data_3AU
#

_chem_comp.id                                   3AU
_chem_comp.name                                 "3-[(3S)-3-amino-3-carboxypropyl]uridine 5'-(dihydrogen phosphate)"
_chem_comp.type                                 "RNA linking"
_chem_comp.pdbx_type                            ATOMN
_chem_comp.formula                              "C13 H20 N3 O11 P"
_chem_comp.mon_nstd_parent_comp_id              U
_chem_comp.pdbx_synonyms                        ?
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2011-01-18
_chem_comp.pdbx_modified_date                   2021-05-11
_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                       425.285
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    3AU
_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       3IZV
_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
3AU  P       P       P  0  1  N  N  N  -0.125  -0.116  -0.035   5.480  -1.929   0.134  P       3AU   1  
3AU  N1      N1      N  0  1  N  N  N   5.652  -1.219  -2.784  -0.405   1.003   0.477  N1      3AU   2  
3AU  C2      C2      C  0  1  N  N  N   6.991  -1.466  -3.013  -1.682   1.024   0.053  C2      3AU   3  
3AU  O2      O2      O  0  1  N  N  N   7.846  -0.695  -2.508  -1.924   1.306  -1.105  O2      3AU   4  
3AU  N3      N3      N  0  1  N  N  N   7.418  -2.533  -3.780  -2.695   0.739   0.892  N3      3AU   5  
3AU  C4      C4      C  0  1  N  N  N   6.481  -3.379  -4.323  -2.444   0.425   2.179  C4      3AU   6  
3AU  O4      O4      O  0  1  N  N  N   6.792  -4.386  -5.006  -3.360   0.166   2.938  O4      3AU   7  
3AU  C5      C5      C  0  1  N  N  N   5.112  -3.151  -4.126  -1.105   0.398   2.639  C5      3AU   8  
3AU  C6      C6      C  0  1  N  N  N   4.725  -2.052  -3.352  -0.108   0.689   1.776  C6      3AU   9  
3AU  "C1'"   "C1'"   C  0  1  N  N  R   5.204  -0.074  -1.994   0.677   1.312  -0.461  "C1'"   3AU  10  
3AU  C10     C10     C  0  1  N  N  N   8.839  -2.789  -3.989  -4.076   0.770   0.405  C10     3AU  11  
3AU  C11     C11     C  0  1  N  N  N   9.411  -3.682  -2.853  -4.462  -0.613  -0.124  C11     3AU  12  
3AU  C12     C12     C  0  1  N  N  S  10.929  -4.000  -2.979  -5.905  -0.580  -0.633  C12     3AU  13  
3AU  C13     C13     C  0  1  N  N  N  11.382  -4.806  -1.852  -6.244  -1.906  -1.265  C13     3AU  14  
3AU  "C2'"   "C2'"   C  0  1  N  N  R   5.015   1.182  -2.868   1.406   2.614  -0.042  "C2'"   3AU  15  
3AU  "O2'"   "O2'"   O  0  1  N  N  N   6.253   1.817  -3.177   0.746   3.763  -0.578  "O2'"   3AU  16  
3AU  "C3'"   "C3'"   C  0  1  N  N  S   4.063   2.062  -2.038   2.800   2.427  -0.688  "C3'"   3AU  17  
3AU  "O3'"   "O3'"   O  0  1  N  N  N   4.753   3.105  -1.349   2.873   3.122  -1.934  "O3'"   3AU  18  
3AU  O30     O30     O  0  1  N  N  N  11.336  -6.027  -1.882  -6.877  -2.727  -0.644  O30     3AU  19  
3AU  O31     O31     O  0  1  N  N  N  11.785  -4.286  -0.817  -5.844  -2.174  -2.518  O31     3AU  20  
3AU  "C4'"   "C4'"   C  0  1  N  N  R   3.413   1.063  -1.042   2.911   0.906  -0.912  "C4'"   3AU  21  
3AU  "O4'"   "O4'"   O  0  1  N  N  N   3.924  -0.243  -1.359   1.712   0.309  -0.391  "O4'"   3AU  22  
3AU  N40     N40     N  0  1  N  N  N  11.223  -4.675  -4.255  -6.815  -0.327   0.492  N40     3AU  23  
3AU  "C5'"   "C5'"   C  0  1  N  N  N   1.866   1.058  -1.108   4.131   0.358  -0.169  "C5'"   3AU  24  
3AU  "O5'"   "O5'"   O  0  1  N  N  N   1.353   0.196  -0.220   4.293  -1.028  -0.476  "O5'"   3AU  25  
3AU  OP1     OP1     O  0  1  N  N  N  -0.851   1.098   0.391   5.455  -1.844   1.611  OP1     3AU  26  
3AU  OP2     OP2     O  0  1  N  N  N  -0.695  -0.618  -1.342   5.279  -3.460  -0.320  OP2     3AU  27  
3AU  H5      H5      H  0  1  N  N  N   4.374  -3.808  -4.561  -0.884   0.149   3.666  H5      3AU  28  
3AU  H6      H6      H  0  1  N  N  N   3.674  -1.856  -3.199   0.919   0.674   2.108  H6      3AU  29  
3AU  "H1'"   "H1'"   H  0  1  N  N  N   6.001   0.023  -1.242   0.290   1.398  -1.476  "H1'"   3AU  30  
3AU  H10     H10     H  0  1  N  N  N   8.973  -3.304  -4.952  -4.743   1.046   1.222  H10     3AU  31  
3AU  H10A    H10A    H  0  0  N  N  N   9.379  -1.831  -3.998  -4.162   1.503  -0.398  H10A    3AU  32  
3AU  H11     H11     H  0  1  N  N  N   9.256  -3.154  -1.901  -3.795  -0.889  -0.941  H11     3AU  33  
3AU  H11A    H11A    H  0  0  N  N  N   8.865  -4.637  -2.870  -4.376  -1.346   0.678  H11A    3AU  34  
3AU  H12     H12     H  0  1  N  N  N  11.478  -3.047  -2.965  -6.011   0.213  -1.372  H12     3AU  35  
3AU  "H2'"   "H2'"   H  0  1  N  N  N   4.599   0.956  -3.861   1.485   2.684   1.043  "H2'"   3AU  36  
3AU  "HO2'"  "HO2'"  H  0  0  N  N  N   6.091   2.583  -3.715   1.166   4.602  -0.344  "HO2'"  3AU  37  
3AU  "H3'"   "H3'"   H  0  1  N  N  N   3.327   2.584  -2.668   3.583   2.773  -0.013  "H3'"   3AU  38  
3AU  "HO3'"  "HO3'"  H  0  0  N  N  N   4.131   3.622  -0.851   2.750   4.079  -1.858  "HO3'"  3AU  39  
3AU  "H4'"   "H4'"   H  0  1  N  N  N   3.668   1.367  -0.016   2.998   0.694  -1.978  "H4'"   3AU  40  
3AU  HN40    HN40    H  0  0  N  N  N  12.202  -4.868  -4.312  -7.768  -0.236   0.173  HN40    3AU  41  
3AU  HN4A    HN4A    H  0  0  N  N  N  10.711  -5.532  -4.304  -6.735  -1.049   1.192  HN4A    3AU  42  
3AU  "H5'"   "H5'"   H  0  1  N  N  N   1.495   2.068  -0.882   5.022   0.905  -0.479  "H5'"   3AU  43  
3AU  "H5'A"  "H5'A"  H  0  0  N  N  N   1.552   0.760  -2.119   3.987   0.478   0.905  "H5'A"  3AU  44  
3AU  O11     O11     O  0  1  N  N  N  -0.272  -1.193   1.015   6.897  -1.389  -0.410  O11     3AU  45  
3AU  H18     H18     H  0  1  N  N  N  12.002  -4.962  -0.186  -6.086  -3.037  -2.880  H18     3AU  46  
3AU  H19     H19     H  0  1  N  N  N  -1.403  -0.048  -1.619   5.960  -4.061   0.013  H19     3AU  47  
3AU  H20     H20     H  0  1  N  N  N  -0.802  -0.866   1.733   6.984  -1.416  -1.373  H20     3AU  48  
#   #
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
3AU  P      "O5'"   SING  N  N   1  
3AU  P      OP1     DOUB  N  N   2  
3AU  P      OP2     SING  N  N   3  
3AU  N1     C2      SING  N  N   4  
3AU  N1     C6      SING  N  N   5  
3AU  N1     "C1'"   SING  N  N   6  
3AU  C2     O2      DOUB  N  N   7  
3AU  C2     N3      SING  N  N   8  
3AU  N3     C4      SING  N  N   9  
3AU  N3     C10     SING  N  N  10  
3AU  C4     O4      DOUB  N  N  11  
3AU  C4     C5      SING  N  N  12  
3AU  C5     C6      DOUB  N  N  13  
3AU  C5     H5      SING  N  N  14  
3AU  C6     H6      SING  N  N  15  
3AU  "C1'"  "C2'"   SING  N  N  16  
3AU  "C1'"  "O4'"   SING  N  N  17  
3AU  "C1'"  "H1'"   SING  N  N  18  
3AU  C10    C11     SING  N  N  19  
3AU  C10    H10     SING  N  N  20  
3AU  C10    H10A    SING  N  N  21  
3AU  C11    C12     SING  N  N  22  
3AU  C11    H11     SING  N  N  23  
3AU  C11    H11A    SING  N  N  24  
3AU  C12    C13     SING  N  N  25  
3AU  C12    N40     SING  N  N  26  
3AU  C12    H12     SING  N  N  27  
3AU  C13    O30     DOUB  N  N  28  
3AU  C13    O31     SING  N  N  29  
3AU  "C2'"  "O2'"   SING  N  N  30  
3AU  "C2'"  "C3'"   SING  N  N  31  
3AU  "C2'"  "H2'"   SING  N  N  32  
3AU  "O2'"  "HO2'"  SING  N  N  33  
3AU  "C3'"  "O3'"   SING  N  N  34  
3AU  "C3'"  "C4'"   SING  N  N  35  
3AU  "C3'"  "H3'"   SING  N  N  36  
3AU  "O3'"  "HO3'"  SING  N  N  37  
3AU  "C4'"  "O4'"   SING  N  N  38  
3AU  "C4'"  "C5'"   SING  N  N  39  
3AU  "C4'"  "H4'"   SING  N  N  40  
3AU  N40    HN40    SING  N  N  41  
3AU  N40    HN4A    SING  N  N  42  
3AU  "C5'"  "O5'"   SING  N  N  43  
3AU  "C5'"  "H5'"   SING  N  N  44  
3AU  "C5'"  "H5'A"  SING  N  N  45  
3AU  P      O11     SING  N  N  46  
3AU  O31    H18     SING  N  N  47  
3AU  OP2    H19     SING  N  N  48  
3AU  O11    H20     SING  N  N  49  
#   #
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
3AU  SMILES            ACDLabs               12.01  "O=C(O)C(N)CCN1C(=O)C=CN(C1=O)C2OC(C(O)C2O)COP(=O)(O)O"  
3AU  SMILES_CANONICAL  CACTVS                3.370  "N[C@@H](CCN1C(=O)C=CN([C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O)C1=O)C(O)=O"  
3AU  SMILES            CACTVS                3.370  "N[CH](CCN1C(=O)C=CN([CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O)C1=O)C(O)=O"  
3AU  SMILES_CANONICAL  "OpenEye OEToolkits"  1.7.0  "C1=CN(C(=O)N(C1=O)CC[C@@H](C(=O)O)N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O"  
3AU  SMILES            "OpenEye OEToolkits"  1.7.0  "C1=CN(C(=O)N(C1=O)CCC(C(=O)O)N)C2C(C(C(O2)COP(=O)(O)O)O)O"  
3AU  InChI             InChI                 1.03   "InChI=1S/C13H20N3O11P/c14-6(12(20)21)1-3-15-8(17)2-4-16(13(15)22)11-10(19)9(18)7(27-11)5-26-28(23,24)25/h2,4,6-7,9-11,18-19H,1,3,5,14H2,(H,20,21)(H2,23,24,25)/t6-,7+,9+,10+,11+/m0/s1"  
3AU  InChIKey          InChI                 1.03   CJKRCYMKRHIIKR-CNYIRLTGSA-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
3AU  "SYSTEMATIC NAME"  ACDLabs               12.01  "3-[(3S)-3-amino-3-carboxypropyl]uridine 5'-(dihydrogen phosphate)"  
3AU  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.7.0  "(2S)-2-azanyl-4-[3-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(phosphonooxymethyl)oxolan-2-yl]-2,6-dioxo-pyrimidin-1-yl]butanoic acid"  
#   #
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
3AU  "Create component"   2011-01-18  RCSB  
3AU  "Modify descriptor"  2011-06-04  RCSB  
3AU  "Modify synonyms"    2020-06-05  PDBE  
3AU  "Modify synonyms"    2021-05-11  RCSB  
##
