data_JSP
#

_chem_comp.id                                   JSP
_chem_comp.name                                 "(1R)-1-(4-amino-1-methyl-2-oxo-1,2-dihydropyrimidin-5-yl)-1,4-anhydro-2-deoxy-5-O-phosphono-D-erythro-pentitol"
_chem_comp.type                                 "DNA linking"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C10 H16 N3 O7 P"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2018-09-20
_chem_comp.pdbx_modified_date                   2019-02-22
_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                       321.224
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    JSP
_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       6MIG
_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
JSP  C1     C1   C  0  1  N  N  N  24.934  4.576  -18.790  -2.289  -0.376   0.197  C1     JSP   1  
JSP  "C1'"  C2   C  0  1  N  N  R  25.096  4.203  -20.300  -1.151  -1.335   0.435  "C1'"  JSP   2  
JSP  C2     C3   C  0  1  N  N  N  24.306  3.799  -17.883  -2.198   0.607  -0.810  C2     JSP   3  
JSP  "C2'"  C4   C  0  1  N  N  N  25.222  5.423  -21.198  -0.905  -2.212  -0.818  "C2'"  JSP   4  
JSP  "C3'"  C5   C  0  1  N  N  S  25.840  4.780  -22.439   0.581  -2.612  -0.648  "C3'"  JSP   5  
JSP  C4     C6   C  0  1  N  N  N  24.678  5.248  -16.232  -4.316   1.354  -0.266  C4     JSP   6  
JSP  "C4'"  C7   C  0  1  N  N  R  26.787  3.736  -21.841   1.152  -1.547   0.308  "C4'"  JSP   7  
JSP  "C5'"  C8   C  0  1  N  N  N  28.273  4.081  -21.841   2.317  -0.817  -0.363  "C5'"  JSP   8  
JSP  C6     C9   C  0  1  N  N  N  25.451  5.743  -18.388  -3.417  -0.449   0.943  C6     JSP   9  
JSP  C7     C10  C  0  1  N  N  N  25.871  7.356  -16.578  -5.659   0.358   1.501  C7     JSP  10  
JSP  N2     N1   N  0  1  N  N  N  23.824  2.700  -18.295  -1.064   0.703  -1.582  N2     JSP  11  
JSP  N3     N2   N  0  1  N  N  N  24.204  4.153  -16.670  -3.213   1.438  -1.008  N3     JSP  12  
JSP  N5     N3   N  0  1  N  N  N  25.331  6.100  -17.093  -4.433   0.426   0.702  N5     JSP  13  
JSP  "O3'"  O1   O  0  1  N  N  N  24.882  4.113  -23.265   0.688  -3.914  -0.067  "O3'"  JSP  14  
JSP  O4     O2   O  0  1  N  N  N  24.552  5.540  -15.061  -5.236   2.129  -0.468  O4     JSP  15  
JSP  "O4'"  O3   O  0  1  N  N  N  26.312  3.500  -20.486   0.092  -0.618   0.598  "O4'"  JSP  16  
JSP  "O5'"  O4   O  0  1  N  N  N  28.565  5.237  -22.632   2.913   0.087   0.570  "O5'"  JSP  17  
JSP  OP1    O5   O  0  1  N  N  N  30.742  6.380  -22.145   5.277   0.184  -0.309  OP1    JSP  18  
JSP  OP2    O6   O  0  1  N  N  N  28.572  7.715  -22.382   3.737   2.086  -0.925  OP2    JSP  19  
JSP  P      P1   P  0  1  N  N  N  29.280  6.494  -21.935   4.171   1.023   0.203  P      JSP  20  
JSP  H1     H1   H  0  1  N  N  N  24.234  3.597  -20.616  -1.352  -1.958   1.307  H1     JSP  21  
JSP  H2     H2   H  0  1  N  N  N  25.884  6.185  -20.761  -1.548  -3.092  -0.810  H2     JSP  22  
JSP  H3     H3   H  0  1  N  N  N  24.242  5.871  -21.416  -1.050  -1.635  -1.732  H3     JSP  23  
JSP  H4     H4   H  0  1  N  N  N  26.413  5.528  -23.007   1.096  -2.579  -1.608  H4     JSP  24  
JSP  H5     H5   H  0  1  N  N  N  26.663  2.808  -22.419   1.492  -2.020   1.230  H5     JSP  25  
JSP  H6     H6   H  0  1  N  N  N  28.834  3.226  -22.245   3.060  -1.543  -0.691  H6     JSP  26  
JSP  H7     H7   H  0  1  N  N  N  28.591  4.272  -20.806   1.949  -0.259  -1.224  H7     JSP  27  
JSP  H8     H8   H  0  1  N  N  N  25.957  6.389  -19.090  -3.511  -1.194   1.719  H8     JSP  28  
JSP  H9     H9   H  0  1  N  N  N  25.656  7.434  -15.502  -5.557   0.998   2.378  H9     JSP  29  
JSP  H10    H10  H  0  1  N  N  N  26.959  7.380  -16.737  -6.503   0.695   0.901  H10    JSP  30  
JSP  H11    H11  H  0  1  N  N  N  25.405  8.200  -17.107  -5.828  -0.671   1.820  H11    JSP  31  
JSP  H12    H12  H  0  1  N  N  N  23.351  2.091  -17.658  -0.324   0.094  -1.435  H12    JSP  32  
JSP  H13    H13  H  0  1  N  N  N  23.917  2.442  -19.257  -1.005   1.381  -2.274  H13    JSP  33  
JSP  H14    H14  H  0  1  N  N  N  24.289  4.752  -23.642   0.343  -4.623  -0.626  H14    JSP  34  
JSP  H16    H16  H  0  1  N  N  N  29.193  8.315  -22.777   3.014   2.671  -0.658  H16    JSP  35  
JSP  OP3    OP3  O  0  1  N  Y  N  28.941  6.286  -20.398   4.658   1.808   1.521  OP3    JSP  36  
JSP  H15    H15  H  0  1  N  Y  N  29.744  6.129  -19.915   5.414   2.392   1.374  H15    JSP  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
JSP  "O3'"  "C3'"  SING  N  N   1  
JSP  "O5'"  P      SING  N  N   2  
JSP  "O5'"  "C5'"  SING  N  N   3  
JSP  "C3'"  "C4'"  SING  N  N   4  
JSP  "C3'"  "C2'"  SING  N  N   5  
JSP  OP2    P      SING  N  N   6  
JSP  OP1    P      DOUB  N  N   7  
JSP  "C4'"  "C5'"  SING  N  N   8  
JSP  "C4'"  "O4'"  SING  N  N   9  
JSP  "C2'"  "C1'"  SING  N  N  10  
JSP  "O4'"  "C1'"  SING  N  N  11  
JSP  "C1'"  C1     SING  N  N  12  
JSP  C1     C6     DOUB  N  N  13  
JSP  C1     C2     SING  N  N  14  
JSP  C6     N5     SING  N  N  15  
JSP  N2     C2     SING  N  N  16  
JSP  C2     N3     DOUB  N  N  17  
JSP  N5     C7     SING  N  N  18  
JSP  N5     C4     SING  N  N  19  
JSP  N3     C4     SING  N  N  20  
JSP  C4     O4     DOUB  N  N  21  
JSP  "C1'"  H1     SING  N  N  22  
JSP  "C2'"  H2     SING  N  N  23  
JSP  "C2'"  H3     SING  N  N  24  
JSP  "C3'"  H4     SING  N  N  25  
JSP  "C4'"  H5     SING  N  N  26  
JSP  "C5'"  H6     SING  N  N  27  
JSP  "C5'"  H7     SING  N  N  28  
JSP  C6     H8     SING  N  N  29  
JSP  C7     H9     SING  N  N  30  
JSP  C7     H10    SING  N  N  31  
JSP  C7     H11    SING  N  N  32  
JSP  N2     H12    SING  N  N  33  
JSP  N2     H13    SING  N  N  34  
JSP  "O3'"  H14    SING  N  N  35  
JSP  OP2    H16    SING  N  N  36  
JSP  P      OP3    SING  N  N  37  
JSP  OP3    H15    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
JSP  SMILES            ACDLabs               12.01  "C1(=CN(C(=O)N=C1N)C)C2CC(C(COP(=O)(O)O)O2)O"  
JSP  InChI             InChI                 1.03   "InChI=1S/C10H16N3O7P/c1-13-3-5(9(11)12-10(13)15)7-2-6(14)8(20-7)4-19-21(16,17)18/h3,6-8,14H,2,4H2,1H3,(H2,11,12,15)(H2,16,17,18)/t6-,7+,8+/m0/s1"  
JSP  InChIKey          InChI                 1.03   NSXSEZCKIMJZGT-XLPZGREQSA-N  
JSP  SMILES_CANONICAL  CACTVS                3.385  "CN1C=C([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=NC1=O)N"  
JSP  SMILES            CACTVS                3.385  "CN1C=C([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=NC1=O)N"  
JSP  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.6  "CN1C=C(C(=NC1=O)N)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O"  
JSP  SMILES            "OpenEye OEToolkits"  2.0.6  "CN1C=C(C(=NC1=O)N)C2CC(C(O2)COP(=O)(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
JSP  "SYSTEMATIC NAME"  ACDLabs               12.01  "(1R)-1-(4-amino-1-methyl-2-oxo-1,2-dihydropyrimidin-5-yl)-1,4-anhydro-2-deoxy-5-O-phosphono-D-erythro-pentitol"  
JSP  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.6  "[(2~{R},3~{S},5~{R})-5-(4-azanyl-1-methyl-2-oxidanylidene-pyrimidin-5-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
JSP  "Create component"  2018-09-20  RCSB  
JSP  "Initial release"   2019-02-27  RCSB  
##
