data_DPB
#

_chem_comp.id                                   DPB
_chem_comp.name                                 "(S)-1-[2'-DEOXY-3',5'-O-(1-PHOSPHONO)BENZYLIDENE-B-D-THREO-PENTOFURANOSYL]THYMINE"
_chem_comp.type                                 "DNA LINKING"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C17 H19 N2 O8 P"
_chem_comp.mon_nstd_parent_comp_id              DT
_chem_comp.pdbx_synonyms                        DPB-T
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2003-09-17
_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                       410.315
_chem_comp.one_letter_code                      T
_chem_comp.three_letter_code                    DPB
_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       ?
_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
DPB  C11     C11   C  0  1  Y  N  N  15.733  41.697  23.918   0.652  -2.395  -0.497  C11     DPB   1  
DPB  C12     C12   C  0  1  Y  N  N  14.414  41.924  23.702  -0.204  -1.350  -0.792  C12     DPB   2  
DPB  C7      C7    C  0  1  Y  N  N  13.729  41.019  22.771  -1.104  -0.905   0.158  C7      DPB   3  
DPB  C8      C8    C  0  1  Y  N  N  14.409  39.916  22.108  -1.155  -1.511   1.400  C8      DPB   4  
DPB  C9      C9    C  0  1  Y  N  N  15.786  39.737  22.379  -0.302  -2.558   1.693  C9      DPB   5  
DPB  C10     C10   C  0  1  Y  N  N  16.548  40.577  23.271   0.602  -3.000   0.745  C10     DPB   6  
DPB  C2      C2    C  0  1  N  N  N   9.461  38.614  27.114   2.916   0.361   1.291  C2      DPB   7  
DPB  N1      N1    N  0  1  N  N  N  10.051  39.745  26.573   2.338   1.136   0.356  N1      DPB   8  
DPB  C6      C6    C  0  1  N  N  N  11.265  40.341  27.035   2.546   0.895  -0.975  C6      DPB   9  
DPB  C5      C5    C  0  1  N  N  N  11.830  39.655  28.127   3.340  -0.130  -1.352  C5      DPB  10  
DPB  C4      C4    C  0  1  N  N  N  11.177  38.464  28.670   3.938  -0.940  -0.358  C4      DPB  11  
DPB  N3      N3    N  0  1  N  N  N  10.065  38.000  28.166   3.711  -0.667   0.943  N3      DPB  12  
DPB  O2      O2    O  0  1  N  N  N   8.406  38.104  26.714   2.716   0.593   2.468  O2      DPB  13  
DPB  O4      O4    O  0  1  N  N  N  11.722  37.888  29.657   4.658  -1.870  -0.674  O4      DPB  14  
DPB  C5M     C5M   C  0  1  N  N  N  13.228  40.277  28.736   3.582  -0.411  -2.813  C5M     DPB  15  
DPB  "C1'"   C1*   C  0  1  N  N  S   9.339  40.366  25.454   1.476   2.249   0.765  "C1'"   DPB  16  
DPB  "O4'"   O4*   O  0  1  N  N  N   9.493  41.773  25.032   0.942   2.918  -0.380  "O4'"   DPB  17  
DPB  "C4'"   C4*   C  0  1  N  N  S   9.617  41.576  23.574  -0.437   2.546  -0.564  "C4'"   DPB  18  
DPB  "C3'"   C3*   C  0  1  N  N  S   9.586  40.535  22.994  -0.955   2.152   0.824  "C3'"   DPB  19  
DPB  "C2'"   C2*   C  0  1  N  N  N   9.465  39.760  24.179   0.297   1.723   1.605  "C2'"   DPB  20  
DPB  "C5'"   C5*   C  0  1  N  N  N  10.673  42.506  23.730  -0.481   1.343  -1.509  "C5'"   DPB  21  
DPB  "O5'"   O5*   O  0  1  N  N  N  11.750  41.700  23.743  -1.760   0.738  -1.461  "O5'"   DPB  22  
DPB  "C6'"   C6*   C  0  1  N  N  S  12.217  41.233  22.459  -2.035   0.237  -0.161  "C6'"   DPB  23  
DPB  "O3'"   O3*   O  0  1  N  N  N  10.913  40.290  22.395  -1.982   1.216   0.844  "O3'"   DPB  24  
DPB  P       P     P  0  1  N  N  N  12.126  42.651  21.108  -3.740  -0.452  -0.188  P       DPB  25  
DPB  OP2     O2P   O  0  1  N  N  N  12.776  41.746  19.977  -4.776   0.699  -0.629  OP2     DPB  26  
DPB  OP1     O1P   O  0  1  N  N  N  13.051  43.751  21.404  -4.095  -0.943   1.163  OP1     DPB  27  
DPB  OP3     O3P   O  0  1  N  Y  N  10.688  42.990  20.726  -3.811  -1.670  -1.237  OP3     DPB  28  
DPB  H11     H11   H  0  1  N  N  N  16.148  42.432  24.628   1.358  -2.739  -1.238  H11     DPB  29  
DPB  H12     H12   H  0  1  N  N  N  13.942  42.767  24.234  -0.165  -0.877  -1.762  H12     DPB  30  
DPB  H8      H8    H  0  1  N  N  N  13.892  39.231  21.415  -1.861  -1.166   2.141  H8      DPB  31  
DPB  H9      H9    H  0  1  N  N  N  16.291  38.900  21.869  -0.341  -3.031   2.663  H9      DPB  32  
DPB  H10     H10   H  0  1  N  N  N  17.622  40.386  23.438   1.269  -3.818   0.974  H10     DPB  33  
DPB  H6      H6    H  0  1  N  N  N  11.721  41.242  26.592   2.079   1.522  -1.720  H6      DPB  34  
DPB  H3      H3    H  0  1  N  N  N   9.670  37.162  28.592   4.120  -1.216   1.631  H3      DPB  35  
DPB  H71     1H5M  H  0  1  N  N  N  13.078  41.349  29.002   4.455   0.147  -3.151  H71     DPB  36  
DPB  H72     2H5M  H  0  1  N  N  N  13.675  39.734  29.601   3.756  -1.478  -2.954  H72     DPB  37  
DPB  H73     3H5M  H  0  1  N  N  N  13.983  40.374  27.921   2.709  -0.106  -3.391  H73     DPB  38  
DPB  "H1'"   H1*   H  0  1  N  N  N   8.399  40.226  26.037   2.063   2.953   1.364  "H1'"   DPB  39  
DPB  "H4'"   H4*   H  0  1  N  N  N   8.817  41.680  22.805  -1.020   3.383  -0.983  "H4'"   DPB  40  
DPB  "H3'"   H3*   H  0  1  N  N  N   8.838  40.391  22.180  -1.339   3.079   1.309  "H3'"   DPB  41  
DPB  "H2'"   1H2*  H  0  1  N  N  N   8.606  39.062  24.045   0.353   0.644   1.721  "H2'"   DPB  42  
DPB  "H2''"  2H2*  H  0  0  N  N  N  10.330  39.057  24.218   0.302   2.195   2.594  "H2''"  DPB  43  
DPB  "H5'"   1H5*  H  0  1  N  N  N  10.580  43.186  24.609   0.315   0.648  -1.275  "H5'"   DPB  44  
DPB  "H5''"  2H5*  H  0  0  N  N  N  10.701  43.322  22.971  -0.308   1.709  -2.533  "H5''"  DPB  45  
DPB  HOP2    2HOP  H  0  0  N  N  N  12.732  42.433  19.322  -4.510   0.990  -1.512  HOP2    DPB  46  
DPB  HOP3    3HOP  H  0  0  N  N  N  10.644  43.677  20.071  -4.719  -2.001  -1.220  HOP3    DPB  47  
#   #
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
DPB  C11    C12     DOUB  Y  N   1  
DPB  C11    C10     SING  Y  N   2  
DPB  C11    H11     SING  N  N   3  
DPB  C12    C7      SING  Y  N   4  
DPB  C12    H12     SING  N  N   5  
DPB  C7     C8      DOUB  Y  N   6  
DPB  C7     "C6'"   SING  N  N   7  
DPB  C8     C9      SING  Y  N   8  
DPB  C8     H8      SING  N  N   9  
DPB  C9     C10     DOUB  Y  N  10  
DPB  C9     H9      SING  N  N  11  
DPB  C10    H10     SING  N  N  12  
DPB  C2     N1      SING  N  N  13  
DPB  C2     N3      SING  N  N  14  
DPB  C2     O2      DOUB  N  N  15  
DPB  N1     C6      SING  N  N  16  
DPB  N1     "C1'"   SING  N  N  17  
DPB  C6     C5      DOUB  N  N  18  
DPB  C6     H6      SING  N  N  19  
DPB  C5     C4      SING  N  N  20  
DPB  C5     C5M     SING  N  N  21  
DPB  C4     N3      SING  N  N  22  
DPB  C4     O4      DOUB  N  N  23  
DPB  N3     H3      SING  N  N  24  
DPB  C5M    H71     SING  N  N  25  
DPB  C5M    H72     SING  N  N  26  
DPB  C5M    H73     SING  N  N  27  
DPB  "C1'"  "O4'"   SING  N  N  28  
DPB  "C1'"  "C2'"   SING  N  N  29  
DPB  "C1'"  "H1'"   SING  N  N  30  
DPB  "O4'"  "C4'"   SING  N  N  31  
DPB  "C4'"  "C3'"   SING  N  N  32  
DPB  "C4'"  "C5'"   SING  N  N  33  
DPB  "C4'"  "H4'"   SING  N  N  34  
DPB  "C3'"  "C2'"   SING  N  N  35  
DPB  "C3'"  "O3'"   SING  N  N  36  
DPB  "C3'"  "H3'"   SING  N  N  37  
DPB  "C2'"  "H2'"   SING  N  N  38  
DPB  "C2'"  "H2''"  SING  N  N  39  
DPB  "C5'"  "O5'"   SING  N  N  40  
DPB  "C5'"  "H5'"   SING  N  N  41  
DPB  "C5'"  "H5''"  SING  N  N  42  
DPB  "O5'"  "C6'"   SING  N  N  43  
DPB  "C6'"  "O3'"   SING  N  N  44  
DPB  "C6'"  P       SING  N  N  45  
DPB  P      OP2     SING  N  N  46  
DPB  P      OP1     DOUB  N  N  47  
DPB  P      OP3     SING  N  N  48  
DPB  OP2    HOP2    SING  N  N  49  
DPB  OP3    HOP3    SING  N  N  50  
#   #
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
DPB  SMILES            ACDLabs               10.04  "O=C1C(=CN(C(=O)N1)C4OC2C(OC(OC2)(c3ccccc3)P(=O)(O)O)C4)C"  
DPB  SMILES_CANONICAL  CACTVS                3.341  "CC1=CN([C@@H]2C[C@@H]3O[C@@](OC[C@@H]3O2)(c4ccccc4)[P](O)(O)=O)C(=O)NC1=O"  
DPB  SMILES            CACTVS                3.341  "CC1=CN([CH]2C[CH]3O[C](OC[CH]3O2)(c4ccccc4)[P](O)(O)=O)C(=O)NC1=O"  
DPB  SMILES_CANONICAL  "OpenEye OEToolkits"  1.5.0  "CC1=CN(C(=O)NC1=O)[C@@H]2C[C@H]3[C@@H](O2)CO[C@](O3)(c4ccccc4)P(=O)(O)O"  
DPB  SMILES            "OpenEye OEToolkits"  1.5.0  "CC1=CN(C(=O)NC1=O)C2CC3C(O2)COC(O3)(c4ccccc4)P(=O)(O)O"  
DPB  InChI             InChI                 1.03   "InChI=1S/C17H19N2O8P/c1-10-8-19(16(21)18-15(10)20)14-7-12-13(26-14)9-25-17(27-12,28(22,23)24)11-5-3-2-4-6-11/h2-6,8,12-14H,7,9H2,1H3,(H,18,20,21)(H2,22,23,24)/t12-,13-,14-,17-/m0/s1"  
DPB  InChIKey          InChI                 1.03   WTZFKHNHHRPQOU-WSMBLCCSSA-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
DPB  "SYSTEMATIC NAME"  ACDLabs               10.04  "1-{2-deoxy-3,5-O-[phenyl(phosphono)methylidene]-beta-L-threo-pentofuranosyl}-5-methylpyrimidine-2,4(1H,3H)-dione"  
DPB  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.5.0  "[(2S,4aS,6S,7aS)-6-(5-methyl-2,4-dioxo-pyrimidin-1-yl)-2-phenyl-4a,6,7,7a-tetrahydro-4H-furo[3,2-d][1,3]dioxin-2-yl]phosphonic acid"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
DPB  "Create component"   2003-09-17  RCSB  
DPB  "Modify descriptor"  2011-06-04  RCSB  
DPB  "Modify synonyms"    2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     DPB
_pdbx_chem_comp_synonyms.name        DPB-T
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
