data_9RC
#

_chem_comp.id                                   9RC
_chem_comp.name                                 "5'-O-[(S)-hydroxy(4-nitrophenoxy)phosphoryl]thymidine"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C16 H18 N3 O10 P"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        PNP-TMP
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2018-06-28
_chem_comp.pdbx_modified_date                   2020-06-17
_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                       443.302
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    9RC
_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       6A4D
_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
9RC  OAJ  O1   O   0  1  N  N  N  -15.167  -31.961  -19.707   3.648  -0.124  -1.584  OAJ  9RC   1  
9RC  CAE  C1   C   0  1  N  N  N  -14.499  -32.964  -19.968   4.433  -0.688  -0.847  CAE  9RC   2  
9RC  NAI  N1   N   0  1  N  N  N  -15.049  -34.218  -19.756   5.107  -1.765  -1.295  NAI  9RC   3  
9RC  CAL  C2   C   0  1  N  N  N  -14.312  -35.372  -20.053   5.981  -2.402  -0.490  CAL  9RC   4  
9RC  OAS  O2   O   0  1  N  N  N  -14.847  -36.466  -19.842   6.591  -3.376  -0.894  OAS  9RC   5  
9RC  CAT  C3   C   0  1  N  N  N  -13.018  -35.261  -20.584   6.185  -1.928   0.828  CAT  9RC   6  
9RC  CAU  C4   C   0  1  N  N  N  -12.252  -36.393  -20.910   7.157  -2.621   1.747  CAU  9RC   7  
9RC  CAF  C5   C   0  1  N  N  N  -12.491  -33.996  -20.773   5.497  -0.846   1.251  CAF  9RC   8  
9RC  NAB  N2   N   0  1  N  N  N  -13.257  -32.852  -20.457   4.622  -0.225   0.402  NAB  9RC   9  
9RC  CAA  C6   C   0  1  N  N  R  -12.730  -31.496  -20.628   3.875   0.949   0.860  CAA  9RC  10  
9RC  OAC  O3   O   0  1  N  N  N  -12.635  -31.146  -21.984   2.469   0.754   0.633  OAC  9RC  11  
9RC  CAD  C7   C   0  1  N  N  N  -11.311  -31.431  -20.123   4.302   2.190   0.052  CAD  9RC  12  
9RC  CAH  C8   C   0  1  N  N  S  -10.879  -30.140  -20.692   2.989   2.689  -0.598  CAH  9RC  13  
9RC  OAK  O4   O   0  1  N  N  N  -11.180  -29.150  -19.744   2.908   4.115  -0.555  OAK  9RC  14  
9RC  CAG  C9   C   0  1  N  N  R  -11.761  -30.004  -21.923   1.911   2.046   0.311  CAG  9RC  15  
9RC  CAR  C10  C   0  1  N  N  N  -10.886  -30.106  -23.128   0.591   1.888  -0.447  CAR  9RC  16  
9RC  OAQ  O5   O   0  1  N  N  N  -11.766  -30.160  -24.240  -0.387   1.305   0.417  OAQ  9RC  17  
9RC  PAP  P1   P   0  1  N  N  N  -11.153  -30.316  -25.686  -1.896   0.995  -0.051  PAP  9RC  18  
9RC  OAO  O6   O   0  1  N  N  N  -12.410  -30.089  -26.657  -1.872   0.146  -1.263  OAO  9RC  19  
9RC  OAN  O7   O   0  1  N  N  N  -10.770  -31.740  -25.818  -2.652   2.378  -0.379  OAN  9RC  20  
9RC  OAM  O8   O   0  1  N  N  N  -10.019  -29.242  -25.603  -2.676   0.224   1.128  OAM  9RC  21  
9RC  CAV  C11  C   0  1  Y  N  N   -8.970  -28.713  -26.346  -3.929  -0.179   0.791  CAV  9RC  22  
9RC  CAW  C12  C   0  1  Y  N  N   -8.194  -27.635  -25.783  -4.128  -1.431   0.227  CAW  9RC  23  
9RC  CAY  C13  C   0  1  Y  N  N   -7.131  -27.011  -26.531  -5.403  -1.838  -0.114  CAY  9RC  24  
9RC  CBA  C14  C   0  1  Y  N  N   -6.807  -27.472  -27.845  -6.480  -0.999   0.105  CBA  9RC  25  
9RC  NBB  N3   N   1  1  N  N  N   -5.825  -26.978  -28.690  -7.845  -1.439  -0.262  NBB  9RC  26  
9RC  OBD  O9   O  -1  1  N  N  N   -4.829  -27.950  -29.539  -8.019  -2.538  -0.757  OBD  9RC  27  
9RC  OBC  O10  O   0  1  N  N  N   -5.780  -25.622  -28.925  -8.795  -0.701  -0.069  OBC  9RC  28  
9RC  CAZ  C15  C   0  1  Y  N  N   -7.584  -28.526  -28.336  -6.285   0.249   0.667  CAZ  9RC  29  
9RC  CAX  C16  C   0  1  Y  N  N   -8.646  -29.151  -27.641  -5.012   0.659   1.015  CAX  9RC  30  
9RC  H1   H1   H   0  1  N  N  N  -15.976  -34.300  -19.389   4.962  -2.083  -2.199  H1   9RC  31  
9RC  H2   H2   H   0  1  N  N  N  -12.831  -37.303  -20.694   7.610  -3.466   1.227  H2   9RC  32  
9RC  H3   H3   H   0  1  N  N  N  -11.996  -36.367  -21.979   7.936  -1.920   2.048  H3   9RC  33  
9RC  H4   H4   H   0  1  N  N  N  -11.329  -36.396  -20.312   6.630  -2.980   2.631  H4   9RC  34  
9RC  H5   H5   H   0  1  N  N  N  -11.490  -33.883  -21.164   5.639  -0.470   2.253  H5   9RC  35  
9RC  H6   H6   H   0  1  N  N  N  -13.351  -30.775  -20.076   4.062   1.116   1.921  H6   9RC  36  
9RC  H7   H7   H   0  1  N  N  N  -10.706  -32.266  -20.506   4.714   2.953   0.713  H7   9RC  37  
9RC  H8   H8   H   0  1  N  N  N  -11.272  -31.423  -19.024   5.029   1.916  -0.712  H8   9RC  38  
9RC  H9   H9   H   0  1  N  N  N   -9.815  -30.155  -20.970   2.900   2.328  -1.623  H9   9RC  39  
9RC  H10  H10  H   0  1  N  N  N  -10.617  -29.255  -18.986   3.616   4.564  -1.036  H10  9RC  40  
9RC  H11  H11  H   0  1  N  N  N  -12.316  -29.054  -21.908   1.768   2.638   1.215  H11  9RC  41  
9RC  H12  H12  H   0  1  N  N  N  -10.273  -31.018  -23.080   0.244   2.867  -0.780  H12  9RC  42  
9RC  H13  H13  H   0  1  N  N  N  -10.230  -29.226  -23.201   0.743   1.243  -1.311  H13  9RC  43  
9RC  H14  H14  H   0  1  N  N  N  -11.351  -32.169  -26.435  -2.705   2.985   0.372  H14  9RC  44  
9RC  H15  H15  H   0  1  N  N  N   -8.413  -27.289  -24.784  -3.287  -2.086   0.055  H15  9RC  45  
9RC  H16  H16  H   0  1  N  N  N   -6.577  -26.192  -26.097  -5.559  -2.812  -0.553  H16  9RC  46  
9RC  H17  H17  H   0  1  N  N  N   -7.355  -28.892  -29.326  -7.127   0.902   0.837  H17  9RC  47  
9RC  H18  H18  H   0  1  N  N  N   -9.201  -29.955  -28.101  -4.860   1.634   1.454  H18  9RC  48  
#   #
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
9RC  OBD  NBB  SING  N  N   1  
9RC  OBC  NBB  DOUB  N  N   2  
9RC  NBB  CBA  SING  N  N   3  
9RC  CAZ  CBA  DOUB  Y  N   4  
9RC  CAZ  CAX  SING  Y  N   5  
9RC  CBA  CAY  SING  Y  N   6  
9RC  CAX  CAV  DOUB  Y  N   7  
9RC  OAO  PAP  DOUB  N  N   8  
9RC  CAY  CAW  DOUB  Y  N   9  
9RC  CAV  CAW  SING  Y  N  10  
9RC  CAV  OAM  SING  N  N  11  
9RC  OAN  PAP  SING  N  N  12  
9RC  PAP  OAM  SING  N  N  13  
9RC  PAP  OAQ  SING  N  N  14  
9RC  OAQ  CAR  SING  N  N  15  
9RC  CAR  CAG  SING  N  N  16  
9RC  OAC  CAG  SING  N  N  17  
9RC  OAC  CAA  SING  N  N  18  
9RC  CAG  CAH  SING  N  N  19  
9RC  CAU  CAT  SING  N  N  20  
9RC  CAF  CAT  DOUB  N  N  21  
9RC  CAF  NAB  SING  N  N  22  
9RC  CAH  CAD  SING  N  N  23  
9RC  CAH  OAK  SING  N  N  24  
9RC  CAA  NAB  SING  N  N  25  
9RC  CAA  CAD  SING  N  N  26  
9RC  CAT  CAL  SING  N  N  27  
9RC  NAB  CAE  SING  N  N  28  
9RC  CAL  OAS  DOUB  N  N  29  
9RC  CAL  NAI  SING  N  N  30  
9RC  CAE  NAI  SING  N  N  31  
9RC  CAE  OAJ  DOUB  N  N  32  
9RC  NAI  H1   SING  N  N  33  
9RC  CAU  H2   SING  N  N  34  
9RC  CAU  H3   SING  N  N  35  
9RC  CAU  H4   SING  N  N  36  
9RC  CAF  H5   SING  N  N  37  
9RC  CAA  H6   SING  N  N  38  
9RC  CAD  H7   SING  N  N  39  
9RC  CAD  H8   SING  N  N  40  
9RC  CAH  H9   SING  N  N  41  
9RC  OAK  H10  SING  N  N  42  
9RC  CAG  H11  SING  N  N  43  
9RC  CAR  H12  SING  N  N  44  
9RC  CAR  H13  SING  N  N  45  
9RC  OAN  H14  SING  N  N  46  
9RC  CAW  H15  SING  N  N  47  
9RC  CAY  H16  SING  N  N  48  
9RC  CAZ  H17  SING  N  N  49  
9RC  CAX  H18  SING  N  N  50  
#   #
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
9RC  SMILES            ACDLabs               12.01  "O=C1NC(=O)C(C)=CN1C2CC(O)C(O2)COP(Oc3ccc([N+]([O-])=O)cc3)(=O)O"  
9RC  InChI             InChI                 1.03   "InChI=1S/C16H18N3O10P/c1-9-7-18(16(22)17-15(9)21)14-6-12(20)13(28-14)8-27-30(25,26)29-11-4-2-10(3-5-11)19(23)24/h2-5,7,12-14,20H,6,8H2,1H3,(H,25,26)(H,17,21,22)/t12-,13+,14+/m0/s1"  
9RC  InChIKey          InChI                 1.03   RWOAVOYBVRQNIZ-BFHYXJOUSA-N  
9RC  SMILES_CANONICAL  CACTVS                3.385  "CC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(=O)Oc3ccc(cc3)[N+]([O-])=O)O2)C(=O)NC1=O"  
9RC  SMILES            CACTVS                3.385  "CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(=O)Oc3ccc(cc3)[N+]([O-])=O)O2)C(=O)NC1=O"  
9RC  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.6  "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)Oc3ccc(cc3)[N+](=O)[O-])O"  
9RC  SMILES            "OpenEye OEToolkits"  2.0.6  "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)Oc3ccc(cc3)[N+](=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
9RC  "SYSTEMATIC NAME"  ACDLabs               12.01  "5'-O-[(S)-hydroxy(4-nitrophenoxy)phosphoryl]thymidine"  
9RC  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.6  "[(2~{R},3~{S},5~{R})-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-oxidanyl-oxolan-2-yl]methyl (4-nitrophenyl) 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
9RC  "Create component"  2018-06-28  PDBJ  
9RC  "Initial release"   2019-03-13  RCSB  
9RC  "Modify synonyms"   2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     9RC
_pdbx_chem_comp_synonyms.name        PNP-TMP
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
