data_DDN
#

_chem_comp.id                                   DDN
_chem_comp.name                                 "3,4-DIHYDRO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE"
_chem_comp.type                                 "DNA LINKING"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C9 H15 N2 O8 P"
_chem_comp.mon_nstd_parent_comp_id              DU
_chem_comp.pdbx_synonyms                        "((2R,3S,5R)-3-HYDROXY-5-(4-HYDROXY-2-OXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-TETRAHYDROFURAN-2-YL)METHYL DIHYDROGEN PHOSPHATE"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2004-12-14
_chem_comp.pdbx_modified_date                   2021-03-13
_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                       310.198
_chem_comp.one_letter_code                      U
_chem_comp.three_letter_code                    DDN
_chem_comp.pdbx_model_coordinates_details       ?
_chem_comp.pdbx_model_coordinates_missing_flag  N
_chem_comp.pdbx_ideal_coordinates_details       ?
_chem_comp.pdbx_ideal_coordinates_missing_flag  N
_chem_comp.pdbx_model_coordinates_db_code       1VQ2
_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
DDN  OP3     O3P   O  0  1  N  Y  N  81.603   5.502  15.525  -3.513  -1.588  -1.240  OP3     DDN   1  
DDN  P       P     P  0  1  N  N  N  81.104   6.559  16.500  -3.914  -1.012   0.063  P       DDN   2  
DDN  OP1     O1P   O  0  1  N  N  N  81.184   6.110  17.930  -4.477  -2.181   1.016  OP1     DDN   3  
DDN  OP2     O2P   O  0  1  N  N  N  81.744   7.909  16.231  -5.064   0.091  -0.170  OP2     DDN   4  
DDN  "O5'"   O5*   O  0  1  N  N  N  79.511   6.767  16.211  -2.639  -0.318   0.759  "O5'"   DDN   5  
DDN  "C5'"   C5*   C  0  1  N  N  N  78.688   7.541  17.107  -2.117   0.623  -0.180  "C5'"   DDN   6  
DDN  "C4'"   C4*   C  0  1  N  N  R  77.479   8.062  16.349  -0.896   1.321   0.422  "C4'"   DDN   7  
DDN  "O4'"   O4*   O  0  1  N  N  N  76.410   8.400  17.232   0.186   0.378   0.600  "O4'"   DDN   8  
DDN  "C3'"   C3*   C  0  1  N  N  S  77.747   9.312  15.493  -0.336   2.380  -0.553  "C3'"   DDN   9  
DDN  "O3'"   O3*   O  0  1  N  N  N  76.949   9.301  14.345  -0.802   3.684  -0.198  "O3'"   DDN  10  
DDN  "C2'"   C2*   C  0  1  N  N  N  77.415  10.490  16.322   1.196   2.286  -0.377  "C2'"   DDN  11  
DDN  "C1'"   C1*   C  0  1  N  N  R  76.539   9.824  17.340   1.384   1.181   0.687  "C1'"   DDN  12  
DDN  N1      N1    N  0  1  N  N  N  75.921   9.989  18.846   2.566   0.373   0.379  N1      DDN  13  
DDN  C2      C2    C  0  1  N  N  N  74.822  10.856  19.020   2.557  -0.367  -0.738  C2      DDN  14  
DDN  O2      O2    O  0  1  N  N  N  74.237  11.417  18.093   1.577  -0.340  -1.457  O2      DDN  15  
DDN  N3      N3    N  0  1  N  N  N  74.538  11.168  20.353   3.610  -1.132  -1.091  N3      DDN  16  
DDN  C4      C4    C  0  1  N  N  R  75.573  10.985  21.525   4.787  -1.152  -0.207  C4      DDN  17  
DDN  O4      O4    O  0  1  N  N  N  76.020  12.231  22.079   5.011  -2.504   0.196  O4      DDN  18  
DDN  C5      C5    C  0  1  N  N  N  76.840  10.235  21.035   4.729  -0.297   1.042  C5      DDN  19  
DDN  C6      C6    C  0  1  N  N  N  76.985   9.896  19.719   3.634   0.408   1.262  C6      DDN  20  
DDN  H1P     H1P   H  0  1  N  N  N  80.873   6.770  18.539  -5.238  -2.569   0.563  H1P     DDN  21  
DDN  H2P     H2P   H  0  1  N  N  N  81.433   8.569  16.840  -5.297   0.440   0.701  H2P     DDN  22  
DDN  "H5'"   1H5*  H  0  1  N  N  N  79.259   8.358  17.607  -2.880   1.365  -0.414  "H5'"   DDN  23  
DDN  "H5''"  2H5*  H  0  0  N  N  N  78.401   6.968  18.020  -1.824   0.103  -1.092  "H5''"  DDN  24  
DDN  "H4'"   H4*   H  0  1  N  N  N  77.214   7.214  15.675  -1.156   1.785   1.374  "H4'"   DDN  25  
DDN  "H3'"   H3*   H  0  1  N  N  N  78.813   9.338  15.167  -0.618   2.141  -1.579  "H3'"   DDN  26  
DDN  H1      H1    H  0  1  N  N  N  77.115  10.073  13.816  -0.398   4.304  -0.821  H1      DDN  27  
DDN  "H2'"   1H2*  H  0  1  N  N  N  76.972  11.361  15.785   1.671   1.998  -1.315  "H2'"   DDN  28  
DDN  "H2''"  2H2*  H  0  0  N  N  N  78.279  11.071  16.721   1.598   3.233  -0.019  "H2''"  DDN  29  
DDN  "H1'"   H1*   H  0  1  N  N  N  76.274  10.840  16.964   1.474   1.622   1.680  "H1'"   DDN  30  
DDN  HN3     HN3   H  0  1  N  N  N  73.589  11.524  20.469   3.590  -1.659  -1.905  HN3     DDN  31  
DDN  H4      H4    H  0  1  N  N  N  75.028  10.405  22.306   5.650  -0.832  -0.792  H4      DDN  32  
DDN  HO4     HO4   H  0  1  N  N  N  76.645  12.121  22.786   5.045  -3.034  -0.612  HO4     DDN  33  
DDN  H5      H5    H  0  1  N  N  N  77.692   9.923  21.662   5.558  -0.266   1.732  H5      DDN  34  
DDN  H6      H6    H  0  1  N  N  N  77.967   9.545  19.359   3.570   1.025   2.146  H6      DDN  35  
#   #
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
DDN  OP3    P       DOUB  N  N   1  
DDN  P      OP1     SING  N  N   2  
DDN  P      OP2     SING  N  N   3  
DDN  P      "O5'"   SING  N  N   4  
DDN  OP1    H1P     SING  N  N   5  
DDN  OP2    H2P     SING  N  N   6  
DDN  "O5'"  "C5'"   SING  N  N   7  
DDN  "C5'"  "C4'"   SING  N  N   8  
DDN  "C5'"  "H5'"   SING  N  N   9  
DDN  "C5'"  "H5''"  SING  N  N  10  
DDN  "C4'"  "O4'"   SING  N  N  11  
DDN  "C4'"  "C3'"   SING  N  N  12  
DDN  "C4'"  "H4'"   SING  N  N  13  
DDN  "O4'"  "C1'"   SING  N  N  14  
DDN  "C3'"  "O3'"   SING  N  N  15  
DDN  "C3'"  "C2'"   SING  N  N  16  
DDN  "C3'"  "H3'"   SING  N  N  17  
DDN  "O3'"  H1      SING  N  N  18  
DDN  "C2'"  "C1'"   SING  N  N  19  
DDN  "C2'"  "H2'"   SING  N  N  20  
DDN  "C2'"  "H2''"  SING  N  N  21  
DDN  "C1'"  N1      SING  N  N  22  
DDN  "C1'"  "H1'"   SING  N  N  23  
DDN  N1     C2      SING  N  N  24  
DDN  N1     C6      SING  N  N  25  
DDN  C2     O2      DOUB  N  N  26  
DDN  C2     N3      SING  N  N  27  
DDN  N3     C4      SING  N  N  28  
DDN  N3     HN3     SING  N  N  29  
DDN  C4     O4      SING  N  N  30  
DDN  C4     C5      SING  N  N  31  
DDN  C4     H4      SING  N  N  32  
DDN  O4     HO4     SING  N  N  33  
DDN  C5     C6      DOUB  N  N  34  
DDN  C5     H5      SING  N  N  35  
DDN  C6     H6      SING  N  N  36  
#   #
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
DDN  SMILES            ACDLabs               10.04  "O=C1NC(O)C=CN1C2OC(C(O)C2)COP(=O)(O)O"  
DDN  SMILES_CANONICAL  CACTVS                3.341  "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=C[C@@H](O)NC2=O"  
DDN  SMILES            CACTVS                3.341  "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=C[CH](O)NC2=O"  
DDN  SMILES_CANONICAL  "OpenEye OEToolkits"  1.5.0  "C1[C@@H]([C@H](O[C@H]1N2C=C[C@H](NC2=O)O)COP(=O)(O)O)O"  
DDN  SMILES            "OpenEye OEToolkits"  1.5.0  "C1C(C(OC1N2C=CC(NC2=O)O)COP(=O)(O)O)O"  
DDN  InChI             InChI                 1.03   "InChI=1S/C9H15N2O8P/c12-5-3-8(11-2-1-7(13)10-9(11)14)19-6(5)4-18-20(15,16)17/h1-2,5-8,12-13H,3-4H2,(H,10,14)(H2,15,16,17)/t5-,6+,7+,8+/m0/s1"  
DDN  InChIKey          InChI                 1.03   ILSIYJVILUIVPM-LXGUWJNJSA-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
DDN  "SYSTEMATIC NAME"  ACDLabs               10.04  "(4R)-1-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-4-hydroxy-3,4-dihydropyrimidin-2(1H)-one"  
DDN  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.5.0  "[(2R,3S,5R)-3-hydroxy-5-[(4R)-4-hydroxy-2-oxo-3,4-dihydropyrimidin-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
DDN  "Create component"   2004-12-14  RCSB  
DDN  "Modify descriptor"  2011-06-04  RCSB  
DDN  "Modify synonyms"    2021-03-13  RCSB  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     DDN
_pdbx_chem_comp_synonyms.name        "((2R,3S,5R)-3-HYDROXY-5-(4-HYDROXY-2-OXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)-TETRAHYDROFURAN-2-YL)METHYL DIHYDROGEN PHOSPHATE"
_pdbx_chem_comp_synonyms.provenance  PDB
_pdbx_chem_comp_synonyms.type        ?
##