data_PDU
#

_chem_comp.id                                   PDU
_chem_comp.name                                 "5(1-PROPYNYL)-2'-DEOXYURIDINE-5-MONOPHOSPHATE"
_chem_comp.type                                 "DNA linking"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C12 H15 N2 O8 P"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    1999-07-08
_chem_comp.pdbx_modified_date                   2021-07-21
_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                       346.230
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    PDU
_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       1P3X
_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
PDU  P       P1   P  0  1  N  N  N   1.020  11.691  3.054   4.635  -1.265  -0.129  P       PDU   1  
PDU  OP2     O1   O  0  1  N  N  N   1.721  12.834  3.687   5.944  -0.327  -0.153  OP1     PDU   2  
PDU  OP1     O2   O  0  1  N  N  N   0.582  11.825  1.647   4.404  -1.754   1.248  OP2     PDU   3  
PDU  "O5'"   O3   O  0  1  N  N  N   2.048  10.406  3.133   3.357  -0.415  -0.618  "O5'"   PDU   4  
PDU  "C5'"   C1   C  0  1  N  N  N   1.591   9.163  3.678   2.840   0.701   0.109  "C5'"   PDU   5  
PDU  "C4'"   C2   C  0  1  N  N  R   2.528   8.011  4.010   1.630   1.274  -0.631  "C4'"   PDU   6  
PDU  "O4'"   O4   O  0  1  N  N  N   1.717   6.998  4.676   0.537   0.331  -0.627  "O4'"   PDU   7  
PDU  "C3'"   C3   C  0  1  N  N  S   3.183   7.373  2.808   1.054   2.496   0.130  "C3'"   PDU   8  
PDU  "O3'"   O5   O  0  1  N  N  N   4.540   6.989  3.080   1.731   3.697  -0.249  "O3'"   PDU   9  
PDU  "C2'"   C4   C  0  1  N  N  N   2.318   6.165  2.681  -0.417   2.515  -0.352  "C2'"   PDU  10  
PDU  "C1'"   C5   C  0  1  N  N  R   1.906   5.711  4.066  -0.667   1.081  -0.858  "C1'"   PDU  11  
PDU  N1      N1   N  0  1  N  N  N   0.664   4.890  3.874  -1.779   0.479  -0.119  N1      PDU  12  
PDU  C2      C6   C  0  1  N  N  N   0.597   3.545  4.294  -1.646   0.252   1.198  C2      PDU  13  
PDU  O2      O6   O  0  1  N  N  N   1.535   2.975  4.847  -0.603   0.551   1.747  O2      PDU  14  
PDU  N3      N2   N  0  1  N  N  N  -0.614   2.875  4.049  -2.633  -0.297   1.927  N3      PDU  15  
PDU  C4      C7   C  0  1  N  N  N  -1.721   3.433  3.440  -3.802  -0.640   1.344  C4      PDU  16  
PDU  O4      O7   O  0  1  N  N  N  -2.740   2.768  3.262  -4.700  -1.137   1.998  O4      PDU  17  
PDU  C5      C8   C  0  1  N  N  N  -1.557   4.817  3.050  -3.967  -0.399  -0.097  C5      PDU  18  
PDU  C5A     C9   C  0  1  N  N  N  -2.658   5.457  2.396  -5.189  -0.739  -0.762  C5A     PDU  19  
PDU  C5B     C10  C  0  1  N  N  N  -3.619   5.948  1.895  -6.190  -1.018  -1.308  C5B     PDU  20  
PDU  C5M     C11  C  0  1  N  N  N  -4.841   6.513  1.336  -7.446  -1.368  -1.992  C5M     PDU  21  
PDU  C6      C12  C  0  1  N  N  N  -0.405   5.489  3.266  -2.931   0.167  -0.782  C6      PDU  22  
PDU  OP3     O8   O  0  1  N  Y  N  -0.326  11.391  3.961   4.855  -2.519  -1.115  O1      PDU  23  
PDU  HOP2    H1   H  0  1  N  N  N   1.799  13.544  3.061   6.155   0.030  -1.027  H1      PDU  24  
PDU  "H5'"   H2   H  0  1  N  N  N   1.075   9.415  4.616   2.537   0.376   1.105  "H5'"   PDU  25  
PDU  "H5''"  H3   H  0  0  N  N  N   0.864   8.764  2.955   3.610   1.467   0.195  "H5''"  PDU  26  
PDU  "H4'"   H4   H  0  1  N  N  N   3.309   8.372  4.695   1.899   1.546  -1.651  "H4'"   PDU  27  
PDU  "H3'"   H5   H  0  1  N  N  N   3.102   8.020  1.922   1.109   2.345   1.208  "H3'"   PDU  28  
PDU  H2      H6   H  0  1  N  N  N   5.080   7.767  3.159   1.406   4.490   0.200  H2      PDU  29  
PDU  "H2''"  H7   H  0  0  N  N  N   1.423   6.412  2.091  -1.086   2.750   0.475  "H2''"  PDU  30  
PDU  "H2'"   H8   H  0  1  N  N  N   2.877   5.361  2.180  -0.543   3.233  -1.163  "H2'"   PDU  31  
PDU  "H1'"   H9   H  0  1  N  N  N   2.704   5.128  4.550  -0.894   1.099  -1.924  "H1'"   PDU  32  
PDU  H3      H10  H  0  1  N  N  N  -0.679   1.920  4.338  -2.505  -0.448   2.877  H3      PDU  33  
PDU  H71     H11  H  0  1  N  N  N  -4.591   7.143  0.470  -8.141  -1.804  -1.275  H71     PDU  34  
PDU  H72     H12  H  0  1  N  N  N  -5.509   5.699  1.017  -7.887  -0.469  -2.424  H72     PDU  35  
PDU  H73     H13  H  0  1  N  N  N  -5.346   7.123  2.100  -7.240  -2.088  -2.783  H73     PDU  36  
PDU  H6      H14  H  0  1  N  N  N  -0.327   6.519  2.952  -3.018   0.358  -1.841  H6      PDU  37  
PDU  HOP3    H15  H  0  1  N  Y  N  -1.090  11.368  3.397   5.609  -3.076  -0.879  H4      PDU  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
PDU  C5M    C5B     SING  N  N   1  
PDU  OP1    P       DOUB  N  N   2  
PDU  C5B    C5A     TRIP  N  N   3  
PDU  C5A    C5      SING  N  N   4  
PDU  "C2'"  "C3'"   SING  N  N   5  
PDU  "C2'"  "C1'"   SING  N  N   6  
PDU  "C3'"  "O3'"   SING  N  N   7  
PDU  "C3'"  "C4'"   SING  N  N   8  
PDU  C5     C6      DOUB  N  N   9  
PDU  C5     C4      SING  N  N  10  
PDU  P      "O5'"   SING  N  N  11  
PDU  P      OP2     SING  N  N  12  
PDU  "O5'"  "C5'"   SING  N  N  13  
PDU  O4     C4      DOUB  N  N  14  
PDU  C6     N1      SING  N  N  15  
PDU  C4     N3      SING  N  N  16  
PDU  "C5'"  "C4'"   SING  N  N  17  
PDU  N1     "C1'"   SING  N  N  18  
PDU  N1     C2      SING  N  N  19  
PDU  "C4'"  "O4'"   SING  N  N  20  
PDU  N3     C2      SING  N  N  21  
PDU  "C1'"  "O4'"   SING  N  N  22  
PDU  C2     O2      DOUB  N  N  23  
PDU  P      OP3     SING  N  N  24  
PDU  OP2    HOP2    SING  N  N  25  
PDU  "C5'"  "H5'"   SING  N  N  26  
PDU  "C5'"  "H5''"  SING  N  N  27  
PDU  "C4'"  "H4'"   SING  N  N  28  
PDU  "C3'"  "H3'"   SING  N  N  29  
PDU  "O3'"  H2      SING  N  N  30  
PDU  "C2'"  "H2''"  SING  N  N  31  
PDU  "C2'"  "H2'"   SING  N  N  32  
PDU  "C1'"  "H1'"   SING  N  N  33  
PDU  N3     H3      SING  N  N  34  
PDU  C5M    H71     SING  N  N  35  
PDU  C5M    H72     SING  N  N  36  
PDU  C5M    H73     SING  N  N  37  
PDU  C6     H6      SING  N  N  38  
PDU  OP3    HOP3    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
PDU  InChI             InChI                 1.03   "InChI=1S/C12H15N2O8P/c1-2-3-7-5-14(12(17)13-11(7)16)10-4-8(15)9(22-10)6-21-23(18,19)20/h5,8-10,15H,4,6H2,1H3,(H,13,16,17)(H2,18,19,20)/t8-,9+,10+/m0/s1"  
PDU  InChIKey          InChI                 1.03   NUOBVCABUBRVOG-IVZWLZJFSA-N  
PDU  SMILES_CANONICAL  CACTVS                3.385  "CC#CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O"  
PDU  SMILES            CACTVS                3.385  "CC#CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O"  
PDU  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "CC#CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O"  
PDU  SMILES            "OpenEye OEToolkits"  2.0.7  "CC#CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)O)O"  
#
_pdbx_chem_comp_identifier.comp_id          PDU
_pdbx_chem_comp_identifier.type             "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program          "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version  2.0.7
_pdbx_chem_comp_identifier.identifier       "[(2~{R},3~{S},5~{R})-5-[2,4-bis(oxidanylidene)-5-prop-1-ynyl-pyrimidin-1-yl]-3-oxidanyl-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
PDU  "Create component"    1999-07-08  EBI   
PDU  "Modify descriptor"   2011-06-04  RCSB  
PDU  "Other modification"  2021-07-21  RCSB  
##
