data_2DT
#

_chem_comp.id                                   2DT
_chem_comp.name                                 "3'-DEOXYTHYMIDINE-5'-MONOPHOSPHATE"
_chem_comp.type                                 "DNA LINKING"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C10 H15 N2 O7 P"
_chem_comp.mon_nstd_parent_comp_id              DT
_chem_comp.pdbx_synonyms                        "2',3'-DIDEOXYTHYMIDINE-5'-MONOPHOSPHATE"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    1999-07-07
_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                       306.209
_chem_comp.one_letter_code                      T
_chem_comp.three_letter_code                    2DT
_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       3BDP
_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
2DT  P       P     P  0  1  N  N  N  17.858  46.724  34.563   0.760  -0.138  -4.202  P       2DT   1  
2DT  OP1     O1P   O  0  1  N  N  N  18.351  46.697  35.969   1.665   0.929  -3.722  OP1     2DT   2  
2DT  OP2     O2P   O  0  1  N  N  N  17.623  48.032  33.871   1.622  -1.286  -4.930  OP2     2DT   3  
2DT  OP3     O3P   O  0  1  N  Y  N  18.962  45.940  33.719  -0.296   0.483  -5.246  OP3     2DT   4  
2DT  "O5'"   O5*   O  0  1  N  N  N  16.532  45.853  34.412  -0.031  -0.772  -2.952  "O5'"   2DT   5  
2DT  N1      N1    N  0  1  N  N  N  15.120  42.269  35.391  -0.529  -0.306   2.235  N1      2DT   6  
2DT  C6      C6    C  0  1  N  N  N  16.065  43.061  36.008  -0.372  -1.162   3.291  C6      2DT   7  
2DT  C2      C2    C  0  1  N  N  N  14.891  40.973  35.808   0.107   0.878   2.213  C2      2DT   8  
2DT  O2      O2    O  0  1  N  N  N  14.031  40.268  35.320  -0.047   1.624   1.266  O2      2DT   9  
2DT  N3      N3    N  0  1  N  N  N  15.694  40.545  36.847   0.913   1.249   3.225  N3      2DT  10  
2DT  C4      C4    C  0  1  N  N  N  16.648  41.276  37.517   1.091   0.435   4.286  C4      2DT  11  
2DT  O4      O4    O  0  1  N  N  N  17.267  40.769  38.444   1.820   0.770   5.202  O4      2DT  12  
2DT  C5      C5    C  0  1  N  N  N  16.826  42.644  37.039   0.430  -0.815   4.320  C5      2DT  13  
2DT  C5M     C5M   C  0  1  N  N  N  17.838  43.518  37.714   0.616  -1.745   5.491  C5M     2DT  14  
2DT  "C2'"   C2*   C  0  1  N  N  N  13.122  43.666  34.603  -2.533   0.350   0.967  "C2'"   2DT  15  
2DT  "C5'"   C5*   C  0  1  N  N  N  15.781  45.861  33.177  -0.773   0.289  -2.351  "C5'"   2DT  16  
2DT  "C4'"   C4*   C  0  1  N  N  S  14.637  44.873  33.227  -1.553  -0.248  -1.149  "C4'"   2DT  17  
2DT  "O4'"   O4*   O  0  1  N  N  N  15.184  43.555  33.429  -0.651  -0.683  -0.106  "O4'"   2DT  18  
2DT  "C1'"   C1*   C  0  1  N  N  R  14.322  42.783  34.256  -1.401  -0.682   1.119  "C1'"   2DT  19  
2DT  "C3'"   C3*   C  0  1  N  N  N  13.626  45.074  34.352  -2.369   0.883  -0.476  "C3'"   2DT  20  
2DT  HOP2    2HOP  H  0  0  N  N  N  17.308  48.049  32.974   2.079  -0.865  -5.671  HOP2    2DT  21  
2DT  HOP3    3HOP  H  0  0  N  N  N  18.647  45.957  32.822  -0.865  -0.243  -5.534  HOP3    2DT  22  
2DT  H6      H6    H  0  1  N  N  N  16.222  44.093  35.654  -0.887  -2.112   3.301  H6      2DT  23  
2DT  HN3     HN3   H  0  1  N  N  N  15.568  39.580  37.154   1.365   2.107   3.193  HN3     2DT  24  
2DT  H71     1H5M  H  0  1  N  N  N  18.467  43.173  38.567   1.295  -1.290   6.212  H71     2DT  25  
2DT  H72     2H5M  H  0  1  N  N  N  18.526  43.900  36.925  -0.347  -1.929   5.965  H72     2DT  26  
2DT  H73     3H5M  H  0  1  N  N  N  17.311  44.444  38.041   1.035  -2.689   5.142  H73     2DT  27  
2DT  "H2'"   1H2*  H  0  1  N  N  N  12.186  43.407  34.054  -3.505  -0.127   1.089  "H2'"   2DT  28  
2DT  "H2''"  2H2*  H  0  0  N  N  N  12.709  43.500  35.625  -2.412   1.159   1.688  "H2''"  2DT  29  
2DT  "H5'"   1H5*  H  0  1  N  N  N  15.426  46.886  32.919  -1.470   0.704  -3.080  "H5'"   2DT  30  
2DT  "H5''"  2H5*  H  0  0  N  N  N  16.439  45.681  32.295  -0.088   1.069  -2.019  "H5''"  2DT  31  
2DT  "H4'"   H4*   H  0  1  N  N  N  14.096  45.020  32.263  -2.208  -1.065  -1.453  "H4'"   2DT  32  
2DT  "H1'"   H1*   H  0  1  N  N  N  13.897  41.873  33.770  -1.823  -1.672   1.296  "H1'"   2DT  33  
2DT  "H3'1"  1H3*  H  0  0  N  N  N  12.829  45.823  34.136  -3.339   1.004  -0.959  "H3'1"  2DT  34  
2DT  "H3'2"  2H3*  H  0  0  N  N  N  14.026  45.594  35.253  -1.813   1.821  -0.484  "H3'2"  2DT  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
2DT  P      OP1     DOUB  N  N   1  
2DT  P      OP2     SING  N  N   2  
2DT  P      OP3     SING  N  N   3  
2DT  P      "O5'"   SING  N  N   4  
2DT  OP2    HOP2    SING  N  N   5  
2DT  OP3    HOP3    SING  N  N   6  
2DT  "O5'"  "C5'"   SING  N  N   7  
2DT  N1     C6      SING  N  N   8  
2DT  N1     C2      SING  N  N   9  
2DT  N1     "C1'"   SING  N  N  10  
2DT  C6     C5      DOUB  N  N  11  
2DT  C6     H6      SING  N  N  12  
2DT  C2     O2      DOUB  N  N  13  
2DT  C2     N3      SING  N  N  14  
2DT  N3     C4      SING  N  N  15  
2DT  N3     HN3     SING  N  N  16  
2DT  C4     O4      DOUB  N  N  17  
2DT  C4     C5      SING  N  N  18  
2DT  C5     C5M     SING  N  N  19  
2DT  C5M    H71     SING  N  N  20  
2DT  C5M    H72     SING  N  N  21  
2DT  C5M    H73     SING  N  N  22  
2DT  "C2'"  "C1'"   SING  N  N  23  
2DT  "C2'"  "C3'"   SING  N  N  24  
2DT  "C2'"  "H2'"   SING  N  N  25  
2DT  "C2'"  "H2''"  SING  N  N  26  
2DT  "C5'"  "C4'"   SING  N  N  27  
2DT  "C5'"  "H5'"   SING  N  N  28  
2DT  "C5'"  "H5''"  SING  N  N  29  
2DT  "C4'"  "O4'"   SING  N  N  30  
2DT  "C4'"  "C3'"   SING  N  N  31  
2DT  "C4'"  "H4'"   SING  N  N  32  
2DT  "O4'"  "C1'"   SING  N  N  33  
2DT  "C1'"  "H1'"   SING  N  N  34  
2DT  "C3'"  "H3'1"  SING  N  N  35  
2DT  "C3'"  "H3'2"  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
2DT  SMILES            ACDLabs               10.04  "O=C1NC(=O)N(C=C1C)C2OC(CC2)COP(=O)(O)O"  
2DT  SMILES_CANONICAL  CACTVS                3.341  "CC1=CN([C@H]2CC[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O"  
2DT  SMILES            CACTVS                3.341  "CC1=CN([CH]2CC[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O"  
2DT  SMILES_CANONICAL  "OpenEye OEToolkits"  1.5.0  "CC1=CN(C(=O)NC1=O)[C@H]2CC[C@H](O2)COP(=O)(O)O"  
2DT  SMILES            "OpenEye OEToolkits"  1.5.0  "CC1=CN(C(=O)NC1=O)C2CCC(O2)COP(=O)(O)O"  
2DT  InChI             InChI                 1.03   "InChI=1S/C10H15N2O7P/c1-6-4-12(10(14)11-9(6)13)8-3-2-7(19-8)5-18-20(15,16)17/h4,7-8H,2-3,5H2,1H3,(H,11,13,14)(H2,15,16,17)/t7-,8+/m0/s1"  
2DT  InChIKey          InChI                 1.03   WVNRRNJFRREKAR-JGVFFNPUSA-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
2DT  "SYSTEMATIC NAME"  ACDLabs               10.04  "[(2S,5R)-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl dihydrogen phosphate"  
2DT  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.5.0  "[(2S,5R)-5-(5-methyl-2,4-dioxo-pyrimidin-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
2DT  "Create component"   1999-07-07  RCSB  
2DT  "Modify descriptor"  2011-06-04  RCSB  
2DT  "Modify synonyms"    2021-03-13  RCSB  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     2DT
_pdbx_chem_comp_synonyms.name        "2',3'-DIDEOXYTHYMIDINE-5'-MONOPHOSPHATE"
_pdbx_chem_comp_synonyms.provenance  PDB
_pdbx_chem_comp_synonyms.type        ?
##