data_DDY
# 
_chem_comp.id                                    DDY 
_chem_comp.name                                  "2',3'-DIDEOXYCYTOSINE-5'-DIPHOSPATE" 
_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                    2008-10-14 
_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        ? 
_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 5.814  1.587  0.003  C4     DDY 1  
DDY PB     PB   P 0 1 N N N 20.514 15.607 1.186  -5.037 0.622  -0.271 PB     DDY 2  
DDY PA     PA   P 0 1 N N R 19.132 13.536 -0.290 -2.580 -0.089 0.106  PA     DDY 3  
DDY C2     C2   C 0 1 N N N 15.067 15.663 -5.521 3.916  0.403  0.583  C2     DDY 4  
DDY C5     C5   C 0 1 N N N 16.593 17.602 -4.146 5.926  0.824  -1.177 C5     DDY 5  
DDY O2     O2   O 0 1 N N N 14.418 14.816 -6.136 3.005  0.207  1.370  O2     DDY 6  
DDY O3B    O3B  O 0 1 N N N 21.838 14.771 0.875  -5.244 -0.434 0.745  O3B    DDY 7  
DDY O1B    O1B  O 0 1 N N N 20.075 15.239 2.546  -5.018 2.062  0.448  O1B    DDY 8  
DDY O2B    O2B  O 0 1 N N N 20.776 17.031 0.909  -6.234 0.574  -1.347 O2B    DDY 9  
DDY O3A    O3A  O 0 1 N N N 19.441 15.088 0.072  -3.632 0.377  -1.020 O3A    DDY 10 
DDY O1A    O1A  O 0 1 N N N 19.029 12.708 0.916  -3.210 -1.104 0.980  O1A    DDY 11 
DDY O2A    O2A  O 0 1 N N N 20.091 13.113 -1.332 -2.141 1.183  0.990  O2A    DDY 12 
DDY "O5'"  O5*  O 0 1 N N N 17.685 13.681 -0.970 -1.282 -0.724 -0.604 "O5'"  DDY 13 
DDY "C5'"  C5*  C 0 1 N N N 16.531 12.998 -0.473 -0.443 -1.223 0.440  "C5'"  DDY 14 
DDY "C4'"  C4*  C 0 1 N N S 15.468 12.955 -1.578 0.816  -1.843 -0.169 "C4'"  DDY 15 
DDY "O4'"  O4*  O 0 1 N N N 15.112 14.292 -2.030 1.679  -0.820 -0.715 "O4'"  DDY 16 
DDY "C3'"  C3*  C 0 1 N N N 15.996 12.392 -2.667 1.685  -2.505 0.930  "C3'"  DDY 17 
DDY "C2'"  C2*  C 0 1 N N N 15.758 13.102 -3.753 3.094  -2.482 0.287  "C2'"  DDY 18 
DDY "C1'"  C1*  C 0 1 N N R 15.038 14.183 -3.479 2.999  -1.384 -0.790 "C1'"  DDY 19 
DDY N1     N1   N 0 1 N N N 15.488 15.420 -4.191 4.000  -0.345 -0.532 N1     DDY 20 
DDY C6     C6   C 0 1 N N N 16.258 16.396 -3.513 5.011  -0.142 -1.423 C6     DDY 21 
DDY N4     N4   N 0 1 N N N 16.462 18.991 -6.061 6.733  2.572  0.281  N4     DDY 22 
DDY N3     N3   N 0 1 N N N 15.407 16.875 -6.145 4.812  1.353  0.842  N3     DDY 23 
DDY H5     H5   H 0 1 N N N 17.191 18.361 -3.613 6.736  1.002  -1.870 H5     DDY 24 
DDY H1B    H1B  H 0 1 N N N 19.287 15.737 2.731  -4.881 2.720  -0.248 H1B    DDY 25 
DDY H2B    H2B  H 0 1 N N N 19.988 17.529 1.094  -7.055 0.724  -0.858 H2B    DDY 26 
DDY H2A    H2A  H 0 1 N N N 19.910 12.205 -1.544 -1.736 1.818  0.384  H2A    DDY 27 
DDY "H5'1" 1H5* H 0 0 N N N 16.145 13.446 0.472  -0.983 -1.981 1.009  "H5'1" DDY 28 
DDY "H5'2" 2H5* H 0 0 N N N 16.774 11.985 -0.076 -0.161 -0.405 1.103  "H5'2" DDY 29 
DDY "H4'"  H4*  H 0 1 N N N 14.591 12.410 -1.156 0.551  -2.569 -0.938 "H4'"  DDY 30 
DDY "H3'1" 1H3* H 0 0 N N N 15.649 11.339 -2.787 1.361  -3.528 1.119  "H3'1" DDY 31 
DDY "H3'2" 2H3* H 0 0 N N N 17.087 12.204 -2.537 1.667  -1.917 1.847  "H3'2" DDY 32 
DDY "H2'1" 1H2* H 0 0 N N N 15.280 12.484 -4.548 3.321  -3.445 -0.169 "H2'1" DDY 33 
DDY "H2'2" 2H2* H 0 0 N N N 16.703 13.365 -4.284 3.848  -2.223 1.030  "H2'2" DDY 34 
DDY "H1'"  H1*  H 0 1 N N N 13.990 14.081 -3.847 3.161  -1.818 -1.777 "H1'"  DDY 35 
DDY H6     H6   H 0 1 N N N 16.601 16.215 -2.480 5.078  -0.743 -2.319 H6     DDY 36 
DDY HN41   1HN4 H 0 0 N N N 17.473 19.123 -6.023 6.650  3.098  1.092  HN41   DDY 37 
DDY HN42   2HN4 H 0 0 N N N 16.151 19.164 -7.017 7.466  2.738  -0.332 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              10.04 O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)CC2                                                                                                                            
DDY InChI            InChI                1.02b InChI=1/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/f/h14-15,17H,10H2 
DDY InChIKey         InChI                1.02b FVSQWXITYSICAK-BAJFBQQNDV                                                                                                                                                 
DDY SMILES_CANONICAL CACTVS               3.341 NC1=NC(=O)N(C=C1)[C@H]2CC[C@@H](CO[P@](O)(=O)O[P](O)(O)=O)O2                                                                                                              
DDY SMILES           CACTVS               3.341 NC1=NC(=O)N(C=C1)[CH]2CC[CH](CO[P](O)(=O)O[P](O)(O)=O)O2                                                                                                                  
DDY SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C1C[C@@H](O[C@@H]1CO[P@@](=O)(O)OP(=O)(O)O)N2C=CC(=NC2=O)N                                                                                                                
DDY SMILES           "OpenEye OEToolkits" 1.5.0 C1CC(OC1COP(=O)(O)OP(=O)(O)O)N2C=CC(=NC2=O)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              10.04 "[(2S,5R)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl trihydrogen diphosphate" 
DDY "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2S,5R)-5-(4-amino-2-oxo-pyrimidin-1-yl)oxolan-2-yl]methyl phosphono hydrogen phosphate"        
# 
