data_3ZO
#

_chem_comp.id                                   3ZO
_chem_comp.name                                 "2'-DEOXY-XANTHOSINE-5'-MONOPHOSPHATE"
_chem_comp.type                                 "DNA LINKING"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C10 H13 N4 O8 P"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        "2'-deoxy-5'-2,3-dihydroxanthylic acid"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2014-12-24
_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                       348.206
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    3ZO
_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       2MWZ
_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
3ZO  P       P       P  0  1  N  N  N  22.814  28.577  18.277   5.086   0.776   0.350  P       3ZO   1  
3ZO  "C5'"   "C5'"   C  0  1  N  N  N  22.563  27.049  20.438   3.037  -0.716  -0.495  "C5'"   3ZO   2  
3ZO  "O5'"   "O5'"   O  0  1  N  N  N  22.395  28.332  19.817   3.658   0.056   0.534  "O5'"   3ZO   3  
3ZO  "C4'"   "C4'"   C  0  1  N  N  R  22.343  27.120  21.952   1.697  -1.255   0.009  "C4'"   3ZO   4  
3ZO  "O4'"   "O4'"   O  0  1  N  N  N  23.303  28.012  22.537   0.746  -0.178   0.158  "O4'"   3ZO   5  
3ZO  "C3'"   "C3'"   C  0  1  N  N  S  20.951  27.627  22.366   1.066  -2.195  -1.042  "C3'"   3ZO   6  
3ZO  "O3'"   "O3'"   O  0  1  N  N  N  20.445  26.821  23.439   1.326  -3.561  -0.712  "O3'"   3ZO   7  
3ZO  "C2'"   "C2'"   C  0  1  N  N  N  21.219  29.035  22.876  -0.448  -1.896  -0.952  "C2'"   3ZO   8  
3ZO  "C1'"   "C1'"   C  0  1  N  N  R  22.606  28.852  23.454  -0.552  -0.811   0.142  "C1'"   3ZO   9  
3ZO  N1      N1      N  0  1  N  N  N  25.504  31.539  26.607  -5.634   0.426   0.444  N1      3ZO  10  
3ZO  C2      C2      C  0  1  N  N  N  24.911  30.314  26.780  -5.004  -0.656   0.931  C2      3ZO  11  
3ZO  O2      O2      O  0  1  N  N  N  25.111  29.768  27.854  -5.652  -1.493   1.530  O2      3ZO  12  
3ZO  N3      N3      N  0  1  N  N  N  24.171  29.714  25.859  -3.681  -0.846   0.778  N3      3ZO  13  
3ZO  C4      C4      C  0  1  Y  N  N  24.073  30.450  24.735  -2.910   0.074   0.107  C4      3ZO  14  
3ZO  C5      C5      C  0  1  Y  N  N  24.632  31.674  24.473  -3.514   1.211  -0.417  C5      3ZO  15  
3ZO  C6      C6      C  0  1  N  N  N  25.421  32.308  25.466  -4.957   1.378  -0.233  C6      3ZO  16  
3ZO  O6      O6      O  0  1  N  N  N  25.987  33.391  25.418  -5.531   2.356  -0.674  O6      3ZO  17  
3ZO  N7      N7      N  0  1  Y  N  N  24.294  32.097  23.195  -2.546   1.942  -1.020  N7      3ZO  18  
3ZO  C8      C8      C  0  1  Y  N  N  23.554  31.126  22.733  -1.407   1.325  -0.896  C8      3ZO  19  
3ZO  N9      N9      N  0  1  Y  N  N  23.377  30.095  23.616  -1.590   0.163  -0.204  N9      3ZO  20  
3ZO  OP1     OP1     O  0  1  N  N  N  22.475  27.360  17.503   6.094  -0.226  -0.065  OP1     3ZO  21  
3ZO  OP2     OP2     O  0  1  N  N  N  22.272  29.890  17.858   4.969   1.919  -0.778  OP2     3ZO  22  
3ZO  OP3     OP3     O  0  1  N  Y  N  24.421  28.692  18.352   5.535   1.443   1.745  OP3     3ZO  23  
3ZO  "H5''"  "H5''"  H  0  0  N  N  N  21.837  26.345  20.005   2.870  -0.088  -1.370  "H5''"  3ZO  24  
3ZO  "H5'"   "H5'"   H  0  1  N  N  N  23.584  26.689  20.243   3.685  -1.550  -0.765  "H5'"   3ZO  25  
3ZO  "H4'"   "H4'"   H  0  1  N  N  N  22.478  26.111  22.368   1.831  -1.779   0.955  "H4'"   3ZO  26  
3ZO  "H3'"   "H3'"   H  0  1  N  N  N  20.271  27.645  21.502   1.442  -1.963  -2.038  "H3'"   3ZO  27  
3ZO  H2      H2      H  0  1  N  N  N  19.585  27.135  23.694   0.952  -4.195  -1.339  H2      3ZO  28  
3ZO  "H2'"   "H2'"   H  0  1  N  N  N  21.212  29.772  22.060  -0.819  -1.516  -1.904  "H2'"   3ZO  29  
3ZO  "H2''"  "H2''"  H  0  0  N  N  N  20.493  29.334  23.646  -0.997  -2.790  -0.656  "H2''"  3ZO  30  
3ZO  "H1'"   "H1'"   H  0  1  N  N  N  22.518  28.350  24.429  -0.764  -1.266   1.109  "H1'"   3ZO  31  
3ZO  H1      H1      H  0  1  N  N  N  26.039  31.903  27.369  -6.590   0.522   0.577  H1      3ZO  32  
3ZO  H3      H3      H  0  1  N  N  N  23.737  28.822  25.983  -3.266  -1.642   1.146  H3      3ZO  33  
3ZO  H8      H8      H  0  1  N  N  N  23.121  31.135  21.744  -0.462   1.678  -1.281  H8      3ZO  34  
3ZO  H4      H4      H  0  1  N  N  N  21.732  29.778  17.084   4.326   2.610  -0.572  H4      3ZO  35  
3ZO  HOP3    HOP3    H  0  0  N  N  N  24.813  27.962  17.888   6.389   1.895   1.708  HOP3    3ZO  36  
#   #
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
3ZO  OP1    P       DOUB  N  N   1  
3ZO  OP2    P       SING  N  N   2  
3ZO  P      "O5'"   SING  N  N   3  
3ZO  "O5'"  "C5'"   SING  N  N   4  
3ZO  "C5'"  "C4'"   SING  N  N   5  
3ZO  "C4'"  "C3'"   SING  N  N   6  
3ZO  "C4'"  "O4'"   SING  N  N   7  
3ZO  "C3'"  "C2'"   SING  N  N   8  
3ZO  "C3'"  "O3'"   SING  N  N   9  
3ZO  "O4'"  "C1'"   SING  N  N  10  
3ZO  C8     N7      DOUB  Y  N  11  
3ZO  C8     N9      SING  Y  N  12  
3ZO  "C2'"  "C1'"   SING  N  N  13  
3ZO  N7     C5      SING  Y  N  14  
3ZO  "C1'"  N9      SING  N  N  15  
3ZO  N9     C4      SING  Y  N  16  
3ZO  C5     C4      DOUB  Y  N  17  
3ZO  C5     C6      SING  N  N  18  
3ZO  C4     N3      SING  N  N  19  
3ZO  O6     C6      DOUB  N  N  20  
3ZO  C6     N1      SING  N  N  21  
3ZO  N3     C2      SING  N  N  22  
3ZO  N1     C2      SING  N  N  23  
3ZO  C2     O2      DOUB  N  N  24  
3ZO  P      OP3     SING  N  N  25  
3ZO  "C5'"  "H5''"  SING  N  N  26  
3ZO  "C5'"  "H5'"   SING  N  N  27  
3ZO  "C4'"  "H4'"   SING  N  N  28  
3ZO  "C3'"  "H3'"   SING  N  N  29  
3ZO  "O3'"  H2      SING  N  N  30  
3ZO  "C2'"  "H2'"   SING  N  N  31  
3ZO  "C2'"  "H2''"  SING  N  N  32  
3ZO  "C1'"  "H1'"   SING  N  N  33  
3ZO  N1     H1      SING  N  N  34  
3ZO  N3     H3      SING  N  N  35  
3ZO  C8     H8      SING  N  N  36  
3ZO  OP2    H4      SING  N  N  37  
3ZO  OP3    HOP3    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
3ZO  SMILES            ACDLabs               12.01  "O=P(O)(O)OCC3OC(n1cnc2c1NC(=O)NC2=O)CC3O"  
3ZO  InChI             InChI                 1.03   "InChI=1S/C10H13N4O8P/c15-4-1-6(22-5(4)2-21-23(18,19)20)14-3-11-7-8(14)12-10(17)13-9(7)16/h3-6,15H,1-2H2,(H2,18,19,20)(H2,12,13,16,17)/t4-,5+,6+/m0/s1"  
3ZO  InChIKey          InChI                 1.03   RTWWRSBEQVIVBY-KVQBGUIXSA-N  
3ZO  SMILES_CANONICAL  CACTVS                3.385  "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)n2cnc3C(=O)NC(=O)Nc23"  
3ZO  SMILES            CACTVS                3.385  "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)n2cnc3C(=O)NC(=O)Nc23"  
3ZO  SMILES_CANONICAL  "OpenEye OEToolkits"  1.7.6  "c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)NC(=O)NC2=O"  
3ZO  SMILES            "OpenEye OEToolkits"  1.7.6  "c1nc2c(n1C3CC(C(O3)COP(=O)(O)O)O)NC(=O)NC2=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
3ZO  "SYSTEMATIC NAME"  ACDLabs               12.01  "2'-deoxy-5'-2,3-dihydroxanthylic acid"  
3ZO  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.7.6  "[(2R,3S,5R)-5-[2,6-bis(oxidanylidene)-3H-purin-9-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
3ZO  "Create component"  2014-12-24  RCSB  
3ZO  "Modify name"       2015-04-15  RCSB  
3ZO  "Modify synonyms"   2015-04-15  RCSB  
3ZO  "Initial release"   2015-10-14  RCSB  
3ZO  "Modify synonyms"   2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     3ZO
_pdbx_chem_comp_synonyms.name        "2'-deoxy-5'-2,3-dihydroxanthylic acid"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
