data_A6C
#

_chem_comp.id                                   A6C
_chem_comp.name                                 "2-(4-amino-2-oxopyrimidin-1(2H)-yl)-1,5-anhydro-2-deoxy-6-O-phosphono-D-altritol"
_chem_comp.type                                 "RNA linking"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C10 H16 N3 O8 P"
_chem_comp.mon_nstd_parent_comp_id              C
_chem_comp.pdbx_synonyms                        "((2R,3S,4S,5R)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydro-2H-pyran-2-yl)methyl dihydrogen phosphate"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2010-08-26
_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                       337.223
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    A6C
_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       3OK2
_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
A6C  P       P       P  0  1  N  N  N  -0.737   3.176  -36.736   4.255   0.743  -0.058  P       A6C   1  
A6C  N1      N1      N  0  1  N  N  N   4.213   3.844  -34.003  -2.569  -0.041   0.581  N1      A6C   2  
A6C  C2      C2      C  0  1  N  N  N   5.268   3.242  -33.257  -3.673  -0.050  -0.189  C2      A6C   3  
A6C  O2      O2      O  0  1  N  N  N   6.262   3.952  -32.985  -4.183  -1.115  -0.494  O2      A6C   4  
A6C  N3      N3      N  0  1  N  N  N   5.219   1.880  -32.984  -4.219   1.085  -0.622  N3      A6C   5  
A6C  C4      C4      C  0  1  N  N  N   4.134   1.149  -33.349  -3.685   2.257  -0.305  C4      A6C   6  
A6C  N4      N4      N  0  1  N  N  N   4.087  -0.143  -32.976  -4.258   3.423  -0.758  N4      A6C   7  
A6C  C5      C5      C  0  1  N  N  N   3.022   1.765  -34.055  -2.528   2.302   0.499  C5      A6C   8  
A6C  C6      C6      C  0  1  N  N  N   3.119   3.085  -34.399  -1.985   1.139   0.932  C6      A6C   9  
A6C  "C1'"   "C1'"   C  0  1  N  N  R   4.354   5.317  -34.376  -1.995  -1.305   1.047  "C1'"   A6C  10  
A6C  "C2'"   "C2'"   C  0  1  N  N  S   4.664   5.499  -35.883  -1.512  -2.123  -0.155  "C2'"   A6C  11  
A6C  "O2'"   "O2'"   O  0  1  N  N  N   5.031   6.871  -36.037  -1.014  -3.385   0.295  "O2'"   A6C  12  
A6C  "C3'"   "C3'"   C  0  1  N  N  S   3.453   5.157  -36.746  -0.396  -1.353  -0.866  "C3'"   A6C  13  
A6C  "O3'"   "O3'"   O  0  1  N  N  N   3.630   5.203  -38.152   0.112  -2.138  -1.947  "O3'"   A6C  14  
A6C  "C4'"   "C4'"   C  0  1  N  N  R   2.171   5.882  -36.301   0.730  -1.065   0.130  "C4'"   A6C  15  
A6C  "O4'"   "O4'"   O  0  1  N  N  N   2.002   5.720  -34.898   0.207  -0.329   1.238  "O4'"   A6C  16  
A6C  "C5'"   "C5'"   C  0  1  N  N  N   0.902   5.307  -36.944   1.822  -0.243  -0.558  "C5'"   A6C  17  
A6C  "O5'"   "O5'"   O  0  1  N  N  N   0.706   3.927  -36.631   2.924  -0.074   0.336  "O5'"   A6C  18  
A6C  "C6'"   "C6'"   C  0  1  N  N  N   3.113   6.141  -34.090  -0.808  -1.019   1.970  "C6'"   A6C  19  
A6C  OP1     OP1     O  0  1  N  N  N  -1.280   3.404  -38.098   3.885   2.104  -0.504  OP1     A6C  20  
A6C  OP2     OP2     O  0  1  N  N  N  -0.537   1.855  -36.147   5.223   0.842   1.225  OP2     A6C  21  
A6C  OP3     OP3     O  0  1  N  Y  N  -1.698   3.929  -35.711   5.021  -0.023  -1.250  OP3     A6C  22  
A6C  HN4     HN4     H  0  1  N  N  N   4.837  -0.538  -32.446  -5.054   3.390  -1.311  HN4     A6C  23  
A6C  HN4A    HN4A    H  0  0  N  N  N   3.302  -0.708  -33.229  -3.865   4.279  -0.525  HN4A    A6C  24  
A6C  H5      H5      H  0  1  N  N  N   2.140   1.193  -34.302  -2.081   3.248   0.766  H5      A6C  25  
A6C  H6      H6      H  0  1  N  N  N   2.336   3.543  -34.985  -1.099   1.147   1.550  H6      A6C  26  
A6C  "H1'"   "H1'"   H  0  1  N  N  N   5.183   5.672  -33.746  -2.752  -1.870   1.592  "H1'"   A6C  27  
A6C  "H2'"   "H2'"   H  0  1  N  N  N   5.468   4.824  -36.210  -2.342  -2.283  -0.844  "H2'"   A6C  28  
A6C  "HO2'"  "HO2'"  H  0  0  N  N  N   5.234   7.044  -36.949  -0.691  -3.955  -0.416  "HO2'"  A6C  29  
A6C  "H3'"   "H3'"   H  0  1  N  N  N   3.327   4.083  -36.544  -0.790  -0.413  -1.252  "H3'"   A6C  30  
A6C  "HO3'"  "HO3'"  H  0  0  N  Y  N   2.815   4.973  -38.582   0.824  -1.711  -2.443  "HO3'"  A6C  31  
A6C  "H4'"   "H4'"   H  0  1  N  N  N   2.294   6.932  -36.605   1.151  -2.005   0.485  "H4'"   A6C  32  
A6C  "H5'"   "H5'"   H  0  1  N  N  N   0.036   5.875  -36.573   2.159  -0.765  -1.454  "H5'"   A6C  33  
A6C  "H5'A"  "H5'A"  H  0  0  N  N  N   0.989   5.407  -38.036   1.424   0.733  -0.833  "H5'A"  A6C  34  
A6C  "H6'"   "H6'"   H  0  1  N  N  N   2.845   6.022  -33.030  -1.137  -0.401   2.805  "H6'"   A6C  35  
A6C  "H6'A"  "H6'A"  H  0  0  N  N  N   3.331   7.197  -34.309  -0.407  -1.959   2.349  "H6'A"  A6C  36  
A6C  HOP2    HOP2    H  0  0  N  N  N  -0.806   1.187  -36.767   6.046   1.322   1.060  HOP2    A6C  37  
A6C  HOP3    HOP3    H  0  0  N  Y  N  -2.400   4.354  -36.189   5.294  -0.923  -1.027  HOP3    A6C  38  
#   #
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
A6C  OP1    P       DOUB  N  N   1  
A6C  P      "O5'"   SING  N  N   2  
A6C  P      OP2     SING  N  N   3  
A6C  P      OP3     SING  N  N   4  
A6C  C6     N1      SING  N  N   5  
A6C  "C1'"  N1      SING  N  N   6  
A6C  N1     C2      SING  N  N   7  
A6C  C2     O2      DOUB  N  N   8  
A6C  C2     N3      SING  N  N   9  
A6C  C4     N3      DOUB  N  N  10  
A6C  C5     C4      SING  N  N  11  
A6C  C4     N4      SING  N  N  12  
A6C  N4     HN4     SING  N  N  13  
A6C  N4     HN4A    SING  N  N  14  
A6C  C6     C5      DOUB  N  N  15  
A6C  C5     H5      SING  N  N  16  
A6C  C6     H6      SING  N  N  17  
A6C  "C2'"  "C1'"   SING  N  N  18  
A6C  "C1'"  "C6'"   SING  N  N  19  
A6C  "C1'"  "H1'"   SING  N  N  20  
A6C  "C3'"  "C2'"   SING  N  N  21  
A6C  "O2'"  "C2'"   SING  N  N  22  
A6C  "C2'"  "H2'"   SING  N  N  23  
A6C  "O2'"  "HO2'"  SING  N  N  24  
A6C  "O3'"  "C3'"   SING  N  N  25  
A6C  "C3'"  "C4'"   SING  N  N  26  
A6C  "C3'"  "H3'"   SING  N  N  27  
A6C  "O3'"  "HO3'"  SING  N  N  28  
A6C  "C5'"  "C4'"   SING  N  N  29  
A6C  "C4'"  "O4'"   SING  N  N  30  
A6C  "C4'"  "H4'"   SING  N  N  31  
A6C  "O4'"  "C6'"   SING  N  N  32  
A6C  "C5'"  "O5'"   SING  N  N  33  
A6C  "C5'"  "H5'"   SING  N  N  34  
A6C  "C5'"  "H5'A"  SING  N  N  35  
A6C  "C6'"  "H6'"   SING  N  N  36  
A6C  "C6'"  "H6'A"  SING  N  N  37  
A6C  OP2    HOP2    SING  N  N  38  
A6C  OP3    HOP3    SING  N  N  39  
#   #
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
A6C  SMILES            ACDLabs               12.01  "O=P(O)(O)OCC2OCC(N1C(=O)N=C(N)C=C1)C(O)C2O"  
A6C  SMILES_CANONICAL  CACTVS                3.370  "NC1=NC(=O)N(C=C1)[C@@H]2CO[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O"  
A6C  SMILES            CACTVS                3.370  "NC1=NC(=O)N(C=C1)[CH]2CO[CH](CO[P](O)(O)=O)[CH](O)[CH]2O"  
A6C  SMILES_CANONICAL  "OpenEye OEToolkits"  1.7.0  "C1[C@H]([C@@H]([C@@H]([C@H](O1)COP(=O)(O)O)O)O)N2C=CC(=NC2=O)N"  
A6C  SMILES            "OpenEye OEToolkits"  1.7.0  "C1C(C(C(C(O1)COP(=O)(O)O)O)O)N2C=CC(=NC2=O)N"  
A6C  InChI             InChI                 1.03   "InChI=1S/C10H16N3O8P/c11-7-1-2-13(10(16)12-7)5-3-20-6(9(15)8(5)14)4-21-22(17,18)19/h1-2,5-6,8-9,14-15H,3-4H2,(H2,11,12,16)(H2,17,18,19)/t5-,6-,8+,9-/m1/s1"  
A6C  InChIKey          InChI                 1.03   VRGYQABDDBPVLA-MTSNSDSCSA-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
A6C  "SYSTEMATIC NAME"  ACDLabs               12.01  "2-(4-amino-2-oxopyrimidin-1(2H)-yl)-1,5-anhydro-2-deoxy-6-O-phosphono-D-altritol"  
A6C  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.7.0  "[(2R,3S,4S,5R)-5-(4-azanyl-2-oxo-pyrimidin-1-yl)-3,4-dihydroxy-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
A6C  "Create component"   2010-08-26  RCSB  
A6C  "Modify descriptor"  2011-06-04  RCSB  
A6C  "Modify synonyms"    2021-03-13  RCSB  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     A6C
_pdbx_chem_comp_synonyms.name        "((2R,3S,4S,5R)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydro-2H-pyran-2-yl)methyl dihydrogen phosphate"
_pdbx_chem_comp_synonyms.provenance  PDB
_pdbx_chem_comp_synonyms.type        ?
##
