data_DDY
#

_chem_comp.id                                   DDY
_chem_comp.name                                 "2',3'-DIDEOXYCYTOSINE-5'-DIPHOSPHATE"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C9 H15 N3 O9 P2"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        DDCDP
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2004-04-19
_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                       371.178
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    DDY
_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       1S9F
_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
DDY  C4      C4      C  0  1  N  N  N  16.165  17.840  -5.459   5.720  -1.713  -0.249  C4      DDY   1  
DDY  PB      PB      P  0  1  N  N  N  20.514  15.607   1.186  -5.058  -0.877   0.440  PB      DDY   2  
DDY  PA      PA      P  0  1  N  N  N  19.132  13.536  -0.290  -2.592   0.397  -0.601  PA      DDY   3  
DDY  C2      C2      C  0  1  N  N  N  15.067  15.663  -5.521   3.994  -0.219  -0.606  C2      DDY   4  
DDY  C5      C5      C  0  1  N  N  N  16.593  17.602  -4.146   5.655  -1.453   1.135  C5      DDY   5  
DDY  O2      O2      O  0  1  N  N  N  14.418  14.816  -6.136   3.243   0.346  -1.385  O2      DDY   6  
DDY  O3B     O3B     O  0  1  N  N  N  21.838  14.771   0.875  -5.893   0.227  -0.084  O3B     DDY   7  
DDY  O1B     O1B     O  0  1  N  N  N  20.075  15.239   2.546  -5.508  -1.221   1.947  O1B     DDY   8  
DDY  O2B     O2B     O  0  1  N  N  N  20.776  17.031   0.909  -5.247  -2.180  -0.487  O2B     DDY   9  
DDY  O3A     O3A     O  0  1  N  N  N  19.441  15.088   0.072  -3.511  -0.431   0.430  O3A     DDY  10  
DDY  O1A     O1A     O  0  1  N  N  N  19.029  12.708   0.916  -3.324   1.599  -1.059  O1A     DDY  11  
DDY  O2A     O2A     O  0  1  N  N  N  20.091  13.113  -1.332  -2.239  -0.531  -1.869  O2A     DDY  12  
DDY  "O5'"   "O5'"   O  0  1  N  N  N  17.685  13.681  -0.970  -1.231   0.844   0.133  "O5'"   DDY  13  
DDY  "C5'"   "C5'"   C  0  1  N  N  N  16.531  12.998  -0.473  -0.253   1.682  -0.486  "C5'"   DDY  14  
DDY  "C4'"   "C4'"   C  0  1  N  N  S  15.468  12.955  -1.578   0.909   1.910   0.483  "C4'"   DDY  15  
DDY  "O4'"   "O4'"   O  0  1  N  N  N  15.112  14.292  -2.030   1.621   0.677   0.722  "O4'"   DDY  16  
DDY  "C3'"   "C3'"   C  0  1  N  N  N  15.996  12.392  -2.667   1.981   2.828  -0.157  "C3'"   DDY  17  
DDY  "C2'"   "C2'"   C  0  1  N  N  N  15.758  13.102  -3.753   3.258   2.429   0.623  "C2'"   DDY  18  
DDY  "C1'"   "C1'"   C  0  1  N  N  R  15.038  14.183  -3.479   2.933   1.033   1.190  "C1'"   DDY  19  
DDY  N1      N1      N  0  1  N  N  N  15.488  15.420  -4.191   3.915   0.059   0.708  N1      DDY  20  
DDY  C6      C6      C  0  1  N  N  N  16.258  16.396  -3.513   4.744  -0.562   1.594  C6      DDY  21  
DDY  N4      N4      N  0  1  N  N  N  16.462  18.991  -6.061   6.636  -2.613  -0.742  N4      DDY  22  
DDY  N3      N3      N  0  1  N  N  N  15.407  16.875  -6.145   4.888  -1.088  -1.073  N3      DDY  23  
DDY  H5      H5      H  0  1  N  N  N  17.178  18.344  -3.624   6.322  -1.957   1.819  H5      DDY  24  
DDY  H1B     H1B     H  0  1  N  N  N  20.676  14.600   2.911  -6.431  -1.498   2.028  H1B     DDY  25  
DDY  H2B     H2B     H  0  1  N  N  N  21.671  17.136   0.608  -4.728  -2.944  -0.202  H2B     DDY  26  
DDY  H2A     H2A     H  0  1  N  N  N  20.530  12.317  -1.055  -1.758  -1.339  -1.643  H2A     DDY  27  
DDY  "H5'1"  "H5'1"  H  0  0  N  N  N  16.804  11.973  -0.181   0.117   1.202  -1.391  "H5'1"  DDY  28  
DDY  "H5'2"  "H5'2"  H  0  0  N  N  N  16.133  13.531   0.403  -0.705   2.641  -0.742  "H5'2"  DDY  29  
DDY  "H4'"   "H4'"   H  0  1  N  N  N  14.603  12.417  -1.162   0.549   2.333   1.421  "H4'"   DDY  30  
DDY  "H3'1"  "H3'1"  H  0  0  N  N  N  17.085  12.313  -2.530   2.092   2.615  -1.220  "H3'1"  DDY  31  
DDY  "H3'2"  "H3'2"  H  0  0  N  N  N  15.555  11.393  -2.796   1.740   3.879   0.005  "H3'2"  DDY  32  
DDY  "H2'1"  "H2'1"  H  0  0  N  N  N  16.718  13.416  -4.189   4.115   2.378  -0.049  "H2'1"  DDY  33  
DDY  "H2'2"  "H2'2"  H  0  0  N  N  N  15.203  12.479  -4.470   3.447   3.134   1.432  "H2'2"  DDY  34  
DDY  "H1'"   "H1'"   H  0  1  N  N  N  14.004  14.082  -3.842   2.942   1.064   2.279  "H1'"   DDY  35  
DDY  H6      H6      H  0  1  N  N  N  16.589  16.211  -2.502   4.675  -0.347   2.650  H6      DDY  36  
DDY  HN41    HN41    H  0  0  N  N  N  16.146  19.163  -6.994   7.240  -3.071  -0.137  HN41    DDY  37  
DDY  HN42    HN42    H  0  0  N  N  N  17.001  19.682  -5.580   6.678  -2.789  -1.695  HN42    DDY  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
DDY  C4     C5      SING  N  N   1  
DDY  C4     N4      SING  N  N   2  
DDY  C4     N3      DOUB  N  N   3  
DDY  PB     O3B     DOUB  N  N   4  
DDY  PB     O1B     SING  N  N   5  
DDY  PB     O2B     SING  N  N   6  
DDY  PB     O3A     SING  N  N   7  
DDY  PA     O3A     SING  N  N   8  
DDY  PA     O1A     DOUB  N  N   9  
DDY  PA     O2A     SING  N  N  10  
DDY  PA     "O5'"   SING  N  N  11  
DDY  C2     O2      DOUB  N  N  12  
DDY  C2     N1      SING  N  N  13  
DDY  C2     N3      SING  N  N  14  
DDY  C5     C6      DOUB  N  N  15  
DDY  C5     H5      SING  N  N  16  
DDY  O1B    H1B     SING  N  N  17  
DDY  O2B    H2B     SING  N  N  18  
DDY  O2A    H2A     SING  N  N  19  
DDY  "O5'"  "C5'"   SING  N  N  20  
DDY  "C5'"  "C4'"   SING  N  N  21  
DDY  "C5'"  "H5'1"  SING  N  N  22  
DDY  "C5'"  "H5'2"  SING  N  N  23  
DDY  "C4'"  "O4'"   SING  N  N  24  
DDY  "C4'"  "C3'"   SING  N  N  25  
DDY  "C4'"  "H4'"   SING  N  N  26  
DDY  "O4'"  "C1'"   SING  N  N  27  
DDY  "C3'"  "C2'"   SING  N  N  28  
DDY  "C3'"  "H3'1"  SING  N  N  29  
DDY  "C3'"  "H3'2"  SING  N  N  30  
DDY  "C2'"  "C1'"   SING  N  N  31  
DDY  "C2'"  "H2'1"  SING  N  N  32  
DDY  "C2'"  "H2'2"  SING  N  N  33  
DDY  "C1'"  N1      SING  N  N  34  
DDY  "C1'"  "H1'"   SING  N  N  35  
DDY  N1     C6      SING  N  N  36  
DDY  C6     H6      SING  N  N  37  
DDY  N4     HN41    SING  N  N  38  
DDY  N4     HN42    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
DDY  SMILES            ACDLabs               12.01  "O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)CC2"  
DDY  SMILES_CANONICAL  CACTVS                3.370  "NC1=NC(=O)N(C=C1)[C@H]2CC[C@@H](CO[P](O)(=O)O[P](O)(O)=O)O2"  
DDY  SMILES            CACTVS                3.370  "NC1=NC(=O)N(C=C1)[CH]2CC[CH](CO[P](O)(=O)O[P](O)(O)=O)O2"  
DDY  SMILES_CANONICAL  "OpenEye OEToolkits"  1.7.0  "C1C[C@@H](O[C@@H]1CO[P@@](=O)(O)OP(=O)(O)O)N2C=CC(=NC2=O)N"  
DDY  SMILES            "OpenEye OEToolkits"  1.7.0  "C1CC(OC1COP(=O)(O)OP(=O)(O)O)N2C=CC(=NC2=O)N"  
DDY  InChI             InChI                 1.03   "InChI=1S/C9H15N3O9P2/c10-7-3-4-12(9(13)11-7)8-2-1-6(20-8)5-19-23(17,18)21-22(14,15)16/h3-4,6,8H,1-2,5H2,(H,17,18)(H2,10,11,13)(H2,14,15,16)/t6-,8+/m0/s1"  
DDY  InChIKey          InChI                 1.03   FVSQWXITYSICAK-POYBYMJQSA-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
DDY  "SYSTEMATIC NAME"  ACDLabs               12.01  "[(2S,5R)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl trihydrogen diphosphate"  
DDY  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.7.0  "[(2S,5R)-5-(4-azanyl-2-oxo-pyrimidin-1-yl)oxolan-2-yl]methyl phosphono 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
DDY  "Create component"   2004-04-19  RCSB  
DDY  "Modify descriptor"  2011-06-04  RCSB  
DDY  "Modify synonyms"    2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     DDY
_pdbx_chem_comp_synonyms.name        DDCDP
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
