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                    2009-01-07 
_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 InChI            InChI                1.02b "InChI=1/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/f/h10,15-16H" 
DDN InChIKey         InChI                1.02b ILSIYJVILUIVPM-ZTOZMHKSDY                                                                                                                                  
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"                                                                                                                    
# 
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" 
# 
