N  34  
523  PA     O2A     DOUB  N  N  35  
523  PA     O1A     SING  N  N  36  
523  PA     O3A     SING  N  N  37  
523  O1A    HO1A    SING  N  N  38  
523  O3A    PB      SING  N  N  39  
523  PB     O2B     DOUB  N  N  40  
523  PB     O3B     SING  N  N  41  
523  PB     O1B     SING  N  N  42  
523  O1B    HO1B    SING  N  N  43  
523  O3B    PG      SING  N  N  44  
523  PG     O1G     DOUB  N  N  45  
523  PG     O3G     SING  N  N  46  
523  PG     O2G     SING  N  N  47  
523  O2G    HO2G    SING  N  N  48  
523  O3G    HO3G    SING  N  N  49  
#   #
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
523  SMILES            ACDLabs               10.04  "O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC2OC([N+]=1C(=O)NC(N)=C(C=1)C)CC2O"  
523  SMILES_CANONICAL  CACTVS                3.341  "CC1=C(N)NC(=O)[N+](=C1)[C@H]2C[C@H](O)[C@@H](CO[P@@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)O2"  
523  SMILES            CACTVS                3.341  "CC1=C(N)NC(=O)[N+](=C1)[CH]2C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)O2"  
523  SMILES_CANONICAL  "OpenEye OEToolkits"  1.5.0  "CC1=C(NC(=O)[N+](=C1)[C@H]2C[C@@H]([C@H](O2)CO[P@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)N"  
523  SMILES            "OpenEye OEToolkits"  1.5.0  "CC1=C(NC(=O)[N+](=C1)C2CC(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)N"  
523  InChI             InChI                 1.03   "InChI=1S/C10H18N3O13P3/c1-5-3-13(10(15)12-9(5)11)8-2-6(14)7(24-8)4-23-28(19,20)26-29(21,22)25-27(16,17)18/h3,6-8,14H,2,4H2,1H3,(H6,11,12,15,16,17,18,19,20,21,22)/p+1/t6-,7+,8+/m0/s1"  
523  InChIKey          InChI                 1.03   VSWHQKSDLZFLRY-XLPZGREQSA-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
523  "SYSTEMATIC NAME"  ACDLabs               10.04  "2'-deoxy-5-methylcytidine 5'-(tetrahydrogen triphosphate)"  
523  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.5.0  "[(2R,3S,5R)-5-(4-amino-5-methyl-2-oxo-3H-pyrimidin-1-ium-1-yl)-3-hydroxy-oxolan-2-yl]methyl (hydroxy-phosphonooxy-phosphoryl) hydrogen 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
523  "Create component"   2007-01-22  PDBJ  
523  "Modify descriptor"  2011-06-04  RCSB  
523  "Modify synonyms"    2021-03-01  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     523
_pdbx_chem_comp_synonyms.name        "5-METHYL-2'-DEOXY-CYTIDINE-5'-TRIPHOSPHATE"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
