data_T3Q
#

_chem_comp.id                                   T3Q
_chem_comp.name                                 "[(3R,4S,5S,6R)-4-amino-3,5-dihydroxy-6-methyloxan-2-yl][hydroxy-[[(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methoxy]phosphoryl] hydrogen phosphate"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C16 H27 N3 O14 P2"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "thymidine-5'-diphosphate-alpha-D-3,6-dideoxy-3-aminoglucose"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2009-02-02
_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                       547.345
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    T3Q
_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       3FSB
_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
T3Q  O4      O4    O  0  1  N  N  N  46.489   -8.906  -13.157  -7.027  -3.605   1.645  O4    T3Q   1  
T3Q  C4      C4    C  0  1  N  N  N  45.506   -9.114  -12.399  -6.480  -2.745   0.978  C4    T3Q   2  
T3Q  N3      N3    N  0  1  N  N  N  44.691  -10.213  -12.584  -6.067  -1.598   1.554  N3    T3Q   3  
T3Q  C2      C2    C  0  1  N  N  N  43.647  -10.401  -11.729  -5.463  -0.647   0.817  C2    T3Q   4  
T3Q  O2      O2    O  0  1  N  N  N  42.941  -11.373  -11.857  -5.095   0.382   1.350  O2    T3Q   5  
T3Q  C5      C5    C  0  1  N  N  N  45.207   -8.209  -11.323  -6.268  -2.942  -0.408  C5    T3Q   6  
T3Q  C5M     C5M   C  0  1  N  N  N  46.083   -7.009  -11.091  -6.715  -4.216  -1.075  C5M   T3Q   7  
T3Q  C6      C6    C  0  1  N  N  N  44.145   -8.425  -10.501  -5.660  -1.972  -1.123  C6    T3Q   8  
T3Q  N1      N1    N  0  1  N  N  N  43.358   -9.549  -10.712  -5.259  -0.820  -0.502  N1    T3Q   9  
T3Q  "C1'"   C1*   C  0  1  N  N  R  42.208   -9.858   -9.821  -4.599   0.232  -1.278  C1*   T3Q  10  
T3Q  "O4'"   O4*   O  0  1  N  N  N  41.717   -8.666   -9.169  -3.338   0.588  -0.671  O4*   T3Q  11  
T3Q  "C2'"   C2*   C  0  1  N  N  N  42.676  -10.794   -8.673  -5.435   1.531  -1.243  C2*   T3Q  12  
T3Q  "C3'"   C3*   C  0  1  N  N  S  41.817  -10.360   -7.447  -4.378   2.656  -1.178  C3*   T3Q  13  
T3Q  "O3'"   O3*   O  0  1  N  N  N  40.594  -11.109   -7.365  -4.480   3.506  -2.323  O3*   T3Q  14  
T3Q  "C4'"   C4*   C  0  1  N  N  R  41.516   -8.858   -7.716  -3.029   1.903  -1.181  C4*   T3Q  15  
T3Q  "C5'"   C5*   C  0  1  N  N  N  42.527   -7.965   -6.976  -2.024   2.607  -0.266  C5*   T3Q  16  
T3Q  "O5'"   O5*   O  0  1  N  N  N  43.868   -8.290   -7.386  -0.772   1.921  -0.317  O5*   T3Q  17  
T3Q  PA      PA    P  0  1  N  N  S  44.956   -7.154   -6.906   0.518   2.388   0.526  PA    T3Q  18  
T3Q  O1A     O1A   O  0  1  N  N  N  44.609   -5.807   -7.462   0.165   2.476   1.961  O1A   T3Q  19  
T3Q  O2A     O2A   O  0  1  N  N  N  46.381   -7.695   -7.446   1.007   3.830   0.004  O2A   T3Q  20  
T3Q  O3A     O3A   O  0  1  N  N  N  45.094   -7.090   -5.303   1.704   1.316   0.330  O3A   T3Q  21  
T3Q  PB      PB    P  0  1  N  N  S  44.890   -5.637   -4.582   3.037   0.959   1.159  PB    T3Q  22  
T3Q  O1B     O1B   O  0  1  N  N  N  43.557   -5.029   -4.815   2.655   0.031   2.418  O1B   T3Q  23  
T3Q  O2B     O2B   O  0  1  N  N  N  46.012   -4.521   -4.895   3.667   2.209   1.641  O2B   T3Q  24  
T3Q  O3B     O3B   O  0  1  N  N  N  45.014   -6.128   -3.071   4.067   0.172   0.205  O3B   T3Q  25  
T3Q  O4Q     O4Q   O  0  1  N  N  N  45.290   -6.381    1.445   5.243  -3.625  -1.757  O4Q   T3Q  26  
T3Q  C4Q     C4Q   C  0  1  N  N  S  46.129   -6.456    0.275   5.768  -2.636  -0.869  C4Q   T3Q  27  
T3Q  C5Q     C5Q   C  0  1  N  N  R  45.980   -5.203   -0.627   4.863  -2.518   0.359  C5Q   T3Q  28  
T3Q  O5Q     O5Q   O  0  1  N  N  N  46.863   -5.320   -1.759   5.358  -1.488   1.217  O5Q   T3Q  29  
T3Q  C6Q     C6Q   C  0  1  N  N  N  46.359   -3.920    0.137   4.851  -3.849   1.114  C6Q   T3Q  30  
T3Q  C3Q     C3Q   C  0  1  N  N  S  45.707   -7.665   -0.555   5.824  -1.283  -1.586  C3Q   T3Q  31  
T3Q  N3Q     N3Q   N  0  1  N  N  N  45.807   -8.888    0.260   6.750  -1.367  -2.723  N3Q   T3Q  32  
T3Q  C2Q     C2Q   C  0  1  N  N  R  46.585   -7.709   -1.823   6.314  -0.216  -0.603  C2Q   T3Q  33  
T3Q  O2Q     O2Q   O  0  1  N  N  N  46.235   -8.799   -2.670   6.303   1.062  -1.240  O2Q   T3Q  34  
T3Q  C1Q     C1Q   C  0  1  N  N  R  46.412   -6.387   -2.595   5.387  -0.192   0.616  C1Q   T3Q  35  
T3Q  HN3     HN3   H  0  1  N  N  N  44.863  -10.857  -13.329  -6.206  -1.457   2.504  HN3   T3Q  36  
T3Q  H5M     H5M   H  0  1  N  N  N  46.297   -6.913  -10.016  -7.181  -4.869  -0.337  H5M   T3Q  37  
T3Q  H5MA    H5MA  H  0  0  N  N  N  47.027   -7.132  -11.643  -7.436  -3.983  -1.859  H5MA  T3Q  38  
T3Q  H5MB    H5MB  H  0  0  N  N  N  45.566   -6.104  -11.444  -5.853  -4.720  -1.512  H5MB  T3Q  39  
T3Q  H6      H6    H  0  1  N  N  N  43.919   -7.736   -9.701  -5.489  -2.105  -2.182  H6    T3Q  40  
T3Q  "H1'"   H1*   H  0  1  N  N  N  41.428  -10.315  -10.448  -4.446  -0.096  -2.307  H1*   T3Q  41  
T3Q  "H2'"   H2*   H  0  1  N  N  N  42.504  -11.851   -8.926  -6.035   1.623  -2.148  H2*   T3Q  42  
T3Q  "H2'A"  H2*A  H  0  0  N  N  N  43.755  -10.709   -8.478  -6.071   1.552  -0.358  H2*A  T3Q  43  
T3Q  "H3'"   H3*   H  0  1  N  N  N  42.338  -10.535   -6.494  -4.492   3.235  -0.262  H3*   T3Q  44  
T3Q  "HO3'"  HO3*  H  0  0  N  N  N  40.384  -11.274   -6.453  -5.332   3.957  -2.403  HO3*  T3Q  45  
T3Q  "H4'"   H4*   H  0  1  N  N  N  40.502   -8.595   -7.379  -2.635   1.834  -2.196  H4*   T3Q  46  
T3Q  "H5'"   H5*   H  0  1  N  N  N  42.321   -6.911   -7.213  -1.888   3.636  -0.599  H5*   T3Q  47  
T3Q  "H5'A"  H5*A  H  0  0  N  N  N  42.431   -8.133   -5.893  -2.400   2.603   0.757  H5*A  T3Q  48  
T3Q  HO2A    HO2A  H  0  0  N  N  N  46.343   -7.801   -8.389   1.255   3.847  -0.930  HO2A  T3Q  49  
T3Q  HO1B    HO1B  H  0  0  N  N  N  43.118   -4.899   -3.983   2.236  -0.807   2.176  HO1B  T3Q  50  
T3Q  HO4Q    HO4Q  H  0  0  N  N  N  45.833   -6.365    2.224   5.177  -4.508  -1.367  HO4Q  T3Q  51  
T3Q  H4Q     H4Q   H  0  1  N  N  N  47.172   -6.530    0.618   6.772  -2.924  -0.556  H4Q   T3Q  52  
T3Q  H5Q     H5Q   H  0  1  N  N  N  44.930   -5.141   -0.948   3.849  -2.271   0.042  H5Q   T3Q  53  
T3Q  H6Q     H6Q   H  0  1  N  N  N  46.449   -4.145    1.210   5.864  -4.095   1.432  H6Q   T3Q  54  
T3Q  H6QA    H6QA  H  0  0  N  N  N  47.320   -3.539   -0.240   4.206  -3.765   1.989  H6QA  T3Q  55  
T3Q  H6QB    H6QB  H  0  0  N  N  N  45.578   -3.160   -0.014   4.474  -4.635   0.459  H6QB  T3Q  56  
T3Q  H3Q     H3Q   H  0  1  N  N  N  44.656   -7.589   -0.872   4.829  -1.020  -1.945  H3Q   T3Q  57  
T3Q  HN3Q    HN3Q  H  0  0  N  N  N  45.830   -9.688   -0.340   6.804  -0.486  -3.212  HN3Q  T3Q  58  
T3Q  HN3A    HN3A  H  0  0  N  N  N  46.644   -8.857    0.806   7.665  -1.670  -2.422  HN3A  T3Q  59  
T3Q  H2Q     H2Q   H  0  1  N  N  N  47.632   -7.846   -1.514   7.329  -0.455  -0.283  H2Q   T3Q  60  
T3Q  HO2Q    HO2Q  H  0  0  N  N  N  46.157   -8.492   -3.566   6.602   1.787  -0.674  HO2Q  T3Q  61  
T3Q  H1Q     H1Q   H  0  1  N  N  N  47.014   -6.460   -3.513   5.755   0.536   1.339  H1Q   T3Q  62  
#   #
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
T3Q  O4     C4      DOUB  N  N   1  
T3Q  N3     C4      SING  N  N   2  
T3Q  C4     C5      SING  N  N   3  
T3Q  N3     C2      SING  N  N   4  
T3Q  N3     HN3     SING  N  N   5  
T3Q  O2     C2      DOUB  N  N   6  
T3Q  C2     N1      SING  N  N   7  
T3Q  C5     C5M     SING  N  N   8  
T3Q  C5     C6      DOUB  N  N   9  
T3Q  C5M    H5M     SING  N  N  10  
T3Q  C5M    H5MA    SING  N  N  11  
T3Q  C5M    H5MB    SING  N  N  12  
T3Q  N1     C6      SING  N  N  13  
T3Q  C6     H6      SING  N  N  14  
T3Q  N1     "C1'"   SING  N  N  15  
T3Q  "C1'"  "O4'"   SING  N  N  16  
T3Q  "C1'"  "C2'"   SING  N  N  17  
T3Q  "C1'"  "H1'"   SING  N  N  18  
T3Q  "O4'"  "C4'"   SING  N  N  19  
T3Q  "C2'"  "C3'"   SING  N  N  20  
T3Q  "C2'"  "H2'"   SING  N  N  21  
T3Q  "C2'"  "H2'A"  SING  N  N  22  
T3Q  "C4'"  "C3'"   SING  N  N  23  
T3Q  "C3'"  "O3'"   SING  N  N  24  
T3Q  "C3'"  "H3'"   SING  N  N  25  
T3Q  "O3'"  "HO3'"  SING  N  N  26  
T3Q  "C4'"  "C5'"   SING  N  N  27  
T3Q  "C4'"  "H4'"   SING  N  N  28  
T3Q  "O5'"  "C5'"   SING  N  N  29  
T3Q  "C5'"  "H5'"   SING  N  N  30  
T3Q  "C5'"  "H5'A"  SING  N  N  31  
T3Q  "O5'"  PA      SING  N  N  32  
T3Q  O1A    PA      DOUB  N  N  33  
T3Q  O2A    PA      SING  N  N  34  
T3Q  PA     O3A     SING  N  N  35  
T3Q  O2A    HO2A    SING  N  N  36  
T3Q  O3A    PB      SING  N  N  37  
T3Q  O2B    PB      DOUB  N  N  38  
T3Q  O1B    PB      SING  N  N  39  
T3Q  PB     O3B     SING  N  N  40  
T3Q  O1B    HO1B    SING  N  N  41  
T3Q  O3B    C1Q     SING  N  N  42  
T3Q  C4Q    O4Q     SING  N  N  43  
T3Q  O4Q    HO4Q    SING  N  N  44  
T3Q  C5Q    C4Q     SING  N  N  45  
T3Q  C3Q    C4Q     SING  N  N  46  
T3Q  C4Q    H4Q     SING  N  N  47  
T3Q  O5Q    C5Q     SING  N  N  48  
T3Q  C5Q    C6Q     SING  N  N  49  
T3Q  C5Q    H5Q     SING  N  N  50  
T3Q  C1Q    O5Q     SING  N  N  51  
T3Q  C6Q    H6Q     SING  N  N  52  
T3Q  C6Q    H6QA    SING  N  N  53  
T3Q  C6Q    H6QB    SING  N  N  54  
T3Q  C2Q    C3Q     SING  N  N  55  
T3Q  C3Q    N3Q     SING  N  N  56  
T3Q  C3Q    H3Q     SING  N  N  57  
T3Q  N3Q    HN3Q    SING  N  N  58  
T3Q  N3Q    HN3A    SING  N  N  59  
T3Q  O2Q    C2Q     SING  N  N  60  
T3Q  C1Q    C2Q     SING  N  N  61  
T3Q  C2Q    H2Q     SING  N  N  62  
T3Q  O2Q    HO2Q    SING  N  N  63  
T3Q  C1Q    H1Q     SING  N  N  64  
#   #
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
T3Q  SMILES            ACDLabs               10.04  "O=P(OC1OC(C(O)C(N)C1O)C)(O)OP(=O)(O)OCC3OC(N2C=C(C(=O)NC2=O)C)CC3O"  
T3Q  SMILES_CANONICAL  CACTVS                3.341  "C[C@H]1O[C@H](O[P@@](O)(=O)O[P@](O)(=O)OC[C@H]2O[C@H](C[C@@H]2O)N3C=C(C)C(=O)NC3=O)[C@H](O)[C@@H](N)[C@@H]1O"  
T3Q  SMILES            CACTVS                3.341  "C[CH]1O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH](C[CH]2O)N3C=C(C)C(=O)NC3=O)[CH](O)[CH](N)[CH]1O"  
T3Q  SMILES_CANONICAL  "OpenEye OEToolkits"  1.5.0  "C[C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]2[C@H](C[C@@H](O2)N3C=C(C(=O)NC3=O)C)O)O)N)O"  
T3Q  SMILES            "OpenEye OEToolkits"  1.5.0  "CC1C(C(C(C(O1)OP(=O)(O)OP(=O)(O)OCC2C(CC(O2)N3C=C(C(=O)NC3=O)C)O)O)N)O"  
T3Q  InChI             InChI                 1.03   "InChI=1S/C16H27N3O14P2/c1-6-4-19(16(24)18-14(6)23)10-3-8(20)9(31-10)5-29-34(25,26)33-35(27,28)32-15-13(22)11(17)12(21)7(2)30-15/h4,7-13,15,20-22H,3,5,17H2,1-2H3,(H,25,26)(H,27,28)(H,18,23,24)/t7-,8+,9-,10-,11+,12-,13-,15-/m1/s1"  
T3Q  InChIKey          InChI                 1.03   KVYJLJOGNUNRJK-HALQBZCBSA-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
T3Q  "SYSTEMATIC NAME"  ACDLabs               10.04  "(2R,3R,4S,5S,6R)-4-amino-3,5-dihydroxy-6-methyltetrahydro-2H-pyran-2-yl [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)tetrahydrofuran-2-yl]methyl dihydrogen diphosphate (non-preferred name)"  
T3Q  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.5.0  "[[(2R,3R,4S,5S,6R)-4-amino-3,5-dihydroxy-6-methyl-oxan-2-yl]oxy-hydroxy-phosphoryl] [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl hydrogen 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
T3Q  "Create component"   2009-02-02  RCSB  
T3Q  "Modify descriptor"  2011-06-04  RCSB  
T3Q  "Modify synonyms"    2021-03-13  RCSB  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     T3Q
_pdbx_chem_comp_synonyms.name        "thymidine-5'-diphosphate-alpha-D-3,6-dideoxy-3-aminoglucose"
_pdbx_chem_comp_synonyms.provenance  PDB
_pdbx_chem_comp_synonyms.type        ?
##
