data_NDU
#

_chem_comp.id                                   NDU
_chem_comp.name                                 "2'-DEOXY-5-NITROURIDINE 5'-MONOPHOSPHATE"
_chem_comp.type                                 "DNA LINKING"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C9 H14 N3 O10 P"
_chem_comp.mon_nstd_parent_comp_id              DU
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2007-10-27
_chem_comp.pdbx_modified_date                   2019-05-07
_chem_comp.pdbx_ambiguous_flag                  ?
_chem_comp.pdbx_release_status                  REL
_chem_comp.pdbx_replaced_by                     ?
_chem_comp.pdbx_replaces                        ?
_chem_comp.formula_weight                       355.195
_chem_comp.one_letter_code                      U
_chem_comp.three_letter_code                    NDU
_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       2VF0
_chem_comp.pdbx_subcomponent_list               ?
_chem_comp.pdbx_processing_site                 EBI
#   #
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
NDU  P       P       P   0  1  N  N  N  15.190  24.243  25.855  -4.291   1.194   0.147  P       NDU   1  
NDU  OP1     OP1     O   0  1  N  N  N  14.052  25.000  25.279  -5.489   0.331   0.251  OP1     NDU   2  
NDU  OP2     OP2     O   0  1  N  N  N  16.168  25.119  26.563  -4.598   2.419  -0.852  OP2     NDU   3  
NDU  OP3     OP3     O   0  1  N  N  N  15.687  23.295  24.822  -3.917   1.770   1.603  OP3     NDU   4  
NDU  "O5'"   "O5'"   O   0  1  N  N  N  14.758  23.340  27.090  -3.056   0.333  -0.423  "O5'"   NDU   5  
NDU  "C5'"   "C5'"   C   0  1  N  N  N  15.423  22.370  27.854  -2.608  -0.881   0.183  "C5'"   NDU   6  
NDU  "C4'"   "C4'"   C   0  1  N  N  R  14.865  22.227  29.256  -1.423  -1.438  -0.608  "C4'"   NDU   7  
NDU  "C3'"   "C3'"   C   0  1  N  N  S  15.129  23.279  30.328  -1.001  -2.814  -0.046  "C3'"   NDU   8  
NDU  "O3'"   "O3'"   O   0  1  N  N  N  14.049  23.447  31.235  -1.556  -3.868  -0.835  "O3'"   NDU   9  
NDU  "C2'"   "C2'"   C   0  1  N  N  N  16.394  22.809  31.025   0.540  -2.808  -0.158  "C2'"   NDU  10  
NDU  "C1'"   "C1'"   C   0  1  N  N  R  16.214  21.283  30.990   0.867  -1.430  -0.774  "C1'"   NDU  11  
NDU  "O4'"   "O4'"   O   0  1  N  N  N  15.309  21.010  29.888  -0.262  -0.596  -0.433  "O4'"   NDU  12  
NDU  N1      N1      N   0  1  N  N  N  17.535  20.612  31.200   2.096  -0.888  -0.188  N1      NDU  13  
NDU  C2      C2      C   0  1  N  N  N  18.144  20.306  32.483   2.125  -0.572   1.117  C2      NDU  14  
NDU  O2      O2      O   0  1  N  N  N  18.066  21.020  33.439   1.164  -0.838   1.812  O2      NDU  15  
NDU  N3      N3      N   0  1  N  N  N  18.862  19.104  32.614   3.189   0.030   1.672  N3      NDU  16  
NDU  C4      C4      C   0  1  N  N  N  19.339  18.261  31.574   4.165   0.555   0.908  C4      NDU  17  
NDU  O4      O4      O   0  1  N  N  N  20.254  17.484  31.735   5.156   1.023   1.426  O4      NDU  18  
NDU  C5      C5      C   0  1  N  N  R  18.607  18.369  30.165   4.024   0.561  -0.594  C5      NDU  19  
NDU  C6      C6      C   0  1  N  N  N  17.814  19.765  29.851   3.278  -0.705  -1.033  C6      NDU  20  
NDU  N5      N5      N   1  1  N  N  N  18.831  17.494  29.096   3.273   1.747  -1.010  N5      NDU  21  
NDU  O51     O51     O  -1  1  N  N  N  19.445  16.416  29.225   3.784   2.561  -1.759  O51     NDU  22  
NDU  O52     O52     O   0  1  N  N  N  18.472  17.650  27.908   2.136   1.920  -0.609  O52     NDU  23  
NDU  HP2     HP2     H   0  1  N  N  N  16.901  25.305  25.988  -5.332   2.982  -0.570  HP2     NDU  24  
NDU  HP3     HP3     H   0  1  N  N  N  15.793  23.753  23.996  -3.140   2.346   1.611  HP3     NDU  25  
NDU  "H51'"  "1H5'"  H   0  0  N  N  N  15.323  21.401  27.343  -2.300  -0.682   1.209  "H51'"  NDU  26  
NDU  "H52'"  "2H5'"  H   0  0  N  N  N  16.472  22.688  27.949  -3.420  -1.609   0.182  "H52'"  NDU  27  
NDU  "H4'"   "H4'"   H   0  1  N  N  N  13.802  22.302  28.985  -1.677  -1.521  -1.664  "H4'"   NDU  28  
NDU  "H3'"   "H3'"   H   0  1  N  N  N  15.243  24.278  29.881  -1.310  -2.913   0.994  "H3'"   NDU  29  
NDU  HA      HA      H   0  1  N  N  N  14.384  23.485  32.123  -1.323  -4.755  -0.526  HA      NDU  30  
NDU  "H21'"  "1H2'"  H   0  0  N  N  N  17.304  23.133  30.499   0.995  -2.904   0.828  "H21'"  NDU  31  
NDU  "H22'"  "2H2'"  H   0  0  N  N  N  16.523  23.219  32.037   0.878  -3.610  -0.814  "H22'"  NDU  32  
NDU  "H1'"   "H1'"   H   0  1  N  N  N  15.690  20.787  31.820   0.966  -1.512  -1.856  "H1'"   NDU  33  
NDU  H611    1H61    H   0  0  N  N  N  16.850  19.525  29.379   3.934  -1.570  -0.933  H611    NDU  34  
NDU  H612    2H61    H   0  0  N  N  N  18.443  20.375  29.186   2.969  -0.601  -2.073  H612    NDU  35  
NDU  H3      H3      H   0  1  N  N  N  19.060  18.808  33.548   3.256   0.088   2.638  H3      NDU  36  
NDU  H5      H5      H   0  1  N  N  N  17.934  17.572  30.515   5.013   0.576  -1.052  H5      NDU  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
NDU  P      OP1     DOUB  N  N   1  
NDU  P      OP2     SING  N  N   2  
NDU  P      OP3     SING  N  N   3  
NDU  P      "O5'"   SING  N  N   4  
NDU  "O5'"  "C5'"   SING  N  N   5  
NDU  "C5'"  "C4'"   SING  N  N   6  
NDU  "C4'"  "C3'"   SING  N  N   7  
NDU  "C4'"  "O4'"   SING  N  N   8  
NDU  "C3'"  "O3'"   SING  N  N   9  
NDU  "C3'"  "C2'"   SING  N  N  10  
NDU  "C2'"  "C1'"   SING  N  N  11  
NDU  "C1'"  "O4'"   SING  N  N  12  
NDU  "C1'"  N1      SING  N  N  13  
NDU  N1     C2      SING  N  N  14  
NDU  N1     C6      SING  N  N  15  
NDU  C2     O2      DOUB  N  N  16  
NDU  C2     N3      SING  N  N  17  
NDU  N3     C4      SING  N  N  18  
NDU  C4     O4      DOUB  N  N  19  
NDU  C4     C5      SING  N  N  20  
NDU  C5     C6      SING  N  N  21  
NDU  C5     N5      SING  N  N  22  
NDU  N5     O51     SING  N  N  23  
NDU  N5     O52     DOUB  N  N  24  
NDU  OP2    HP2     SING  N  N  25  
NDU  OP3    HP3     SING  N  N  26  
NDU  "C5'"  "H51'"  SING  N  N  27  
NDU  "C5'"  "H52'"  SING  N  N  28  
NDU  "C4'"  "H4'"   SING  N  N  29  
NDU  "C3'"  "H3'"   SING  N  N  30  
NDU  "O3'"  HA      SING  N  N  31  
NDU  "C2'"  "H21'"  SING  N  N  32  
NDU  "C2'"  "H22'"  SING  N  N  33  
NDU  "C1'"  "H1'"   SING  N  N  34  
NDU  C6     H611    SING  N  N  35  
NDU  C6     H612    SING  N  N  36  
NDU  N3     H3      SING  N  N  37  
NDU  C5     H5      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
NDU  SMILES            ACDLabs               10.04  "[O-][N+](=O)C1C(=O)NC(=O)N(C1)C2OC(C(O)C2)COP(=O)(O)O"  
NDU  SMILES_CANONICAL  CACTVS                3.341  "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C[C@H](C(=O)NC2=O)[N+]([O-])=O"  
NDU  SMILES            CACTVS                3.341  "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C[CH](C(=O)NC2=O)[N+]([O-])=O"  
NDU  SMILES_CANONICAL  "OpenEye OEToolkits"  1.5.0  "C1[C@@H]([C@H](O[C@H]1N2CC(C(=O)NC2=O)[N+](=O)[O-])COP(=O)(O)O)O"  
NDU  SMILES            "OpenEye OEToolkits"  1.5.0  "C1C(C(OC1N2CC(C(=O)NC2=O)[N+](=O)[O-])COP(=O)(O)O)O"  
NDU  InChI             InChI                 1.03   "InChI=1S/C9H14N3O10P/c13-5-1-7(22-6(5)3-21-23(18,19)20)11-2-4(12(16)17)8(14)10-9(11)15/h4-7,13H,1-3H2,(H,10,14,15)(H2,18,19,20)/t4-,5+,6-,7-/m1/s1"  
NDU  InChIKey          InChI                 1.03   ZYBJIJYGXJSDTC-XZBKPIIZSA-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
NDU  "SYSTEMATIC NAME"  ACDLabs               10.04  "2'-deoxy-5-nitrouridine 5'-(dihydrogen phosphate)"  
NDU  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.5.0  "[(2R,3S,5R)-3-hydroxy-5-(5-nitro-2,4-dioxo-1,3-diazinan-1-yl)oxolan-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
NDU  "Create component"        2007-10-27  EBI   
NDU  "Modify descriptor"       2011-06-04  RCSB  
NDU  "Modify one letter code"  2019-05-07  EBI   
##
