data_NDN
#

_chem_comp.id                                   NDN
_chem_comp.name                                 "2'-DEOXY-5-NITROURIDINE 5'-(DIHYDROGEN PHOSPHATE)"
_chem_comp.type                                 "DNA LINKING"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C9 H12 N3 O10 P"
_chem_comp.mon_nstd_parent_comp_id              DU
_chem_comp.pdbx_synonyms                        "[(2R,3S,5R)-3-HYDROXY-5-(5-NITRO-2,4-DIOXO-PYRIMIDIN-1-YL)OXOLAN-2-YL]METHYL DIHYDROGEN PHOSPHATE"
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2007-11-07
_chem_comp.pdbx_modified_date                   2020-06-17
_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                       353.179
_chem_comp.one_letter_code                      U
_chem_comp.three_letter_code                    NDN
_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       3B5B
_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
NDN  P     P     P   0  1  N  N  N  46.433  28.257  24.564  -4.772  -1.098   0.304  P     NDN   1  
NDN  OP1   OP1   O   0  1  N  N  N  47.700  27.548  24.968  -5.899  -0.182   0.018  OP1   NDN   2  
NDN  OP2   OP2   O   0  1  N  N  N  45.494  28.422  25.721  -5.133  -2.010   1.581  OP2   NDN   3  
NDN  OP3   OP3   O   0  1  N  Y  N  45.849  27.841  23.248  -4.510  -2.043  -0.973  OP3   NDN   4  
NDN  OR5   OR5   O   0  1  N  N  N  46.936  29.734  24.272  -3.447  -0.237   0.616  OR5   NDN   5  
NDN  CR5   CR5   C   0  1  N  N  N  46.361  30.943  23.895  -2.930   0.747  -0.281  CR5   NDN   6  
NDN  CR4   CR4   C   0  1  N  N  R  46.859  32.042  24.811  -1.669   1.372   0.320  CR4   NDN   7  
NDN  CR3   CR3   C   0  1  N  N  S  46.554  32.079  26.296  -1.163   2.526  -0.574  CR3   NDN   8  
NDN  OR3   OR3   O   0  1  N  N  N  47.488  32.815  27.038  -1.596   3.786  -0.058  OR3   NDN   9  
NDN  CR2   CR2   C   0  1  N  N  N  45.163  32.742  26.356   0.377   2.411  -0.500  CR2   NDN  10  
NDN  CR1   CR1   C   0  1  N  N  R  45.360  33.822  25.239   0.618   1.201   0.430  CR1   NDN  11  
NDN  OR1   OR1   O   0  1  N  N  N  46.374  33.303  24.361  -0.589   0.413   0.332  OR1   NDN  12  
NDN  N1    N1    N   0  1  N  N  N  44.024  34.350  24.714   1.773   0.426  -0.030  N1    NDN  13  
NDN  C2    C2    C   0  1  N  N  N  43.216  35.326  25.294   1.724  -0.202  -1.218  C2    NDN  14  
NDN  O2    O2    O   0  1  N  N  N  43.416  35.695  26.380   0.720  -0.120  -1.899  O2    NDN  15  
NDN  N3    N3    N   0  1  N  N  N  42.162  35.840  24.534   2.772  -0.919  -1.665  N3    NDN  16  
NDN  C4    C4    C   0  1  N  N  N  42.097  35.908  23.145   3.893  -1.020  -0.923  C4    NDN  17  
NDN  O4    O4    O   0  1  N  N  N  41.389  36.685  22.533   4.841  -1.669  -1.327  O4    NDN  18  
NDN  C5    C5    C   0  1  N  N  N  43.004  34.921  22.371   3.957  -0.364   0.330  C5    NDN  19  
NDN  C6    C6    C   0  1  N  N  N  44.138  34.276  23.195   2.895   0.354   0.752  C6    NDN  20  
NDN  N5    N5    N   1  1  N  N  N  43.089  34.783  21.069   5.177  -0.459   1.164  N5    NDN  21  
NDN  O51   O51   O   0  1  N  N  N  42.206  35.225  20.299   5.224   0.108   2.241  O51   NDN  22  
NDN  O52   O52   O  -1  1  N  N  N  44.027  34.233  20.465   6.133  -1.105   0.774  O52   NDN  23  
NDN  HOP3  HOP3  H   0  0  N  N  N  44.907  27.753  23.333  -3.783  -2.670  -0.856  HOP3  NDN  24  
NDN  HOP2  HOP2  H   0  0  N  N  N  45.991  28.457  26.530  -5.922  -2.556   1.464  HOP2  NDN  25  
NDN  HR5   HR5   H   0  1  N  N  N  46.641  31.175  22.857  -2.684   0.277  -1.234  HR5   NDN  26  
NDN  HR5A  HR5A  H   0  0  N  N  N  45.266  30.869  23.970  -3.679   1.522  -0.441  HR5A  NDN  27  
NDN  HR4   HR4   H   0  1  N  N  N  47.933  31.814  24.739  -1.869   1.733   1.328  HR4   NDN  28  
NDN  HR3   HR3   H   0  1  N  N  N  46.591  31.073  26.740  -1.506   2.394  -1.600  HR3   NDN  29  
NDN  HOR3  HOR3  H   0  0  N  Y  N  48.256  32.982  26.505  -1.305   4.546  -0.581  HOR3  NDN  30  
NDN  HR2   HR2   H   0  1  N  N  N  44.341  32.043  26.142   0.794   2.221  -1.489  HR2   NDN  31  
NDN  HR2A  HR2A  H   0  0  N  N  N  44.871  33.133  27.342   0.807   3.316  -0.071  HR2A  NDN  32  
NDN  HR1   HR1   H   0  1  N  N  N  45.764  34.790  25.569   0.770   1.535   1.456  HR1   NDN  33  
NDN  HN3   HN3   H   0  1  N  N  N  41.375  36.195  25.039   2.720  -1.366  -2.525  HN3   NDN  34  
NDN  H6    H6    H   0  1  N  N  N  44.977  33.793  22.716   2.926   0.861   1.704  H6    NDN  35  
#   #
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
NDN  P    OP1   DOUB  N  N   1  
NDN  P    OP2   SING  N  N   2  
NDN  OP3  HOP3  SING  N  N   3  
NDN  OP2  HOP2  SING  N  N   4  
NDN  OP3  P     SING  N  N   5  
NDN  OR5  P     SING  N  N   6  
NDN  CR5  OR5   SING  N  N   7  
NDN  CR5  CR4   SING  N  N   8  
NDN  CR5  HR5   SING  N  N   9  
NDN  CR5  HR5A  SING  N  N  10  
NDN  CR4  CR3   SING  N  N  11  
NDN  CR4  HR4   SING  N  N  12  
NDN  CR3  CR2   SING  N  N  13  
NDN  CR3  OR3   SING  N  N  14  
NDN  CR3  HR3   SING  N  N  15  
NDN  OR3  HOR3  SING  N  N  16  
NDN  CR2  HR2   SING  N  N  17  
NDN  CR2  HR2A  SING  N  N  18  
NDN  CR1  CR2   SING  N  N  19  
NDN  CR1  HR1   SING  N  N  20  
NDN  OR1  CR4   SING  N  N  21  
NDN  OR1  CR1   SING  N  N  22  
NDN  N1   CR1   SING  N  N  23  
NDN  N1   C2    SING  N  N  24  
NDN  C2   O2    DOUB  N  N  25  
NDN  N3   C2    SING  N  N  26  
NDN  N3   HN3   SING  N  N  27  
NDN  C4   N3    SING  N  N  28  
NDN  O4   C4    DOUB  N  N  29  
NDN  C5   C4    SING  N  N  30  
NDN  C5   C6    DOUB  N  N  31  
NDN  C6   N1    SING  N  N  32  
NDN  C6   H6    SING  N  N  33  
NDN  N5   C5    SING  N  N  34  
NDN  O51  N5    DOUB  N  N  35  
NDN  O52  N5    SING  N  N  36  
#   #
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
NDN  SMILES            ACDLabs               10.04  "[O-][N+](=O)C=1C(=O)NC(=O)N(C=1)C2OC(C(O)C2)COP(=O)(O)O"  
NDN  SMILES_CANONICAL  CACTVS                3.341  "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=C(C(=O)NC2=O)[N+]([O-])=O"  
NDN  SMILES            CACTVS                3.341  "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=C(C(=O)NC2=O)[N+]([O-])=O"  
NDN  SMILES_CANONICAL  "OpenEye OEToolkits"  1.5.0  "C1[C@@H]([C@H](O[C@H]1N2C=C(C(=O)NC2=O)[N+](=O)[O-])COP(=O)(O)O)O"  
NDN  SMILES            "OpenEye OEToolkits"  1.5.0  "C1C(C(OC1N2C=C(C(=O)NC2=O)[N+](=O)[O-])COP(=O)(O)O)O"  
NDN  InChI             InChI                 1.03   "InChI=1S/C9H12N3O10P/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/h2,5-7,13H,1,3H2,(H,10,14,15)(H2,18,19,20)/t5-,6+,7+/m0/s1"  
NDN  InChIKey          InChI                 1.03   LVLPVLNNXRTCHP-RRKCRQDMSA-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
NDN  "SYSTEMATIC NAME"  ACDLabs               10.04  "2'-deoxy-5-nitrouridine 5'-(dihydrogen phosphate)"  
NDN  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.5.0  "[(2R,3S,5R)-3-hydroxy-5-(5-nitro-2,4-dioxo-pyrimidin-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
NDN  "Create component"   2007-11-07  RCSB  
NDN  "Modify descriptor"  2011-06-04  RCSB  
NDN  "Modify synonyms"    2020-06-05  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     NDN
_pdbx_chem_comp_synonyms.name        "[(2R,3S,5R)-3-HYDROXY-5-(5-NITRO-2,4-DIOXO-PYRIMIDIN-1-YL)OXOLAN-2-YL]METHYL DIHYDROGEN PHOSPHATE"
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
