data_U23
#

_chem_comp.id                                   U23
_chem_comp.name                                 "URIDINE-5'-MONOPHOSPHATE-2',3'-CYCLIC PHOSPHATE"
_chem_comp.type                                 "RNA linking"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C9 H12 N2 O11 P2"
_chem_comp.mon_nstd_parent_comp_id              U
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2020-07-31
_chem_comp.pdbx_modified_date                   2020-09-04
_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                       386.146
_chem_comp.one_letter_code                      U
_chem_comp.three_letter_code                    U23
_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       7JJU
_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
U23  N1     N1   N  0  1  N  N  N  64.028  46.229  76.004  -2.231  -1.048  -0.222  N1     U23   1  
U23  C2     C1   C  0  1  N  N  N  64.697  45.492  75.077  -3.245  -1.390  -1.038  C2     U23   2  
U23  O2     O1   O  0  1  N  N  N  65.790  45.026  75.348  -3.322  -0.887  -2.142  O2     U23   3  
U23  N3     N2   N  0  1  N  N  N  64.153  45.270  73.845  -4.175  -2.281  -0.649  N3     U23   4  
U23  C4     C2   C  0  1  N  N  N  62.921  45.809  73.571  -4.105  -2.849   0.572  C4     U23   5  
U23  O4     O2   O  0  1  N  N  N  62.413  45.622  72.467  -4.946  -3.656   0.925  O4     U23   6  
U23  C5     C3   C  0  1  N  N  N  62.226  46.576  74.535  -3.043  -2.497   1.441  C5     U23   7  
U23  C6     C4   C  0  1  N  N  N  62.798  46.770  75.734  -2.124  -1.600   1.025  C6     U23   8  
U23  "C1'"  C5   C  0  1  N  N  R  64.649  46.450  77.331  -1.230  -0.079  -0.675  "C1'"  U23   9  
U23  "C2'"  C6   C  0  1  N  N  R  65.698  47.566  77.240  -1.305   1.197   0.190  "C2'"  U23  10  
U23  "C3'"  C7   C  0  1  N  N  R  65.416  48.474  78.430   0.115   1.321   0.795  "C3'"  U23  11  
U23  "O3'"  O3   O  0  1  N  N  N  66.634  48.582  79.153   0.553   2.684   0.754  "O3'"  U23  12  
U23  "C4'"  C8   C  0  1  N  N  R  64.380  47.712  79.233   0.964   0.468  -0.176  "C4'"  U23  13  
U23  "O4'"  O4   O  0  1  N  N  N  63.675  46.885  78.263   0.088  -0.628  -0.516  "O4'"  U23  14  
U23  "C5'"  C9   C  0  1  N  N  N  63.427  48.655  79.907   2.226  -0.046   0.521  "C5'"  U23  15  
U23  "O5'"  O5   O  0  1  N  N  N  62.448  49.090  78.964   3.048  -0.730  -0.426  "O5'"  U23  16  
U23  "O2'"  O6   O  0  1  N  N  N  67.013  47.067  77.411  -1.495   2.324  -0.700  "O2'"  U23  17  
U23  OP1    O7   O  0  1  N  N  N  61.170  50.590  80.519   4.262  -2.349   1.083  OP1    U23  18  
U23  OP2    O8   O  0  1  N  N  N  60.158  49.965  78.411   5.043  -2.194  -1.312  OP2    U23  19  
U23  OP5    O9   O  0  1  N  N  N  68.607  47.253  79.150  -0.179   4.519  -0.875  OP5    U23  20  
U23  OP4    O10  O  0  1  N  N  N  68.344  49.015  77.540  -1.601   4.189   1.209  OP4    U23  21  
U23  P      P1   P  0  1  N  N  N  61.033  49.540  79.506   4.458  -1.403  -0.038  P      U23  22  
U23  P2     P2   P  0  1  N  N  N  67.650  47.975  78.308  -0.680   3.505   0.079  P2     U23  23  
U23  H1     H1   H  0  1  N  N  N  64.640  44.728  73.160  -4.900  -2.516  -1.249  H1     U23  24  
U23  H2     H2   H  0  1  N  N  N  61.257  46.996  74.311  -2.970  -2.941   2.423  H2     U23  25  
U23  H3     H3   H  0  1  N  N  N  62.288  47.353  76.487  -1.307  -1.321   1.674  H3     U23  26  
U23  H4     H4   H  0  1  N  N  N  65.135  45.525  77.675  -1.405   0.172  -1.721  H4     U23  27  
U23  H5     H5   H  0  1  N  N  N  64.881  47.084  79.985   1.223   1.043  -1.066  H5     U23  28  
U23  H6     H6   H  0  1  N  N  N  62.930  48.140  80.742   2.777   0.796   0.940  H6     U23  29  
U23  H7     H7   H  0  1  N  N  N  63.980  49.525  80.290   1.945  -0.731   1.321  H7     U23  30  
U23  H9     H9   H  0  1  N  N  N  59.849  50.848  78.577   5.894  -2.626  -1.151  H9     U23  31  
U23  H11    H11  H  0  1  N  N  N  69.270  49.001  77.751  -2.349   4.690   0.857  H11    U23  32  
U23  OP3    OP3  O  0  1  N  Y  N  60.424  48.220  80.189   5.497  -0.255   0.404  OP3    U23  33  
U23  H12    H12  H  0  1  N  N  N  65.585  48.121  76.297  -2.078   1.132   0.957  H12    U23  34  
U23  H13    H13  H  0  1  N  N  N  65.028  49.450  78.102   0.147   0.928   1.811  H13    U23  35  
U23  H8     H8   H  0  1  N  N  N  60.274  48.382  81.113   5.673   0.402  -0.283  H8     U23  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
U23  N1     C2     SING  N  N   1  
U23  N1     C6     SING  N  N   2  
U23  N1     "C1'"  SING  N  N   3  
U23  C2     O2     DOUB  N  N   4  
U23  C2     N3     SING  N  N   5  
U23  N3     C4     SING  N  N   6  
U23  C4     O4     DOUB  N  N   7  
U23  C4     C5     SING  N  N   8  
U23  C5     C6     DOUB  N  N   9  
U23  "C1'"  "C2'"  SING  N  N  10  
U23  "C1'"  "O4'"  SING  N  N  11  
U23  "C2'"  "C3'"  SING  N  N  12  
U23  "C2'"  "O2'"  SING  N  N  13  
U23  "C3'"  "O3'"  SING  N  N  14  
U23  "C3'"  "C4'"  SING  N  N  15  
U23  "O3'"  P2     SING  N  N  16  
U23  "C4'"  "O4'"  SING  N  N  17  
U23  "C4'"  "C5'"  SING  N  N  18  
U23  "C5'"  "O5'"  SING  N  N  19  
U23  "O5'"  P      SING  N  N  20  
U23  "O2'"  P2     SING  N  N  21  
U23  OP1    P      DOUB  N  N  22  
U23  OP2    P      SING  N  N  23  
U23  OP5    P2     DOUB  N  N  24  
U23  OP4    P2     SING  N  N  25  
U23  N3     H1     SING  N  N  26  
U23  C5     H2     SING  N  N  27  
U23  C6     H3     SING  N  N  28  
U23  "C1'"  H4     SING  N  N  29  
U23  "C4'"  H5     SING  N  N  30  
U23  "C5'"  H6     SING  N  N  31  
U23  "C5'"  H7     SING  N  N  32  
U23  OP2    H9     SING  N  N  33  
U23  OP4    H11    SING  N  N  34  
U23  P      OP3    SING  N  N  35  
U23  "C2'"  H12    SING  N  N  36  
U23  "C3'"  H13    SING  N  N  37  
U23  OP3    H8     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
U23  SMILES            ACDLabs               12.01  "N1(C(=O)NC(=O)C=C1)C3C2C(OP(O2)(=O)O)C(O3)COP(=O)(O)O"  
U23  InChI             InChI                 1.03   "InChI=1S/C9H12N2O11P2/c12-5-1-2-11(9(13)10-5)8-7-6(21-24(17,18)22-7)4(20-8)3-19-23(14,15)16/h1-2,4,6-8H,3H2,(H,17,18)(H,10,12,13)(H2,14,15,16)/t4-,6-,7-,8-/m1/s1"  
U23  InChIKey          InChI                 1.03   PXHRDNPZBBFFEO-XVFCMESISA-N  
U23  SMILES_CANONICAL  CACTVS                3.385  "O[P](O)(=O)OC[C@H]1O[C@H]([C@@H]2O[P](O)(=O)O[C@H]12)N3C=CC(=O)NC3=O"  
U23  SMILES            CACTVS                3.385  "O[P](O)(=O)OC[CH]1O[CH]([CH]2O[P](O)(=O)O[CH]12)N3C=CC(=O)NC3=O"  
U23  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "C1=CN(C(=O)NC1=O)[C@H]2[C@H]3[C@@H]([C@H](O2)COP(=O)(O)O)OP(=O)(O3)O"  
U23  SMILES            "OpenEye OEToolkits"  2.0.7  "C1=CN(C(=O)NC1=O)C2C3C(C(O2)COP(=O)(O)O)OP(=O)(O3)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
U23  "SYSTEMATIC NAME"  ACDLabs               12.01  "[(2S,3aR,4R,6R,6aR)-6-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-2-hydroxy-2-oxotetrahydro-2H-2lambda~5~-furo[3,4-d][1,3,2]dioxaphosphol-4-yl]methyl dihydrogen phosphate"  
U23  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  "[(3~{a}~{R},4~{R},6~{R},6~{a}~{R})-4-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-2-oxidanyl-2-oxidanylidene-3~{a},4,6,6~{a}-tetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-6-yl]methyl dihydrogen phosphate"  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     U23
_pdbx_chem_comp_synonyms.name        "[(2S,3aR,4R,6R,6aR)-6-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-2-hydroxy-2-oxotetrahydro-2H-2lambda~5~-furo[3,4-d][1,3,2]dioxaphosphol-4-yl]methyl dihydrogen phosphate"
_pdbx_chem_comp_synonyms.provenance  PDB
_pdbx_chem_comp_synonyms.type        ?
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
U23  "Create component"  2020-07-31  RCSB  
U23  "Initial release"   2020-09-09  RCSB  
##
