data_XCT
#

_chem_comp.id                                   XCT
_chem_comp.name                                 "4-AMINO-1-(2,3-DIDEOXY-6-O-PHOSPHONO-BETA-D-ERYTHRO-HEXOPYRANOSYL)PYRIMIDIN-2(1H)-ONE"
_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              DC
_chem_comp.pdbx_synonyms                        "2',3'-DI-DEOXY-BETA-D-GLUCOPYRANOSYL CYTOSINE"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2006-06-20
_chem_comp.pdbx_modified_date                   2021-03-13
_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                      C
_chem_comp.three_letter_code                    XCT
_chem_comp.pdbx_model_coordinates_details       ?
_chem_comp.pdbx_model_coordinates_missing_flag  N
_chem_comp.pdbx_ideal_coordinates_details       ?
_chem_comp.pdbx_ideal_coordinates_missing_flag  N
_chem_comp.pdbx_model_coordinates_db_code       2H9S
_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
XCT  OP3     O3P     O  0  1  N  Y  N   3.151   7.855  17.218  -3.576   1.731   1.510  OP3     XCT   1  
XCT  P       P       P  0  1  N  N  N   4.516   7.310  17.808  -3.751   1.344  -0.043  P       XCT   2  
XCT  OP1     O1P     O  0  1  N  N  N   4.700   5.943  17.290  -4.870   0.387  -0.190  OP1     XCT   3  
XCT  OP2     O2P     O  0  1  N  N  N   4.498   7.567  19.267  -4.067   2.674  -0.895  OP2     XCT   4  
XCT  "O6'"   "O6'"   O  0  1  N  N  N   5.650   8.219  17.165  -2.393   0.670  -0.585  "O6'"   XCT   5  
XCT  "C6'"   "C6'"   C  0  1  N  N  N   6.924   8.281  17.689  -2.231  -0.560   0.125  "C6'"   XCT   6  
XCT  "C5'"   "C5'"   C  0  1  N  N  R   7.570   9.579  17.266  -0.951  -1.255  -0.345  "C5'"   XCT   7  
XCT  "O5'"   "O5'"   O  0  1  N  N  N   6.855  10.659  17.892   0.178  -0.457   0.008  "O5'"   XCT   8  
XCT  "C4'"   "C4'"   C  0  1  N  N  S   9.023   9.679  17.685  -0.843  -2.627   0.324  "C4'"   XCT   9  
XCT  "O4'"   "O4'"   O  0  1  N  N  N   9.708   8.606  17.067  -1.989  -3.414  -0.008  "O4'"   XCT  10  
XCT  "C3'"   "C3'"   C  0  1  N  N  N   9.490  11.036  17.221   0.424  -3.329  -0.178  "C3'"   XCT  11  
XCT  "C2'"   "C2'"   C  0  1  N  N  N   8.683  12.173  17.860   1.621  -2.397   0.046  "C2'"   XCT  12  
XCT  "C1'"   "C1'"   C  0  1  N  N  R   7.232  11.943  17.431   1.327  -1.042  -0.602  "C1'"   XCT  13  
XCT  N1      N1      N  0  1  N  N  N   6.291  12.879  18.051   2.479  -0.156  -0.421  N1      XCT  14  
XCT  C2      C2      C  0  1  N  N  N   5.433  13.644  17.270   2.831   0.241   0.815  C2      XCT  15  
XCT  O2      O2      O  0  1  N  N  N   5.545  13.597  16.012   2.185  -0.144   1.776  O2      XCT  16  
XCT  C6      C6      C  0  1  N  N  N   6.218  12.913  19.414   3.188   0.263  -1.507  C6      XCT  17  
XCT  C5      C5      C  0  1  N  N  N   5.367  13.719  20.026   4.247   1.088  -1.328  C5      XCT  18  
XCT  C4      C4      C  0  1  N  N  N   4.497  14.504  19.243   4.594   1.480  -0.018  C4      XCT  19  
XCT  N3      N3      N  0  1  N  N  N   4.560  14.484  17.890   3.874   1.046   1.008  N3      XCT  20  
XCT  N4      N4      N  0  1  N  N  N   3.624  15.316  19.841   5.668   2.312   0.193  N4      XCT  21  
XCT  HOP3    3HOP    H  0  0  N  N  N   2.522   7.964  17.922  -2.838   2.355   1.561  HOP3    XCT  22  
XCT  HOP2    2HOP    H  0  0  N  N  N   4.494   6.740  19.735  -4.885   3.046  -0.539  HOP2    XCT  23  
XCT  "H6'1"  "1H6'"  H  0  0  N  N  N   7.519   7.433  17.318  -3.087  -1.206  -0.067  "H6'1"  XCT  24  
XCT  "H6'2"  "2H6'"  H  0  0  N  N  N   6.874   8.235  18.787  -2.162  -0.356   1.194  "H6'2"  XCT  25  
XCT  "H5'"   "H5'"   H  0  1  N  N  N   7.532   9.626  16.168  -0.984  -1.381  -1.427  "H5'"   XCT  26  
XCT  "H4'"   "H4'"   H  0  1  N  N  N   9.198   9.599  18.768  -0.787  -2.503   1.405  "H4'"   XCT  27  
XCT  H4T     H4T     H  0  1  N  N  N   9.862   8.812  16.153  -1.875  -4.270   0.428  H4T     XCT  28  
XCT  "H3'1"  "1H3'"  H  0  0  N  N  N   9.350  11.090  16.131   0.325  -3.548  -1.241  "H3'1"  XCT  29  
XCT  "H3'2"  "2H3'"  H  0  0  N  N  N  10.548  11.157  17.498   0.573  -4.255   0.377  "H3'2"  XCT  30  
XCT  "H2'1"  "1H2'"  H  0  0  N  N  N   9.048  13.159  17.537   2.512  -2.833  -0.408  "H2'1"  XCT  31  
XCT  "H2'2"  "2H2'"  H  0  0  N  N  N   8.774  12.147  18.956   1.784  -2.263   1.115  "H2'2"  XCT  32  
XCT  "H1'"   "H1'"   H  0  1  N  N  N   7.190  12.068  16.339   1.140  -1.183  -1.666  "H1'"   XCT  33  
XCT  H6      H6      H  0  1  N  N  N   6.863  12.274  19.999   2.905  -0.055  -2.499  H6      XCT  34  
XCT  H5      H5      H  0  1  N  N  N   5.339  13.775  21.104   4.823   1.432  -2.174  H5      XCT  35  
XCT  HN41    1HN4    H  0  0  N  N  N   2.981  15.920  19.370   5.902   2.584   1.094  HN41    XCT  36  
XCT  HN42    2HN4    H  0  0  N  N  N   3.712  15.228  20.833   6.195   2.625  -0.560  HN42    XCT  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
XCT  OP3    P       SING  N  N   1  
XCT  OP3    HOP3    SING  N  N   2  
XCT  P      OP1     DOUB  N  N   3  
XCT  P      OP2     SING  N  N   4  
XCT  P      "O6'"   SING  N  N   5  
XCT  OP2    HOP2    SING  N  N   6  
XCT  "O6'"  "C6'"   SING  N  N   7  
XCT  "C6'"  "C5'"   SING  N  N   8  
XCT  "C6'"  "H6'1"  SING  N  N   9  
XCT  "C6'"  "H6'2"  SING  N  N  10  
XCT  "C5'"  "O5'"   SING  N  N  11  
XCT  "C5'"  "C4'"   SING  N  N  12  
XCT  "C5'"  "H5'"   SING  N  N  13  
XCT  "O5'"  "C1'"   SING  N  N  14  
XCT  "C4'"  "O4'"   SING  N  N  15  
XCT  "C4'"  "C3'"   SING  N  N  16  
XCT  "C4'"  "H4'"   SING  N  N  17  
XCT  "O4'"  H4T     SING  N  N  18  
XCT  "C3'"  "C2'"   SING  N  N  19  
XCT  "C3'"  "H3'1"  SING  N  N  20  
XCT  "C3'"  "H3'2"  SING  N  N  21  
XCT  "C2'"  "C1'"   SING  N  N  22  
XCT  "C2'"  "H2'1"  SING  N  N  23  
XCT  "C2'"  "H2'2"  SING  N  N  24  
XCT  "C1'"  N1      SING  N  N  25  
XCT  "C1'"  "H1'"   SING  N  N  26  
XCT  N1     C2      SING  N  N  27  
XCT  N1     C6      SING  N  N  28  
XCT  C2     O2      DOUB  N  N  29  
XCT  C2     N3      SING  N  N  30  
XCT  C6     C5      DOUB  N  N  31  
XCT  C6     H6      SING  N  N  32  
XCT  C5     C4      SING  N  N  33  
XCT  C5     H5      SING  N  N  34  
XCT  C4     N3      DOUB  N  N  35  
XCT  C4     N4      SING  N  N  36  
XCT  N4     HN41    SING  N  N  37  
XCT  N4     HN42    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
XCT  SMILES            ACDLabs               10.04  "O=C1N=C(N)C=CN1C2OC(C(O)CC2)COP(=O)(O)O"  
XCT  SMILES_CANONICAL  CACTVS                3.341  "NC1=NC(=O)N(C=C1)[C@H]2CC[C@H](O)[C@@H](CO[P](O)(O)=O)O2"  
XCT  SMILES            CACTVS                3.341  "NC1=NC(=O)N(C=C1)[CH]2CC[CH](O)[CH](CO[P](O)(O)=O)O2"  
XCT  SMILES_CANONICAL  "OpenEye OEToolkits"  1.5.0  "C1C[C@@H](O[C@@H]([C@H]1O)COP(=O)(O)O)N2C=CC(=NC2=O)N"  
XCT  SMILES            "OpenEye OEToolkits"  1.5.0  "C1CC(OC(C1O)COP(=O)(O)O)N2C=CC(=NC2=O)N"  
XCT  InChI             InChI                 1.03   "InChI=1S/C10H16N3O7P/c11-8-3-4-13(10(15)12-8)9-2-1-6(14)7(20-9)5-19-21(16,17)18/h3-4,6-7,9,14H,1-2,5H2,(H2,11,12,15)(H2,16,17,18)/t6-,7+,9+/m0/s1"  
XCT  InChIKey          InChI                 1.03   ZOFWVGAMLXMFAU-LKEWCRSYSA-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
XCT  "SYSTEMATIC NAME"  ACDLabs               10.04  "4-amino-1-(2,3-dideoxy-6-O-phosphono-beta-D-erythro-hexopyranosyl)pyrimidin-2(1H)-one"  
XCT  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.5.0  "[(2R,3S,6R)-6-(4-amino-2-oxo-pyrimidin-1-yl)-3-hydroxy-oxan-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
XCT  "Create component"   2006-06-20  RCSB  
XCT  "Modify descriptor"  2011-06-04  RCSB  
XCT  "Modify synonyms"    2021-03-13  RCSB  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     XCT
_pdbx_chem_comp_synonyms.name        "2',3'-DI-DEOXY-BETA-D-GLUCOPYRANOSYL CYTOSINE"
_pdbx_chem_comp_synonyms.provenance  PDB
_pdbx_chem_comp_synonyms.type        ?
##
