data_U4P
#

_chem_comp.id                                   U4P
_chem_comp.name                                 "5'-deoxyuridine"
_chem_comp.type                                 non-polymer
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C9 H12 N2 O5"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2020-04-16
_chem_comp.pdbx_modified_date                   2021-04-16
_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                       228.202
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    U4P
_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       6WKB
_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
U4P  OAC    O1   O  0  1  N  N  N  2.750  -56.622  25.466   0.331   1.364   0.871  OAC    U4P   1  
U4P  CAM    C1   C  0  1  N  N  N  2.726  -57.284  24.229   1.198   0.659   0.393  CAM    U4P   2  
U4P  NAI    N1   N  0  1  N  N  N  1.868  -58.447  24.080   2.487   0.888   0.706  NAI    U4P   3  
U4P  CAL    C2   C  0  1  N  N  N  1.812  -59.128  22.900   3.461   0.115   0.184  CAL    U4P   4  
U4P  OAB    O2   O  0  1  N  N  N  0.986  -60.255  22.753   4.627   0.321   0.467  OAB    U4P   5  
U4P  CAK    C3   C  0  1  N  N  N  2.602  -58.691  21.786   3.115  -0.940  -0.695  CAK    U4P   6  
U4P  CAG    C4   C  0  1  N  N  N  3.433  -57.566  21.916   1.814  -1.147  -0.992  CAG    U4P   7  
U4P  NAR    N2   N  0  1  N  N  N  3.499  -56.853  23.135   0.856  -0.343  -0.437  NAR    U4P   8  
U4P  "C1'"  C5   C  0  1  N  N  R  4.360  -55.734  23.182  -0.555  -0.569  -0.759  "C1'"  U4P   9  
U4P  "O4'"  O3   O  0  1  N  N  N  5.616  -56.025  24.071  -1.153   0.655  -1.219  "O4'"  U4P  10  
U4P  "C4'"  C6   C  0  1  N  N  R  5.688  -54.662  24.813  -2.523   0.653  -0.762  "C4'"  U4P  11  
U4P  "C5'"  C7   C  0  1  N  N  N  6.285  -54.823  26.162  -3.080   2.077  -0.724  "C5'"  U4P  12  
U4P  "C3'"  C8   C  0  1  N  N  S  4.305  -54.199  24.936  -2.425   0.066   0.669  "C3'"  U4P  13  
U4P  "O3'"  O4   O  0  1  N  N  N  4.239  -52.746  25.175  -3.662  -0.534   1.060  "O3'"  U4P  14  
U4P  "C2'"  C9   C  0  1  N  N  R  3.714  -54.516  23.684  -1.319  -1.004   0.507  "C2'"  U4P  15  
U4P  "O2'"  O5   O  0  1  N  N  N  3.996  -53.405  22.734  -1.897  -2.297   0.322  "O2'"  U4P  16  
U4P  H1     H1   H  0  1  N  N  N  1.311  -58.752  24.853   2.716   1.612   1.309  H1     U4P  17  
U4P  H2     H2   H  0  1  N  N  N  2.558  -59.226  20.849   3.882  -1.567  -1.125  H2     U4P  18  
U4P  H3     H3   H  0  1  N  N  N  4.028  -57.242  21.075   1.531  -1.947  -1.660  H3     U4P  19  
U4P  H4     H4   H  0  1  N  N  N  4.729  -55.529  22.166  -0.642  -1.338  -1.527  H4     U4P  20  
U4P  H5     H5   H  0  1  N  N  N  6.281  -53.953  24.216  -3.138   0.015  -1.397  H5     U4P  21  
U4P  H6     H6   H  0  1  N  N  N  6.324  -53.846  26.665  -3.067   2.499  -1.729  H6     U4P  22  
U4P  H7     H7   H  0  1  N  N  N  5.670  -55.516  26.755  -4.105   2.056  -0.352  H7     U4P  23  
U4P  H8     H8   H  0  1  N  N  N  7.304  -55.227  26.066  -2.467   2.690  -0.064  H8     U4P  24  
U4P  H9     H9   H  0  1  N  N  N  3.799  -54.736  25.752  -2.124   0.832   1.384  H9     U4P  25  
U4P  H10    H10  H  0  1  N  N  N  4.636  -52.544  26.014  -4.407   0.082   1.088  H10    U4P  26  
U4P  H11    H11  H  0  1  N  N  N  2.629  -54.667  23.782  -0.655  -1.002   1.372  H11    U4P  27  
U4P  H12    H12  H  0  1  N  N  N  3.583  -52.608  23.046  -2.390  -2.621   1.089  H12    U4P  28  
#   #
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
U4P  CAK    CAG    DOUB  N  N   1  
U4P  CAK    CAL    SING  N  N   2  
U4P  CAG    NAR    SING  N  N   3  
U4P  "O2'"  "C2'"  SING  N  N   4  
U4P  OAB    CAL    DOUB  N  N   5  
U4P  CAL    NAI    SING  N  N   6  
U4P  NAR    "C1'"  SING  N  N   7  
U4P  NAR    CAM    SING  N  N   8  
U4P  "C1'"  "C2'"  SING  N  N   9  
U4P  "C1'"  "O4'"  SING  N  N  10  
U4P  "C2'"  "C3'"  SING  N  N  11  
U4P  "O4'"  "C4'"  SING  N  N  12  
U4P  NAI    CAM    SING  N  N  13  
U4P  CAM    OAC    DOUB  N  N  14  
U4P  "C4'"  "C3'"  SING  N  N  15  
U4P  "C4'"  "C5'"  SING  N  N  16  
U4P  "C3'"  "O3'"  SING  N  N  17  
U4P  NAI    H1     SING  N  N  18  
U4P  CAK    H2     SING  N  N  19  
U4P  CAG    H3     SING  N  N  20  
U4P  "C1'"  H4     SING  N  N  21  
U4P  "C4'"  H5     SING  N  N  22  
U4P  "C5'"  H6     SING  N  N  23  
U4P  "C5'"  H7     SING  N  N  24  
U4P  "C5'"  H8     SING  N  N  25  
U4P  "C3'"  H9     SING  N  N  26  
U4P  "O3'"  H10    SING  N  N  27  
U4P  "C2'"  H11    SING  N  N  28  
U4P  "O2'"  H12    SING  N  N  29  
#   #
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
U4P  SMILES            ACDLabs               12.01  "O=C1NC(=O)C=CN1C2C(C(C(O2)C)O)O"  
U4P  InChI             InChI                 1.03   "InChI=1S/C9H12N2O5/c1-4-6(13)7(14)8(16-4)11-3-2-5(12)10-9(11)15/h2-4,6-8,13-14H,1H3,(H,10,12,15)/t4-,6-,7-,8-/m1/s1"  
U4P  InChIKey          InChI                 1.03   WUBAOANSQGKRHF-XVFCMESISA-N  
U4P  SMILES_CANONICAL  CACTVS                3.385  "C[C@H]1O[C@H]([C@H](O)[C@@H]1O)N2C=CC(=O)NC2=O"  
U4P  SMILES            CACTVS                3.385  "C[CH]1O[CH]([CH](O)[CH]1O)N2C=CC(=O)NC2=O"  
U4P  SMILES_CANONICAL  "OpenEye OEToolkits"  2.0.7  "C[C@@H]1[C@H]([C@H]([C@@H](O1)N2C=CC(=O)NC2=O)O)O"  
U4P  SMILES            "OpenEye OEToolkits"  2.0.7  "CC1C(C(C(O1)N2C=CC(=O)NC2=O)O)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
U4P  "SYSTEMATIC NAME"  ACDLabs               12.01  "5'-deoxyuridine"  
U4P  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  2.0.7  "1-[(2~{R},3~{R},4~{S},5~{R})-5-methyl-3,4-bis(oxidanyl)oxolan-2-yl]pyrimidine-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
U4P  "Create component"  2020-04-16  RCSB  
U4P  "Initial release"   2021-04-21  RCSB  
##
