data_A6U
#

_chem_comp.id                                   A6U
_chem_comp.name                                 "1,5-anhydro-2-deoxy-2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-6-O-phosphono-D-altritol"
_chem_comp.type                                 "RNA linking"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C10 H15 N2 O9 P"
_chem_comp.mon_nstd_parent_comp_id              U
_chem_comp.pdbx_synonyms                        "((2R,3S,4S,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-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                       338.208
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    A6U
_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
A6U  P       P       P  0  1  N  N  N  -4.571   3.528  35.499   4.281   0.668  -0.085  P       A6U   1  
A6U  N1      N1      N  0  1  N  N  N  -1.452   7.880  37.253  -2.551  -0.020   0.585  N1      A6U   2  
A6U  C2      C2      C  0  1  N  N  N  -0.226   8.525  37.449  -3.658  -0.018  -0.180  C2      A6U   3  
A6U  O2      O2      O  0  1  N  N  N  -0.062   9.700  37.772  -4.183  -1.073  -0.477  O2      A6U   4  
A6U  N3      N3      N  0  1  N  N  N   0.849   7.709  37.339  -4.192   1.136  -0.622  N3      A6U   5  
A6U  C4      C4      C  0  1  N  N  N   0.868   6.386  37.002  -3.621   2.315  -0.301  C4      A6U   6  
A6U  O4      O4      O  0  1  N  N  N   1.949   5.838  36.922  -4.104   3.360  -0.700  O4      A6U   7  
A6U  C5      C5      C  0  1  N  N  N  -0.419   5.770  36.783  -2.456   2.328   0.503  C5      A6U   8  
A6U  C6      C6      C  0  1  N  N  N  -1.508   6.515  36.970  -1.945   1.155   0.937  C6      A6U   9  
A6U  "C1'"   "C1'"   C  0  1  N  N  R  -2.776   8.651  37.398  -1.993  -1.292   1.050  "C1'"   A6U  10  
A6U  "C2'"   "C2'"   C  0  1  N  N  S  -3.476   9.055  36.052  -1.527  -2.117  -0.153  "C2'"   A6U  11  
A6U  "O2'"   "O2'"   O  0  1  N  N  N  -4.614   9.920  36.321  -1.042  -3.385   0.295  "O2'"   A6U  12  
A6U  "C3'"   "C3'"   C  0  1  N  N  S  -4.116   7.932  35.312  -0.403  -1.363  -0.871  "C3'"   A6U  13  
A6U  "O3'"   "O3'"   O  0  1  N  N  N  -4.746   8.417  34.107   0.090  -2.157  -1.952  "O3'"   A6U  14  
A6U  "C4'"   "C4'"   C  0  1  N  N  R  -5.057   7.226  36.324   0.732  -1.090   0.121  "C4'"   A6U  15  
A6U  "O4'"   "O4'"   O  0  1  N  N  N  -4.398   6.900  37.569   0.224  -0.346   1.230  "O4'"   A6U  16  
A6U  "C5'"   "C5'"   C  0  1  N  N  N  -5.417   5.872  35.846   1.832  -0.285  -0.573  "C5'"   A6U  17  
A6U  "O5'"   "O5'"   O  0  1  N  N  N  -4.325   4.999  36.032   2.941  -0.129   0.316  "O5'"   A6U  18  
A6U  "C6'"   "C6'"   C  0  1  N  N  N  -3.817   8.003  38.274  -0.797  -1.021   1.967  "C6'"   A6U  19  
A6U  OP1     OP1     O  0  1  N  N  N  -5.682   3.739  34.547   4.840   0.097  -1.331  OP1     A6U  20  
A6U  OP2     OP2     O  0  1  N  N  N  -3.340   2.842  35.013   3.932   2.223  -0.317  OP2     A6U  21  
A6U  OP3     OP3     O  0  1  N  Y  N  -5.084   2.793  36.826   5.361   0.531   1.101  OP3     A6U  22  
A6U  H5      H5      H  0  1  N  N  N  -0.497   4.737  36.477  -1.985   3.262   0.770  H5      A6U  23  
A6U  H6      H6      H  0  1  N  N  N  -2.476   6.041  36.899  -1.057   1.145   1.551  H6      A6U  24  
A6U  "H1'"   "H1'"   H  0  1  N  N  N  -2.404   9.558  37.897  -2.755  -1.845   1.599  "H1'"   A6U  25  
A6U  "H2'"   "H2'"   H  0  1  N  N  N  -2.657   9.501  35.469  -2.361  -2.267  -0.838  "H2'"   A6U  26  
A6U  "HO2'"  "HO2'"  H  0  0  N  N  N  -5.031  10.159  35.502  -0.730  -3.960  -0.416  "HO2'"  A6U  27  
A6U  "H3'"   "H3'"   H  0  1  N  N  N  -3.396   7.187  34.943  -0.786  -0.418  -1.256  "H3'"   A6U  28  
A6U  "HO3'"  "HO3'"  H  0  0  N  Y  N  -5.149   7.691  33.646   0.805  -1.740  -2.452  "HO3'"  A6U  29  
A6U  "H4'"   "H4'"   H  0  1  N  N  N  -5.896   7.928  36.441   1.141  -2.036   0.475  "H4'"   A6U  30  
A6U  "H5'"   "H5'"   H  0  1  N  N  N  -6.283   5.501  36.414   2.157  -0.811  -1.470  "H5'"   A6U  31  
A6U  "H5'A"  "H5'A"  H  0  0  N  N  N  -5.672   5.917  34.777   1.446   0.697  -0.847  "H5'A"  A6U  32  
A6U  "H6'"   "H6'"   H  0  1  N  N  N  -3.348   7.643  39.201  -1.115  -0.398   2.803  "H6'"   A6U  33  
A6U  "H6'A"  "H6'A"  H  0  0  N  N  N  -4.599   8.736  38.523  -0.408  -1.966   2.345  "H6'A"  A6U  34  
A6U  HOP2    HOP2    H  0  0  N  N  N  -3.443   2.618  34.096   3.560   2.662   0.460  HOP2    A6U  35  
A6U  HOP3    HOP3    H  0  0  N  Y  N  -6.017   2.627  36.756   6.195   0.988   0.927  HOP3    A6U  36  
A6U  HN3     HN3     H  0  1  N  N  N   1.738   8.126  37.528  -4.990   1.120  -1.172  HN3     A6U  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
A6U  OP1    P       DOUB  N  N   1  
A6U  OP2    P       SING  N  N   2  
A6U  P      "O5'"   SING  N  N   3  
A6U  P      OP3     SING  N  N   4  
A6U  C6     N1      SING  N  N   5  
A6U  N1     "C1'"   SING  N  N   6  
A6U  N1     C2      SING  N  N   7  
A6U  N3     C2      SING  N  N   8  
A6U  C2     O2      DOUB  N  N   9  
A6U  C4     N3      SING  N  N  10  
A6U  C5     C4      SING  N  N  11  
A6U  O4     C4      DOUB  N  N  12  
A6U  C5     C6      DOUB  N  N  13  
A6U  C5     H5      SING  N  N  14  
A6U  C6     H6      SING  N  N  15  
A6U  "C2'"  "C1'"   SING  N  N  16  
A6U  "C1'"  "C6'"   SING  N  N  17  
A6U  "C1'"  "H1'"   SING  N  N  18  
A6U  "C3'"  "C2'"   SING  N  N  19  
A6U  "C2'"  "O2'"   SING  N  N  20  
A6U  "C2'"  "H2'"   SING  N  N  21  
A6U  "O2'"  "HO2'"  SING  N  N  22  
A6U  "O3'"  "C3'"   SING  N  N  23  
A6U  "C3'"  "C4'"   SING  N  N  24  
A6U  "C3'"  "H3'"   SING  N  N  25  
A6U  "O3'"  "HO3'"  SING  N  N  26  
A6U  "C5'"  "C4'"   SING  N  N  27  
A6U  "C4'"  "O4'"   SING  N  N  28  
A6U  "C4'"  "H4'"   SING  N  N  29  
A6U  "O4'"  "C6'"   SING  N  N  30  
A6U  "C5'"  "O5'"   SING  N  N  31  
A6U  "C5'"  "H5'"   SING  N  N  32  
A6U  "C5'"  "H5'A"  SING  N  N  33  
A6U  "C6'"  "H6'"   SING  N  N  34  
A6U  "C6'"  "H6'A"  SING  N  N  35  
A6U  OP2    HOP2    SING  N  N  36  
A6U  OP3    HOP3    SING  N  N  37  
A6U  N3     HN3     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
A6U  SMILES            ACDLabs               12.01  "O=P(O)(O)OCC2OCC(N1C(=O)NC(=O)C=C1)C(O)C2O"  
A6U  SMILES_CANONICAL  CACTVS                3.370  "O[C@H]1[C@@H](O)[C@@H](CO[C@@H]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O"  
A6U  SMILES            CACTVS                3.370  "O[CH]1[CH](O)[CH](CO[CH]1CO[P](O)(O)=O)N2C=CC(=O)NC2=O"  
A6U  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(=O)NC2=O"  
A6U  SMILES            "OpenEye OEToolkits"  1.7.0  "C1C(C(C(C(O1)COP(=O)(O)O)O)O)N2C=CC(=O)NC2=O"  
A6U  InChI             InChI                 1.03   "InChI=1S/C10H15N2O9P/c13-7-1-2-12(10(16)11-7)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,(H,11,13,16)(H2,17,18,19)/t5-,6-,8+,9-/m1/s1"  
A6U  InChIKey          InChI                 1.03   PXVDRBBXHNVTFS-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
A6U  "SYSTEMATIC NAME"  ACDLabs               12.01  "1,5-anhydro-2-deoxy-2-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-6-O-phosphono-D-altritol"  
A6U  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.7.0  "[(2R,3S,4S,5R)-5-(2,4-dioxopyrimidin-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
A6U  "Create component"   2010-08-26  RCSB  
A6U  "Modify descriptor"  2011-06-04  RCSB  
A6U  "Modify synonyms"    2021-03-13  RCSB  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     A6U
_pdbx_chem_comp_synonyms.name        "((2R,3S,4S,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydro-2H-pyran-2-yl)methyl dihydrogen phosphate"
_pdbx_chem_comp_synonyms.provenance  PDB
_pdbx_chem_comp_synonyms.type        ?
##
