data_9L3
#

_chem_comp.id                                   9L3
_chem_comp.name                                 "[(2R,3S,5R)-5-(4-azanyl-5-methyl-pyrimidin-1-ium-1-yl)-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C10 H17 N3 O6 P"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   1
_chem_comp.pdbx_initial_date                    2018-05-22
_chem_comp.pdbx_modified_date                   2022-03-16
_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                       306.232
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    9L3
_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       5ZRI
_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
9L3  N1     N1   N  1  1  Y  N  N  -17.563  12.818   2.477   2.380  -0.262  -0.327  N1     9L3   1  
9L3  C2     C1   C  0  1  Y  N  N  -16.719  12.932   3.606   2.245   0.490   0.747  C2     9L3   2  
9L3  N3     N2   N  0  1  Y  N  N  -15.415  12.627   3.493   3.229   1.242   1.198  N3     9L3   3  
9L3  C4     C2   C  0  1  Y  N  N  -14.893  12.220   2.326   4.404   1.265   0.576  C4     9L3   4  
9L3  C5     C3   C  0  1  Y  N  N  -15.765  12.078   1.141   4.581   0.480  -0.565  C5     9L3   5  
9L3  C5A    C4   C  0  1  N  N  N  -15.199  11.624  -0.183   5.897   0.470  -1.300  C5A    9L3   6  
9L3  C6     C5   C  0  1  Y  N  N  -17.097  12.415   1.283   3.523  -0.295  -0.998  C6     9L3   7  
9L3  N4     N3   N  0  1  N  N  N  -13.595  11.863   2.234   5.436   2.057   1.052  N4     9L3   8  
9L3  "C1'"  C6   C  0  1  N  N  R  -19.007  13.042   2.615   1.252  -1.078  -0.782  "C1'"  9L3   9  
9L3  "C2'"  C7   C  0  1  N  N  N  -19.442  14.371   2.016   1.158  -2.362   0.065  "C2'"  9L3  10  
9L3  "C3'"  C8   C  0  1  N  N  S  -20.815  14.063   1.449  -0.259  -2.304   0.686  "C3'"  9L3  11  
9L3  "C4'"  C9   C  0  1  N  N  R  -20.773  12.592   1.099  -0.992  -1.328  -0.270  "C4'"  9L3  12  
9L3  "O4'"  O1   O  0  1  N  N  N  -19.701  12.041   1.873   0.023  -0.355  -0.606  "O4'"  9L3  13  
9L3  "O3'"  O2   O  0  1  N  N  N  -21.792  14.231   2.483  -0.876  -3.593   0.670  "O3'"  9L3  14  
9L3  "C5'"  C10  C  0  1  N  N  N  -20.585  12.338  -0.391  -2.168  -0.657   0.443  "C5'"  9L3  15  
9L3  "O5'"  O3   O  0  1  N  N  N  -19.334  12.848  -0.843  -2.895   0.146  -0.489  "O5'"  9L3  16  
9L3  PA     P1   P  0  1  N  N  N  -19.248  13.734  -2.187  -4.199   0.998  -0.082  PA     9L3  17  
9L3  O1A    O4   O  0  1  N  N  N  -19.815  15.090  -1.874  -5.381  -0.004   0.354  O1A    9L3  18  
9L3  O2A    O5   O  0  1  N  N  N  -19.884  12.929  -3.295  -3.869   1.893   1.050  O2A    9L3  19  
9L3  O3A    O6   O  0  1  N  N  N  -17.660  13.824  -2.455  -4.679   1.879  -1.341  O3A    9L3  20  
9L3  H1     H1   H  0  1  N  N  N  -17.120  13.262   4.553   1.301   0.490   1.272  H1     9L3  21  
9L3  H2     H2   H  0  1  N  N  N  -14.856  12.499  -0.755   5.889   1.241  -2.069  H2     9L3  22  
9L3  H3     H3   H  0  1  N  N  N  -14.351  10.946  -0.006   6.707   0.665  -0.597  H3     9L3  23  
9L3  H4     H4   H  0  1  N  N  N  -15.978  11.096  -0.753   6.046  -0.505  -1.764  H4     9L3  24  
9L3  H5     H5   H  0  1  N  N  N  -17.763  12.355   0.435   3.623  -0.916  -1.876  H5     9L3  25  
9L3  H6     H6   H  0  1  N  N  N  -13.158  11.959   3.129   5.305   2.600   1.845  H6     9L3  26  
9L3  H7     H7   H  0  1  N  N  N  -13.532  10.912   1.932   6.291   2.069   0.592  H7     9L3  27  
9L3  H8     H8   H  0  1  N  N  N  -19.295  13.009   3.676   1.383  -1.336  -1.833  H8     9L3  28  
9L3  H9     H9   H  0  1  N  N  N  -18.750  14.691   1.223   1.262  -3.244  -0.567  H9     9L3  29  
9L3  H10    H10  H  0  1  N  N  N  -19.500  15.152   2.789   1.919  -2.361   0.845  H10    9L3  30  
9L3  H11    H11  H  0  1  N  N  N  -21.028  14.679   0.563  -0.224  -1.904   1.699  H11    9L3  31  
9L3  H12    H12  H  0  1  N  N  N  -21.723  12.134   1.410  -1.332  -1.850  -1.165  H12    9L3  32  
9L3  H13    H13  H  0  1  N  N  N  -21.842  15.148   2.726  -0.401  -4.262   1.182  H13    9L3  33  
9L3  H14    H14  H  0  1  N  N  N  -21.396  12.833  -0.945  -2.826  -1.421   0.856  H14    9L3  34  
9L3  H15    H15  H  0  1  N  N  N  -20.620  11.255  -0.578  -1.792  -0.027   1.250  H15    9L3  35  
9L3  H16    H16  H  0  1  N  N  N  -20.546  15.270  -2.454  -5.649  -0.622  -0.341  H16    9L3  36  
9L3  H17    H17  H  0  1  N  N  N  -17.446  13.354  -3.253  -5.462   2.420  -1.167  H17    9L3  37  
#   #
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
9L3  O2A    PA     DOUB  N  N   1  
9L3  O3A    PA     SING  N  N   2  
9L3  PA     O1A    SING  N  N   3  
9L3  PA     "O5'"  SING  N  N   4  
9L3  "O5'"  "C5'"  SING  N  N   5  
9L3  "C5'"  "C4'"  SING  N  N   6  
9L3  C5A    C5     SING  N  N   7  
9L3  "C4'"  "C3'"  SING  N  N   8  
9L3  "C4'"  "O4'"  SING  N  N   9  
9L3  C5     C6     DOUB  Y  N  10  
9L3  C5     C4     SING  Y  N  11  
9L3  C6     N1     SING  Y  N  12  
9L3  "C3'"  "C2'"  SING  N  N  13  
9L3  "C3'"  "O3'"  SING  N  N  14  
9L3  "O4'"  "C1'"  SING  N  N  15  
9L3  "C2'"  "C1'"  SING  N  N  16  
9L3  N4     C4     SING  N  N  17  
9L3  C4     N3     DOUB  Y  N  18  
9L3  N1     "C1'"  SING  N  N  19  
9L3  N1     C2     DOUB  Y  N  20  
9L3  N3     C2     SING  Y  N  21  
9L3  C2     H1     SING  N  N  22  
9L3  C5A    H2     SING  N  N  23  
9L3  C5A    H3     SING  N  N  24  
9L3  C5A    H4     SING  N  N  25  
9L3  C6     H5     SING  N  N  26  
9L3  N4     H6     SING  N  N  27  
9L3  N4     H7     SING  N  N  28  
9L3  "C1'"  H8     SING  N  N  29  
9L3  "C2'"  H9     SING  N  N  30  
9L3  "C2'"  H10    SING  N  N  31  
9L3  "C3'"  H11    SING  N  N  32  
9L3  "C4'"  H12    SING  N  N  33  
9L3  "O3'"  H13    SING  N  N  34  
9L3  "C5'"  H14    SING  N  N  35  
9L3  "C5'"  H15    SING  N  N  36  
9L3  O1A    H16    SING  N  N  37  
9L3  O3A    H17    SING  N  N  38  
#   #
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
9L3  InChI             InChI                 1.03   "InChI=1S/C10H16N3O6P/c1-6-3-13(5-12-10(6)11)9-2-7(14)8(19-9)4-18-20(15,16)17/h3,5,7-9,11,14H,2,4H2,1H3,(H2,15,16,17)/p+1/t7-,8+,9+/m0/s1"  
9L3  InChIKey          InChI                 1.03   RJJVNUWWHKQVPB-DJLDLDEBSA-O  
9L3  SMILES_CANONICAL  CACTVS                3.385  "Cc1c[n+](cnc1N)[C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2"  
9L3  SMILES            CACTVS                3.385  "Cc1c[n+](cnc1N)[CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2"  
9L3  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.6  "Cc1c[n+](cnc1N)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O"  
9L3  SMILES            "OpenEye OEToolkits"  2.0.6  "Cc1c[n+](cnc1N)C2CC(C(O2)COP(=O)(O)O)O"  
#
_pdbx_chem_comp_identifier.comp_id          9L3
_pdbx_chem_comp_identifier.type             "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program          "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version  2.0.6
_pdbx_chem_comp_identifier.identifier       "[(2~{R},3~{S},5~{R})-5-(4-azanyl-5-methyl-pyrimidin-1-ium-1-yl)-3-oxidanyl-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
9L3  "Create component"  2018-05-22  PDBJ  
9L3  "Initial release"   2019-04-24  RCSB  
9L3  "Modify name"       2022-03-16  RCSB  
##
