data_R1T
#

_chem_comp.id                                   R1T
_chem_comp.name                                 "2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-[(1R)-1-HYDROXYETHYL]-3-METHYL-2-THIENYL}ETHYL TRIHYDROGEN DIPHOSPHATE"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C15 H23 N3 O8 P2 S"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "2-[(1R)-1-HYDROXYETHYL]-3-DEAZA-THDP"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2007-06-18
_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                       467.371
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    R1T
_chem_comp.pdbx_model_coordinates_details       ?
_chem_comp.pdbx_model_coordinates_missing_flag  N
_chem_comp.pdbx_ideal_coordinates_details       "Corina V3.40"
_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
R1T  "N1'"   "N1'"   N  0  1  Y  N  N  -20.848  -10.387  17.297   3.704  -2.414   1.094  "N1'"   R1T   1  
R1T  "C2'"   "C2'"   C  0  1  Y  N  N  -21.310   -9.970  18.488   4.761  -3.167   0.861  "C2'"   R1T   2  
R1T  CM2     CM2     C  0  1  N  N  N  -22.018  -10.949  19.385   4.942  -4.439   1.649  CM2     R1T   3  
R1T  "N3'"   "N3'"   N  0  1  Y  N  N  -21.146   -8.696  18.891   5.662  -2.839  -0.042  "N3'"   R1T   4  
R1T  "C4'"   "C4'"   C  0  1  Y  N  N  -20.498   -7.765  18.087   5.534  -1.724  -0.756  "C4'"   R1T   5  
R1T  "N4'"   "N4'"   N  0  1  N  N  N  -20.351   -6.488  18.535   6.484  -1.382  -1.704  "N4'"   R1T   6  
R1T  "C5'"   "C5'"   C  0  1  Y  N  N  -19.991   -8.188  16.782   4.426  -0.904  -0.534  "C5'"   R1T   7  
R1T  "C6'"   "C6'"   C  0  1  Y  N  N  -20.194   -9.541  16.443   3.507  -1.289   0.423  "C6'"   R1T   8  
R1T  "C7'"   "C7'"   C  0  1  N  N  N  -19.205   -7.273  15.776   4.238   0.369  -1.318  "C7'"   R1T   9  
R1T  C3      C3      C  0  1  Y  N  N  -19.993   -6.028  15.253   3.043   1.116  -0.784  C3      R1T  10  
R1T  C2      C2      C  0  1  Y  N  N  -19.698   -4.775  15.690   3.135   1.995   0.215  C2      R1T  11  
R1T  S1      S1      S  0  1  Y  N  N  -20.735   -3.732  14.816   1.545   2.662   0.563  S1      R1T  12  
R1T  C5      C5      C  0  1  Y  N  N  -21.616   -4.935  13.869   0.824   1.681  -0.706  C5      R1T  13  
R1T  C4      C4      C  0  1  Y  N  N  -20.991   -6.136  14.258   1.768   0.947  -1.296  C4      R1T  14  
R1T  CM4     CM4     C  0  1  N  N  N  -21.396   -7.487  13.620   1.470   0.001  -2.431  CM4     R1T  15  
R1T  C6      C6      C  0  1  N  N  N  -22.702   -4.654  12.876  -0.638   1.675  -1.074  C6      R1T  16  
R1T  C7      C7      C  0  1  N  N  N  -24.074   -4.554  13.575  -1.368   0.615  -0.247  C7      R1T  17  
R1T  O7      O7      O  0  1  N  N  N  -25.042   -4.479  12.540  -2.754   0.610  -0.596  O7      R1T  18  
R1T  PA      PA      P  0  1  N  N  S  -26.480   -4.030  13.122  -3.825  -0.384   0.082  PA      R1T  19  
R1T  O1A     O1A     O  0  1  N  N  N  -26.908   -4.884  14.274  -3.781  -0.227   1.553  O1A     R1T  20  
R1T  O2A     O2A     O  0  1  N  N  N  -27.506   -4.242  11.937  -3.467  -1.904  -0.307  O2A     R1T  21  
R1T  O3A     O3A     O  0  1  N  N  N  -26.546   -2.477  13.596  -5.301  -0.026  -0.453  O3A     R1T  22  
R1T  PB      PB      P  0  1  N  N  N  -25.917   -1.348  12.541  -6.788  -0.321   0.089  PB      R1T  23  
R1T  O1B     O1B     O  0  1  N  N  N  -26.421   -1.622  11.102  -6.847  -0.046   1.542  O1B     R1T  24  
R1T  O2B     O2B     O  0  1  N  N  N  -26.439    0.047  13.063  -7.837   0.628  -0.680  O2B     R1T  25  
R1T  O3B     O3B     O  0  1  N  N  N  -24.377   -1.326  12.573  -7.162  -1.863  -0.181  O3B     R1T  26  
R1T  CP1     CP1     C  0  1  N  N  R  -18.601   -4.307  16.676   4.407   2.361   0.937  CP1     R1T  27  
R1T  CP2     CP2     C  0  1  N  N  N  -18.224   -2.828  16.383   4.875   3.743   0.477  CP2     R1T  28  
R1T  OP1     OP1     O  0  1  N  N  N  -19.023   -4.475  18.010   4.166   2.383   2.345  OP1     R1T  29  
R1T  HP1     HP1     H  0  1  N  N  N  -18.264   -4.513  18.580   3.490   3.019   2.619  HP1     R1T  30  
R1T  H1      H1      H  0  1  N  N  N  -17.704   -4.928  16.534   5.177   1.623   0.711  H1      R1T  31  
R1T  H61     1H6     H  0  1  N  N  N  -22.487   -3.701  12.370  -1.068   2.655  -0.871  H61     R1T  32  
R1T  H62     2H6     H  0  1  N  N  N  -22.736   -5.478  12.149  -0.744   1.444  -2.135  H62     R1T  33  
R1T  H71     1H7     H  0  1  N  N  N  -24.251   -5.437  14.207  -0.938  -0.365  -0.450  H71     R1T  34  
R1T  H72     2H7     H  0  1  N  N  N  -24.124   -3.673  14.232  -1.262   0.846   0.814  H72     R1T  35  
R1T  H2A     H2A     H  0  1  N  N  N  -28.389   -4.285  12.286  -3.476  -2.080  -1.258  H2A     R1T  36  
R1T  H2B     H2B     H  0  1  N  N  N  -26.544    0.013  14.007  -8.755   0.505  -0.403  H2B     R1T  37  
R1T  H3B     H3B     H  0  1  N  N  N  -24.041   -1.321  11.684  -7.143  -2.115  -1.115  H3B     R1T  38  
R1T  HM41    1HM4    H  0  0  N  N  N  -21.492   -7.365  12.531   1.314  -1.002  -2.036  HM41    R1T  39  
R1T  HM42    2HM4    H  0  0  N  N  N  -20.625   -8.241  13.838   0.571   0.331  -2.951  HM42    R1T  40  
R1T  HM43    3HM4    H  0  0  N  N  N  -22.359   -7.816  14.038   2.309  -0.009  -3.126  HM43    R1T  41  
R1T  "H7'1"  "1H7'"  H  0  0  N  N  N  -18.307   -6.905  16.293   5.128   0.990  -1.222  "H7'1"  R1T  42  
R1T  "H7'2"  "2H7'"  H  0  0  N  N  N  -18.992   -7.896  14.895   4.075   0.128  -2.369  "H7'2"  R1T  43  
R1T  "H6'"   "H6'"   H  0  1  N  N  N  -19.829   -9.915  15.498   2.637  -0.679   0.622  "H6'"   R1T  44  
R1T  HM21    1HM2    H  0  0  N  N  N  -22.191  -11.888  18.839   4.459  -5.263   1.124  HM21    R1T  45  
R1T  HM22    2HM2    H  0  0  N  N  N  -21.398  -11.149  20.271   6.006  -4.650   1.757  HM22    R1T  46  
R1T  HM23    3HM2    H  0  0  N  N  N  -22.983  -10.526  19.700   4.493  -4.323   2.635  HM23    R1T  47  
R1T  "H4'1"  "1H4'"  H  0  0  N  N  N  -20.315   -6.487  19.534   7.290  -1.913  -1.797  "H4'1"  R1T  48  
R1T  "H4'2"  "2H4'"  H  0  0  N  N  N  -19.503   -6.103  18.171   6.342  -0.612  -2.277  "H4'2"  R1T  49  
R1T  HP21    1HP2    H  0  0  N  N  N  -18.135   -2.277  17.331   4.104   4.481   0.702  HP21    R1T  50  
R1T  HP22    2HP2    H  0  0  N  N  N  -17.264   -2.794  15.848   5.795   4.007   0.999  HP22    R1T  51  
R1T  HP23    3HP2    H  0  0  N  N  N  -19.007   -2.366  15.763   5.058   3.726  -0.597  HP23    R1T  52  
#   #
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
R1T  "N1'"  "C2'"   SING  Y  N   1  
R1T  "N1'"  "C6'"   DOUB  Y  N   2  
R1T  "C2'"  "N3'"   DOUB  Y  N   3  
R1T  "C2'"  CM2     SING  N  N   4  
R1T  CM2    HM21    SING  N  N   5  
R1T  CM2    HM22    SING  N  N   6  
R1T  CM2    HM23    SING  N  N   7  
R1T  "N3'"  "C4'"   SING  Y  N   8  
R1T  "C4'"  "C5'"   DOUB  Y  N   9  
R1T  "C4'"  "N4'"   SING  N  N  10  
R1T  "N4'"  "H4'1"  SING  N  N  11  
R1T  "N4'"  "H4'2"  SING  N  N  12  
R1T  "C5'"  "C7'"   SING  N  N  13  
R1T  "C5'"  "C6'"   SING  Y  N  14  
R1T  "C6'"  "H6'"   SING  N  N  15  
R1T  "C7'"  C3      SING  N  N  16  
R1T  "C7'"  "H7'1"  SING  N  N  17  
R1T  "C7'"  "H7'2"  SING  N  N  18  
R1T  C3     C2      DOUB  Y  N  19  
R1T  C3     C4      SING  Y  N  20  
R1T  C2     CP1     SING  N  N  21  
R1T  C2     S1      SING  Y  N  22  
R1T  S1     C5      SING  Y  N  23  
R1T  C5     C4      DOUB  Y  N  24  
R1T  C5     C6      SING  N  N  25  
R1T  C4     CM4     SING  N  N  26  
R1T  CM4    HM41    SING  N  N  27  
R1T  CM4    HM42    SING  N  N  28  
R1T  CM4    HM43    SING  N  N  29  
R1T  C6     H61     SING  N  N  30  
R1T  C6     H62     SING  N  N  31  
R1T  C6     C7      SING  N  N  32  
R1T  C7     H71     SING  N  N  33  
R1T  C7     H72     SING  N  N  34  
R1T  C7     O7      SING  N  N  35  
R1T  O7     PA      SING  N  N  36  
R1T  PA     O1A     DOUB  N  N  37  
R1T  PA     O2A     SING  N  N  38  
R1T  PA     O3A     SING  N  N  39  
R1T  O2A    H2A     SING  N  N  40  
R1T  O3A    PB      SING  N  N  41  
R1T  PB     O1B     DOUB  N  N  42  
R1T  PB     O2B     SING  N  N  43  
R1T  PB     O3B     SING  N  N  44  
R1T  O2B    H2B     SING  N  N  45  
R1T  O3B    H3B     SING  N  N  46  
R1T  CP1    OP1     SING  N  N  47  
R1T  CP1    H1      SING  N  N  48  
R1T  CP1    CP2     SING  N  N  49  
R1T  CP2    HP21    SING  N  N  50  
R1T  CP2    HP22    SING  N  N  51  
R1T  CP2    HP23    SING  N  N  52  
R1T  OP1    HP1     SING  N  N  53  
#   #
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
R1T  SMILES            ACDLabs               10.04  "O=P(O)(O)OP(=O)(O)OCCc1sc(c(c1C)Cc2cnc(nc2N)C)C(O)C"  
R1T  SMILES_CANONICAL  CACTVS                3.341  "C[C@@H](O)c1sc(CCO[P@@](O)(=O)O[P](O)(O)=O)c(C)c1Cc2cnc(C)nc2N"  
R1T  SMILES            CACTVS                3.341  "C[CH](O)c1sc(CCO[P](O)(=O)O[P](O)(O)=O)c(C)c1Cc2cnc(C)nc2N"  
R1T  SMILES_CANONICAL  "OpenEye OEToolkits"  1.5.0  "Cc1c(sc(c1Cc2cnc(nc2N)C)[C@@H](C)O)CCO[P@](=O)(O)OP(=O)(O)O"  
R1T  SMILES            "OpenEye OEToolkits"  1.5.0  "Cc1c(sc(c1Cc2cnc(nc2N)C)C(C)O)CCOP(=O)(O)OP(=O)(O)O"  
R1T  InChI             InChI                 1.03   "InChI=1S/C15H23N3O8P2S/c1-8-12(6-11-7-17-10(3)18-15(11)16)14(9(2)19)29-13(8)4-5-25-28(23,24)26-27(20,21)22/h7,9,19H,4-6H2,1-3H3,(H,23,24)(H2,16,17,18)(H2,20,21,22)/t9-/m1/s1"  
R1T  InChIKey          InChI                 1.03   ORVRYSKZCUVOLA-SECBINFHSA-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
R1T  "SYSTEMATIC NAME"  ACDLabs               10.04  "2-{4-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-[(1R)-1-hydroxyethyl]-3-methylthiophen-2-yl}ethyl trihydrogen diphosphate"  
R1T  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.5.0  "2-[4-[(4-amino-2-methyl-pyrimidin-5-yl)methyl]-5-(1-hydroxyethyl)-3-methyl-thiophen-2-yl]ethyl phosphono 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
R1T  "Create component"   2007-06-18  RCSB  
R1T  "Modify descriptor"  2011-06-04  RCSB  
R1T  "Modify synonyms"    2021-03-01  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     R1T
_pdbx_chem_comp_synonyms.name        "2-[(1R)-1-HYDROXYETHYL]-3-DEAZA-THDP"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
