data_TDK
#

_chem_comp.id                                   TDK
_chem_comp.name                                 "3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-2-{(1S)-1-HYDROXY-1-[(R)-HYDROXY(METHOXY)PHOSPHORYL]ETHYL}-5-(2-{[(S)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-4-METHYL-1,3-THIAZOL-3-IUM"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C15 H26 N4 O11 P3 S"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "2-PHOSPHONOLACTYLTHIAMIN DIPHOSPHATE"
_chem_comp.pdbx_formal_charge                   1
_chem_comp.pdbx_initial_date                    2005-12-01
_chem_comp.pdbx_modified_date                   2021-03-01
_chem_comp.pdbx_ambiguous_flag                  ?
_chem_comp.pdbx_release_status                  REL
_chem_comp.pdbx_replaced_by                     ?
_chem_comp.pdbx_replaces                        ?
_chem_comp.formula_weight                       563.373
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    TDK
_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       2EZ9
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 PDBJ
#   #
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
TDK  O2B     O2B   O  0  1  N  N  N  85.396  59.796   2.252   8.191   1.676   0.642  O2B     TDK   1  
TDK  PB      PB    P  0  1  N  N  N  84.512  60.096   1.069   7.984   0.351  -0.249  PB      TDK   2  
TDK  O3B     O3B   O  0  1  N  N  N  85.297  60.265  -0.213   8.821   0.488  -1.617  O3B     TDK   3  
TDK  O1B     O1B   O  0  1  N  N  N  83.325  59.159   0.940   8.462  -0.830   0.505  O1B     TDK   4  
TDK  O3A     O3A   O  0  1  N  N  N  83.944  61.558   1.490   6.421   0.173  -0.591  O3A     TDK   5  
TDK  PA      PA    P  0  1  N  N  R  83.807  62.903   0.599   5.138  -0.306   0.256  PA      TDK   6  
TDK  O1A     O1A   O  0  1  N  N  N  84.974  63.034  -0.332   5.151   0.348   1.584  O1A     TDK   7  
TDK  O2A     O2A   O  0  1  N  N  N  83.527  64.051   1.540   5.186  -1.905   0.445  O2A     TDK   8  
TDK  O7      O7    O  0  1  N  N  N  82.507  62.636  -0.313   3.794   0.101  -0.530  O7      TDK   9  
TDK  C7      C7    C  0  1  N  N  N  81.181  62.605   0.252   2.486  -0.094   0.012  C7      TDK  10  
TDK  C6      C6    C  0  1  N  N  N  80.300  61.963  -0.809   1.440   0.400  -0.989  C6      TDK  11  
TDK  C5      C5    C  0  1  Y  N  N  78.784  62.097  -0.682   0.061   0.194  -0.418  C5      TDK  12  
TDK  S1      S1    S  0  1  Y  N  N  77.964  61.181   0.542  -0.938  -1.245  -0.611  S1      TDK  13  
TDK  C4      C4    C  0  1  Y  N  N  77.837  62.828  -1.403  -0.619   1.069   0.330  C4      TDK  14  
TDK  CM4     CM4   C  0  1  N  N  N  78.284  63.740  -2.531  -0.068   2.420   0.707  CM4     TDK  15  
TDK  N3      N3    N  1  1  Y  N  N  76.527  62.645  -1.006  -1.810   0.653   0.711  N3      TDK  16  
TDK  C2      C2    C  0  1  Y  N  N  76.403  61.765   0.040  -2.172  -0.524   0.327  C2      TDK  17  
TDK  CMA     CMA   C  0  1  N  N  S  75.068  61.293   0.629  -3.491  -1.172   0.661  CMA     TDK  18  
TDK  OM1     OM1   O  0  1  N  N  N  74.111  62.350   0.744  -4.551  -0.242   0.431  OM1     TDK  19  
TDK  CMB     CMB   C  0  1  N  N  N  75.247  60.637   2.000  -3.494  -1.594   2.132  CMB     TDK  20  
TDK  PC      PC    P  0  1  N  N  R  74.323  60.027  -0.514  -3.731  -2.640  -0.393  PC      TDK  21  
TDK  OM3     OM3   O  0  1  N  N  N  75.119  58.739  -0.487  -2.471  -3.629  -0.231  OM3     TDK  22  
TDK  OM2     OM2   O  0  1  N  N  N  72.886  59.581   0.101  -5.075  -3.407   0.053  OM2     TDK  23  
TDK  CMC     CMC   C  0  1  N  N  N  72.180  58.484  -0.492  -5.594  -4.539  -0.648  CMC     TDK  24  
TDK  OM4     OM4   O  0  1  N  N  N  74.072  60.594  -1.894  -3.849  -2.219  -1.806  OM4     TDK  25  
TDK  "C7'"   C7*   C  0  1  N  N  N  75.420  63.403  -1.621  -2.684   1.491   1.536  "C7'"   TDK  26  
TDK  "C5'"   C5*   C  0  1  Y  N  N  75.500  64.874  -1.130  -3.674   2.206   0.653  "C5'"   TDK  27  
TDK  "C6'"   C6*   C  0  1  Y  N  N  75.660  65.921  -2.060  -3.248   3.110  -0.300  "C6'"   TDK  28  
TDK  "N1'"   N1*   N  0  1  Y  N  N  75.737  67.213  -1.661  -4.147   3.721  -1.059  "N1'"   TDK  29  
TDK  "C2'"   C2*   C  0  1  Y  N  N  75.666  67.538  -0.353  -5.434   3.477  -0.917  "C2'"   TDK  30  
TDK  CM2     CM2   C  0  1  N  N  N  75.758  68.983   0.059  -6.418   4.196  -1.804  CM2     TDK  31  
TDK  "N3'"   N3*   N  0  1  Y  N  N  75.524  66.582   0.589  -5.885   2.622  -0.021  "N3'"   TDK  32  
TDK  "C4'"   C4*   C  0  1  Y  N  N  75.435  65.259   0.222  -5.044   1.967   0.774  "C4'"   TDK  33  
TDK  "N4'"   N4*   N  0  1  N  N  N  75.284  64.366   1.229  -5.521   1.065   1.712  "N4'"   TDK  34  
TDK  H2B     H2B   H  0  1  N  N  N  86.299  59.733   1.965   7.899   2.490   0.210  H2B     TDK  35  
TDK  H3B     H3B   H  0  1  N  N  N  84.698  60.300  -0.949   9.773   0.599  -1.487  H3B     TDK  36  
TDK  H2A     H2A   H  0  1  N  N  N  83.468  63.724   2.430   5.181  -2.399  -0.386  H2A     TDK  37  
TDK  H71     1H7   H  0  1  N  N  N  80.829  63.613   0.516   2.329  -1.154   0.209  H71     TDK  38  
TDK  H72     2H7   H  0  1  N  N  N  81.166  62.016   1.181   2.391   0.467   0.942  H72     TDK  39  
TDK  H61     1H6   H  0  1  N  N  N  80.488  60.884  -0.704   1.597   1.460  -1.187  H61     TDK  40  
TDK  H62     2H6   H  0  1  N  N  N  80.576  62.428  -1.767   1.535  -0.161  -1.920  H62     TDK  41  
TDK  HM41    1HM4  H  0  0  N  N  N  77.533  63.723  -3.335  -0.347   3.151  -0.052  HM41    TDK  42  
TDK  HM42    2HM4  H  0  0  N  N  N  79.250  63.391  -2.924  -0.476   2.723   1.671  HM42    TDK  43  
TDK  HM43    3HM4  H  0  0  N  N  N  78.392  64.767  -2.152   1.019   2.363   0.774  HM43    TDK  44  
TDK  HM1     HM1   H  0  1  N  N  N  73.899  62.487   1.660  -4.681  -0.017  -0.501  HM1     TDK  45  
TDK  HMB1    1HMB  H  0  0  N  N  N  74.398  60.902   2.647  -3.271  -0.731   2.758  HMB1    TDK  46  
TDK  HMB2    2HMB  H  0  0  N  N  N  76.182  60.993   2.457  -4.475  -1.990   2.395  HMB2    TDK  47  
TDK  HMB3    3HMB  H  0  0  N  N  N  75.290  59.544   1.881  -2.738  -2.363   2.291  HMB3    TDK  48  
TDK  HM3     HM3   H  0  1  N  N  N  75.286  58.451  -1.377  -2.333  -3.946   0.672  HM3     TDK  49  
TDK  HMC1    1HMC  H  0  0  N  N  N  71.218  58.346   0.023  -6.507  -4.881  -0.160  HMC1    TDK  50  
TDK  HMC2    2HMC  H  0  0  N  N  N  72.781  57.568  -0.398  -5.817  -4.258  -1.678  HMC2    TDK  51  
TDK  HMC3    3HMC  H  0  0  N  N  N  71.999  58.696  -1.556  -4.856  -5.340  -0.642  HMC3    TDK  52  
TDK  "H7'1"  1H7*  H  0  0  N  N  N  74.455  62.961  -1.333  -3.220   0.864   2.249  "H7'1"  TDK  53  
TDK  "H7'2"  2H7*  H  0  0  N  N  N  75.509  63.370  -2.717  -2.082   2.223   2.075  "H7'2"  TDK  54  
TDK  "H6'"   H6*   H  0  1  N  N  N  75.723  65.688  -3.113  -2.196   3.318  -0.425  "H6'"   TDK  55  
TDK  HM21    1HM2  H  0  0  N  N  N  74.884  69.530  -0.324  -6.588   3.610  -2.707  HM21    TDK  56  
TDK  HM22    2HM2  H  0  0  N  N  N  76.677  69.424  -0.354  -7.361   4.324  -1.271  HM22    TDK  57  
TDK  HM23    3HM2  H  0  0  N  N  N  75.780  69.051   1.157  -6.018   5.173  -2.074  HM23    TDK  58  
TDK  "H4'1"  1H4*  H  0  0  N  N  N  75.233  64.593   2.202  -4.920   0.419   2.112  "H4'1"  TDK  59  
TDK  "H4'2"  2H4*  H  0  0  N  N  N  75.231  63.444   0.846  -6.457   1.081   1.967  "H4'2"  TDK  60  
#   #
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
TDK  O2B    PB      SING  N  N   1  
TDK  O2B    H2B     SING  N  N   2  
TDK  PB     O3B     SING  N  N   3  
TDK  PB     O1B     DOUB  N  N   4  
TDK  PB     O3A     SING  N  N   5  
TDK  O3B    H3B     SING  N  N   6  
TDK  O3A    PA      SING  N  N   7  
TDK  PA     O1A     DOUB  N  N   8  
TDK  PA     O2A     SING  N  N   9  
TDK  PA     O7      SING  N  N  10  
TDK  O2A    H2A     SING  N  N  11  
TDK  O7     C7      SING  N  N  12  
TDK  C7     C6      SING  N  N  13  
TDK  C7     H71     SING  N  N  14  
TDK  C7     H72     SING  N  N  15  
TDK  C6     C5      SING  N  N  16  
TDK  C6     H61     SING  N  N  17  
TDK  C6     H62     SING  N  N  18  
TDK  C5     S1      SING  Y  N  19  
TDK  C5     C4      DOUB  Y  N  20  
TDK  S1     C2      SING  Y  N  21  
TDK  C4     CM4     SING  N  N  22  
TDK  C4     N3      SING  Y  N  23  
TDK  CM4    HM41    SING  N  N  24  
TDK  CM4    HM42    SING  N  N  25  
TDK  CM4    HM43    SING  N  N  26  
TDK  N3     C2      DOUB  Y  N  27  
TDK  N3     "C7'"   SING  N  N  28  
TDK  C2     CMA     SING  N  N  29  
TDK  CMA    OM1     SING  N  N  30  
TDK  CMA    CMB     SING  N  N  31  
TDK  CMA    PC      SING  N  N  32  
TDK  OM1    HM1     SING  N  N  33  
TDK  CMB    HMB1    SING  N  N  34  
TDK  CMB    HMB2    SING  N  N  35  
TDK  CMB    HMB3    SING  N  N  36  
TDK  PC     OM3     SING  N  N  37  
TDK  PC     OM2     SING  N  N  38  
TDK  PC     OM4     DOUB  N  N  39  
TDK  OM3    HM3     SING  N  N  40  
TDK  OM2    CMC     SING  N  N  41  
TDK  CMC    HMC1    SING  N  N  42  
TDK  CMC    HMC2    SING  N  N  43  
TDK  CMC    HMC3    SING  N  N  44  
TDK  "C7'"  "C5'"   SING  N  N  45  
TDK  "C7'"  "H7'1"  SING  N  N  46  
TDK  "C7'"  "H7'2"  SING  N  N  47  
TDK  "C5'"  "C6'"   DOUB  Y  N  48  
TDK  "C5'"  "C4'"   SING  Y  N  49  
TDK  "C6'"  "N1'"   SING  Y  N  50  
TDK  "C6'"  "H6'"   SING  N  N  51  
TDK  "N1'"  "C2'"   DOUB  Y  N  52  
TDK  "C2'"  CM2     SING  N  N  53  
TDK  "C2'"  "N3'"   SING  Y  N  54  
TDK  CM2    HM21    SING  N  N  55  
TDK  CM2    HM22    SING  N  N  56  
TDK  CM2    HM23    SING  N  N  57  
TDK  "N3'"  "C4'"   DOUB  Y  N  58  
TDK  "C4'"  "N4'"   SING  N  N  59  
TDK  "N4'"  "H4'1"  SING  N  N  60  
TDK  "N4'"  "H4'2"  SING  N  N  61  
#   #
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
TDK  SMILES            ACDLabs               10.04  "O=P(O)(O)OP(=O)(O)OCCc1sc([n+](c1C)Cc2cnc(nc2N)C)C(O)(P(=O)(OC)O)C"  
TDK  InChI             InChI                 1.03   "InChI=1S/C15H25N4O11P3S/c1-9-12(5-6-29-33(26,27)30-32(23,24)25)34-14(15(3,20)31(21,22)28-4)19(9)8-11-7-17-10(2)18-13(11)16/h7,20H,5-6,8H2,1-4H3,(H5-,16,17,18,21,22,23,24,25,26,27)/p+1/t15-/m0/s1"  
TDK  InChIKey          InChI                 1.03   ILGXNMPRCMTAOK-HNNXBMFYSA-O  
TDK  SMILES_CANONICAL  CACTVS                3.385  "CO[P](O)(=O)[C@](C)(O)c1sc(CCO[P](O)(=O)O[P](O)(O)=O)c(C)[n+]1Cc2cnc(C)nc2N"  
TDK  SMILES            CACTVS                3.385  "CO[P](O)(=O)[C](C)(O)c1sc(CCO[P](O)(=O)O[P](O)(O)=O)c(C)[n+]1Cc2cnc(C)nc2N"  
TDK  SMILES_CANONICAL  "OpenEye OEToolkits"  1.7.5  "Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@@](C)(O)[P@@](=O)(O)OC)CCO[P@@](=O)(O)OP(=O)(O)O"  
TDK  SMILES            "OpenEye OEToolkits"  1.7.5  "Cc1c(sc([n+]1Cc2cnc(nc2N)C)C(C)(O)P(=O)(O)OC)CCOP(=O)(O)OP(=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
TDK  "SYSTEMATIC NAME"  ACDLabs               10.04  "3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-2-{(1S)-1-hydroxy-1-[(R)-hydroxy(methoxy)phosphoryl]ethyl}-5-(2-{[(R)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3-thiazol-3-ium"  
TDK  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.5.0  "[(1S)-1-[3-[(4-amino-2-methyl-pyrimidin-5-yl)methyl]-5-[2-(hydroxy-phosphonooxy-phosphoryl)oxyethyl]-4-methyl-1,3-thiazol-3-ium-2-yl]-1-hydroxy-ethyl]-methoxy-phosphinic 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
TDK  "Create component"    2005-12-01  PDBJ  
TDK  "Modify descriptor"   2011-06-04  RCSB  
TDK  "Modify descriptor"   2012-01-05  RCSB  
TDK  "Modify coordinates"  2012-01-05  RCSB  
TDK  "Modify synonyms"     2021-03-01  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     TDK
_pdbx_chem_comp_synonyms.name        "2-PHOSPHONOLACTYLTHIAMIN DIPHOSPHATE"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
