data_URD
#

_chem_comp.id                                   URD
_chem_comp.name                                 "1-((2R,3R,4S,5R)-TETRAHYDRO-3,4-DIHYDROXY-5-(HYDROXYMETHYL)FURAN-2-YL)PYRIDINE-2,4(1H,3H)-DIONE"
_chem_comp.type                                 "RNA LINKING"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C10 H13 N O6"
_chem_comp.mon_nstd_parent_comp_id              U
_chem_comp.pdbx_synonyms                        3-DEAZAURIDINE
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2005-04-08
_chem_comp.pdbx_modified_date                   2021-03-01
_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                       243.213
_chem_comp.one_letter_code                      U
_chem_comp.three_letter_code                    URD
_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       ?
_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
URD  "O5'"   O5*   O  0  1  N  N  N  14.592   1.028  63.327   3.373   2.694   0.738  "O5'"   URD   1  
URD  "C5'"   C5*   C  0  1  N  N  N  13.418   0.500  63.932   3.273   1.671  -0.256  "C5'"   URD   2  
URD  "C4'"   C4*   C  0  1  N  N  R  13.506   0.624  65.434   2.570   0.450   0.339  "C4'"   URD   3  
URD  "O4'"   O4*   O  0  1  N  N  N  14.431  -0.377  65.943   1.201   0.771   0.637  "O4'"   URD   4  
URD  "C1'"   C1*   C  0  1  N  N  R  15.462   0.252  66.679   0.426  -0.425   0.402  "C1'"   URD   5  
URD  N1      N1    N  0  1  N  N  N  16.705  -0.507  66.474  -0.984  -0.092   0.186  N1      URD   6  
URD  C6      C6    C  0  1  N  N  N  17.032  -1.029  65.244  -1.301   0.824  -0.768  C6      URD   7  
URD  C2      C2    C  0  1  N  N  N  17.538  -0.693  67.568  -1.917  -0.709   0.937  C2      URD   8  
URD  O2      O2    O  0  1  N  N  N  17.297  -0.230  68.670  -1.600  -1.522   1.778  O2      URD   9  
URD  C3      C3    C  0  1  N  N  N  18.664  -1.441  67.320  -3.373  -0.354   0.709  C3      URD  10  
URD  C4      C4    C  0  1  N  N  N  19.044  -2.006  66.118  -3.660   0.674  -0.369  C4      URD  11  
URD  O4      O4    O  0  1  N  N  N  19.929  -2.869  66.122  -4.795   1.020  -0.626  O4      URD  12  
URD  C5      C5    C  0  1  N  N  N  18.140  -1.749  65.034  -2.555   1.212  -1.059  C5      URD  13  
URD  "C2'"   C2*   C  0  1  N  N  R  15.512   1.676  66.141   1.055  -1.015  -0.886  "C2'"   URD  14  
URD  "O2'"   O2*   O  0  1  N  N  N  16.190   2.544  67.028   0.835  -2.425  -0.962  "O2'"   URD  15  
URD  "C3'"   C3*   C  0  1  N  N  S  14.024   1.960  65.946   2.561  -0.701  -0.687  "C3'"   URD  16  
URD  "O3'"   O3*   O  0  1  N  N  N  13.379   2.273  67.173   3.246  -1.844  -0.172  "O3'"   URD  17  
URD  "HO5'"  *HO5  H  0  0  N  Y  N  14.444   1.146  62.396   3.821   3.443   0.323  "HO5'"  URD  18  
URD  "H5'"   1H5*  H  0  1  N  N  N  13.322  -0.562  63.664   2.699   2.044  -1.104  "H5'"   URD  19  
URD  "H5''"  2H5*  H  0  0  N  N  N  12.542   1.060  63.573   4.272   1.389  -0.589  "H5''"  URD  20  
URD  "H4'"   H4*   H  0  1  N  N  N  12.470   0.502  65.782   3.082   0.132   1.247  "H4'"   URD  21  
URD  "H1'"   H1*   H  0  1  N  N  N  15.302   0.280  67.767   0.532  -1.121   1.234  "H1'"   URD  22  
URD  H6      H6    H  0  1  N  N  N  16.366  -0.850  64.413  -0.492   1.270  -1.329  H6      URD  23  
URD  H31     1H3   H  0  1  N  N  N  18.411  -2.352  67.882  -3.783   0.017   1.648  H31     URD  24  
URD  H32     2H3   H  0  1  N  N  N  19.493  -0.762  67.567  -3.904  -1.271   0.452  H32     URD  25  
URD  H5      H5    H  0  1  N  N  N  18.354  -2.137  64.049  -2.718   1.946  -1.833  H5      URD  26  
URD  "H2'"   H2*   H  0  1  N  N  N  16.086   1.823  65.214   0.666  -0.514  -1.773  "H2'"   URD  27  
URD  "HO2'"  *HO2  H  0  0  N  N  N  16.342   2.099  67.853   1.248  -2.729  -1.781  "HO2'"  URD  28  
URD  "H3'"   H3*   H  0  1  N  N  N  13.841   2.817  65.281   3.011  -0.378  -1.625  "H3'"   URD  29  
URD  "HO3'"  *HO3  H  0  0  N  Y  N  14.028   2.343  67.863   4.174  -1.591  -0.069  "HO3'"  URD  30  
#   #
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
URD  "O5'"  "C5'"   SING  N  N   1  
URD  "O5'"  "HO5'"  SING  N  N   2  
URD  "C5'"  "C4'"   SING  N  N   3  
URD  "C5'"  "H5'"   SING  N  N   4  
URD  "C5'"  "H5''"  SING  N  N   5  
URD  "C4'"  "O4'"   SING  N  N   6  
URD  "C4'"  "C3'"   SING  N  N   7  
URD  "C4'"  "H4'"   SING  N  N   8  
URD  "O4'"  "C1'"   SING  N  N   9  
URD  "C1'"  N1      SING  N  N  10  
URD  "C1'"  "C2'"   SING  N  N  11  
URD  "C1'"  "H1'"   SING  N  N  12  
URD  N1     C6      SING  N  N  13  
URD  N1     C2      SING  N  N  14  
URD  C6     C5      DOUB  N  N  15  
URD  C6     H6      SING  N  N  16  
URD  C2     O2      DOUB  N  N  17  
URD  C2     C3      SING  N  N  18  
URD  C3     C4      SING  N  N  19  
URD  C3     H31     SING  N  N  20  
URD  C3     H32     SING  N  N  21  
URD  C4     O4      DOUB  N  N  22  
URD  C4     C5      SING  N  N  23  
URD  C5     H5      SING  N  N  24  
URD  "C2'"  "O2'"   SING  N  N  25  
URD  "C2'"  "C3'"   SING  N  N  26  
URD  "C2'"  "H2'"   SING  N  N  27  
URD  "O2'"  "HO2'"  SING  N  N  28  
URD  "C3'"  "O3'"   SING  N  N  29  
URD  "C3'"  "H3'"   SING  N  N  30  
URD  "O3'"  "HO3'"  SING  N  N  31  
#   #
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
URD  SMILES            ACDLabs               10.04  "O=C1C=CN(C(=O)C1)C2OC(C(O)C2O)CO"  
URD  SMILES_CANONICAL  CACTVS                3.341  "OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2C=CC(=O)CC2=O"  
URD  SMILES            CACTVS                3.341  "OC[CH]1O[CH]([CH](O)[CH]1O)N2C=CC(=O)CC2=O"  
URD  SMILES_CANONICAL  "OpenEye OEToolkits"  1.5.0  "C1C(=O)C=CN(C1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO)O)O"  
URD  SMILES            "OpenEye OEToolkits"  1.5.0  "C1C(=O)C=CN(C1=O)C2C(C(C(O2)CO)O)O"  
URD  InChI             InChI                 1.03   "InChI=1S/C10H13NO6/c12-4-6-8(15)9(16)10(17-6)11-2-1-5(13)3-7(11)14/h1-2,6,8-10,12,15-16H,3-4H2/t6-,8-,9-,10-/m1/s1"  
URD  InChIKey          InChI                 1.03   WIRVQQCUKDPURA-PEBGCTIMSA-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
URD  "SYSTEMATIC NAME"  ACDLabs               10.04  "1-beta-D-ribofuranosylpyridine-2,4(1H,3H)-dione"  
URD  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.5.0  "1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]pyridine-2,4-dione"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
URD  "Create component"   2005-04-08  RCSB  
URD  "Modify descriptor"  2011-06-04  RCSB  
URD  "Modify synonyms"    2021-03-01  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     URD
_pdbx_chem_comp_synonyms.name        3-DEAZAURIDINE
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
