data_N3E
#

_chem_comp.id                                   N3E
_chem_comp.name                                 "1-[3-(4-CARBOXYPIPERIDIN-1-YL)-3-DEOXY-BETA-D-ARABINOFURANOSYL]PYRIMIDINE-2,4(1H,3H)-DIONE"
_chem_comp.type                                 NON-POLYMER
_chem_comp.pdbx_type                            HETAIN
_chem_comp.formula                              "C15 H21 N3 O7"
_chem_comp.mon_nstd_parent_comp_id              ?
_chem_comp.pdbx_synonyms                        3-N-PIPERIDINE-4-CARBOXYL-3-DEOXY-ARA-URIDINE
_chem_comp.pdbx_formal_charge                   0
_chem_comp.pdbx_initial_date                    2006-03-17
_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                       355.343
_chem_comp.one_letter_code                      ?
_chem_comp.three_letter_code                    N3E
_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       2G8R
_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
N3E  O2      O2      O  0  1  N  N  N  38.535  1.097  18.145  -2.356  -2.331   1.041  O2      N3E   1  
N3E  C2      C2      C  0  1  Y  N  N  39.394  1.840  17.608  -3.190  -1.547   0.629  C2      N3E   2  
N3E  N3      N3      N  0  1  Y  N  N  40.024  1.424  16.482  -4.464  -1.953   0.479  N3      N3E   3  
N3E  C4      C4      C  0  1  Y  N  N  40.967  2.199  15.886  -5.401  -1.096   0.024  C4      N3E   4  
N3E  O4      O4      O  0  1  N  N  N  41.537  1.796  14.838  -6.553  -1.464  -0.118  O4      N3E   5  
N3E  C5      C5      C  0  1  Y  N  N  41.277  3.443  16.444  -5.032   0.234  -0.289  C5      N3E   6  
N3E  C6      C6      C  0  1  Y  N  N  40.612  3.842  17.606  -3.747   0.616  -0.124  C6      N3E   7  
N3E  N1      N1      N  0  1  Y  N  N  39.684  3.030  18.168  -2.827  -0.284   0.340  N1      N3E   8  
N3E  "C1'"   "C1'"   C  0  1  N  N  R  38.976  3.422  19.396  -1.433   0.130   0.519  "C1'"   N3E   9  
N3E  "O4'"   "O4'"   O  0  1  N  N  N  39.137  4.812  19.701  -1.344   1.563   0.670  "O4'"   N3E  10  
N3E  "C4'"   "C4'"   C  0  1  N  N  S  39.540  4.997  21.070   0.003   1.937   0.337  "C4'"   N3E  11  
N3E  "C5'"   "C5'"   C  0  1  N  N  N  40.923  5.647  21.145   0.010   3.310  -0.339  "C5'"   N3E  12  
N3E  "O5'"   "O5'"   O  0  1  N  N  N  41.229  6.269  19.890  -0.396   4.306   0.602  "O5'"   N3E  13  
N3E  "C2'"   "C2'"   C  0  1  N  N  S  39.454  2.624  20.617  -0.609  -0.150  -0.763  "C2'"   N3E  14  
N3E  "O2'"   "O2'"   O  0  1  N  N  N  40.746  2.039  20.384  -1.386   0.102  -1.935  "O2'"   N3E  15  
N3E  "C3'"   "C3'"   C  0  1  N  N  S  39.561  3.625  21.754   0.551   0.873  -0.634  "C3'"   N3E  16  
N3E  N7      N7      N  0  1  N  N  N  38.373  3.391  22.588   1.747   0.226  -0.077  N7      N3E  17  
N3E  C13     C13     C  0  1  N  N  N  38.623  2.569  23.787   2.782   1.261   0.011  C13     N3E  18  
N3E  C8      C8      C  0  1  N  N  N  37.089  3.916  22.088   2.195  -0.756  -1.070  C8      N3E  19  
N3E  C9      C9      C  0  1  N  N  N  35.973  3.853  23.118   3.450  -1.470  -0.562  C9      N3E  20  
N3E  C10     C10     C  0  1  N  N  N  36.345  3.291  24.491   4.568  -0.442  -0.363  C10     N3E  21  
N3E  C12     C12     C  0  1  N  N  N  37.302  2.113  24.406   4.069   0.659   0.579  C12     N3E  22  
N3E  C11     C11     C  0  1  N  N  N  35.083  3.028  25.269   5.773  -1.115   0.242  C11     N3E  23  
N3E  O13     O13     O  0  1  N  N  N  34.777  1.894  25.738   6.381  -2.117  -0.412  O13     N3E  24  
N3E  O12     O12     O  0  1  N  N  N  34.403  4.054  25.422   6.192  -0.753   1.316  O12     N3E  25  
N3E  HN3     HN3     H  0  1  N  N  N  39.792  0.536  16.085  -4.709  -2.866   0.695  HN3     N3E  26  
N3E  H5      H5      H  0  1  N  N  N  42.016  4.083  15.986  -5.768   0.935  -0.655  H5      N3E  27  
N3E  H6      H6      H  0  1  N  N  N  40.837  4.797  18.056  -3.448   1.627  -0.357  H6      N3E  28  
N3E  "H1'"   "H1'"   H  0  1  N  N  N  37.917  3.206  19.193  -0.991  -0.375   1.378  "H1'"   N3E  29  
N3E  "H4'"   "H4'"   H  0  1  N  N  N  38.829  5.665  21.579   0.614   1.965   1.239  "H4'"   N3E  30  
N3E  "H5'1"  "1H5'"  H  0  0  N  N  N  41.678  4.878  21.366  -0.682   3.303  -1.182  "H5'1"  N3E  31  
N3E  "H5'2"  "2H5'"  H  0  0  N  N  N  40.928  6.406  21.941   1.015   3.534  -0.696  "H5'2"  N3E  32  
N3E  "H5'"   "H5'"   H  0  1  N  N  N  41.297  7.209  20.010  -0.378   5.153   0.137  "H5'"   N3E  33  
N3E  "H2'"   "H2'"   H  0  1  N  N  N  38.755  1.804  20.839  -0.226  -1.171  -0.764  "H2'"   N3E  34  
N3E  H1      H1      H  0  1  N  N  N  40.872  1.910  19.451  -2.138  -0.505  -1.907  H1      N3E  35  
N3E  "H3'"   "H3'"   H  0  1  N  N  N  40.458  3.548  22.385   0.775   1.319  -1.602  "H3'"   N3E  36  
N3E  H131    1H13    H  0  0  N  N  N  39.174  3.171  24.524   2.978   1.664  -0.983  H131    N3E  37  
N3E  H132    2H13    H  0  0  N  N  N  39.212  1.685  23.502   2.439   2.063   0.664  H132    N3E  38  
N3E  H81     1H8     H  0  1  N  N  N  36.786  3.288  21.237   1.405  -1.488  -1.238  H81     N3E  39  
N3E  H82     2H8     H  0  1  N  N  N  37.235  4.968  21.803   2.422  -0.247  -2.007  H82     N3E  40  
N3E  H91     1H9     H  0  1  N  N  N  35.228  3.157  22.705   3.766  -2.215  -1.292  H91     N3E  41  
N3E  H92     2H9     H  0  1  N  N  N  35.615  4.881  23.273   3.231  -1.959   0.388  H92     N3E  42  
N3E  H10     H10     H  0  1  N  N  N  36.925  4.039  25.052   4.838  -0.005  -1.324  H10     N3E  43  
N3E  H121    1H12    H  0  0  N  N  N  37.488  1.720  25.416   4.828   1.437   0.664  H121    N3E  44  
N3E  H122    2H12    H  0  0  N  N  N  36.858  1.325  23.780   3.869   0.234   1.562  H122    N3E  45  
N3E  H13     H13     H  0  1  N  N  N  33.958  1.959  26.216   7.154  -2.549  -0.024  H13     N3E  46  
#   #
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
N3E  O2     C2      DOUB  N  N   1  
N3E  C2     N3      SING  Y  N   2  
N3E  C2     N1      SING  Y  N   3  
N3E  N3     C4      SING  Y  N   4  
N3E  N3     HN3     SING  N  N   5  
N3E  C4     O4      DOUB  N  N   6  
N3E  C4     C5      SING  Y  N   7  
N3E  C5     C6      DOUB  Y  N   8  
N3E  C5     H5      SING  N  N   9  
N3E  C6     N1      SING  Y  N  10  
N3E  C6     H6      SING  N  N  11  
N3E  N1     "C1'"   SING  N  N  12  
N3E  "C1'"  "O4'"   SING  N  N  13  
N3E  "C1'"  "C2'"   SING  N  N  14  
N3E  "C1'"  "H1'"   SING  N  N  15  
N3E  "O4'"  "C4'"   SING  N  N  16  
N3E  "C4'"  "C5'"   SING  N  N  17  
N3E  "C4'"  "C3'"   SING  N  N  18  
N3E  "C4'"  "H4'"   SING  N  N  19  
N3E  "C5'"  "O5'"   SING  N  N  20  
N3E  "C5'"  "H5'1"  SING  N  N  21  
N3E  "C5'"  "H5'2"  SING  N  N  22  
N3E  "O5'"  "H5'"   SING  N  N  23  
N3E  "C2'"  "O2'"   SING  N  N  24  
N3E  "C2'"  "C3'"   SING  N  N  25  
N3E  "C2'"  "H2'"   SING  N  N  26  
N3E  "O2'"  H1      SING  N  N  27  
N3E  "C3'"  N7      SING  N  N  28  
N3E  "C3'"  "H3'"   SING  N  N  29  
N3E  N7     C13     SING  N  N  30  
N3E  N7     C8      SING  N  N  31  
N3E  C13    C12     SING  N  N  32  
N3E  C13    H131    SING  N  N  33  
N3E  C13    H132    SING  N  N  34  
N3E  C8     C9      SING  N  N  35  
N3E  C8     H81     SING  N  N  36  
N3E  C8     H82     SING  N  N  37  
N3E  C9     C10     SING  N  N  38  
N3E  C9     H91     SING  N  N  39  
N3E  C9     H92     SING  N  N  40  
N3E  C10    C12     SING  N  N  41  
N3E  C10    C11     SING  N  N  42  
N3E  C10    H10     SING  N  N  43  
N3E  C12    H121    SING  N  N  44  
N3E  C12    H122    SING  N  N  45  
N3E  C11    O13     SING  N  N  46  
N3E  C11    O12     DOUB  N  N  47  
N3E  O13    H13     SING  N  N  48  
#   #
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
N3E  SMILES            ACDLabs               10.04  "O=C(O)C3CCN(C2C(OC(N1C(=O)NC(=O)C=C1)C2O)CO)CC3"  
N3E  SMILES_CANONICAL  CACTVS                3.341  "OC[C@H]1O[C@H]([C@@H](O)[C@@H]1N2CC[C@H](CC2)C(O)=O)N3C=CC(=O)NC3=O"  
N3E  SMILES            CACTVS                3.341  "OC[CH]1O[CH]([CH](O)[CH]1N2CC[CH](CC2)C(O)=O)N3C=CC(=O)NC3=O"  
N3E  SMILES_CANONICAL  "OpenEye OEToolkits"  1.5.0  "C1CN(CCC1C(=O)O)[C@@H]2[C@H](O[C@H]([C@H]2O)N3C=CC(=O)NC3=O)CO"  
N3E  SMILES            "OpenEye OEToolkits"  1.5.0  "C1CN(CCC1C(=O)O)C2C(OC(C2O)N3C=CC(=O)NC3=O)CO"  
N3E  InChI             InChI                 1.03   "InChI=1S/C15H21N3O7/c19-7-9-11(17-4-1-8(2-5-17)14(22)23)12(21)13(25-9)18-6-3-10(20)16-15(18)24/h3,6,8-9,11-13,19,21H,1-2,4-5,7H2,(H,22,23)(H,16,20,24)/t9-,11-,12+,13-/m1/s1"  
N3E  InChIKey          InChI                 1.03   IBEGWFLXVPJKRI-FOUMNBMASA-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
N3E  "SYSTEMATIC NAME"  ACDLabs               10.04  "1-[3-(4-carboxypiperidin-1-yl)-3-deoxy-beta-D-arabinofuranosyl]pyrimidine-2,4(1H,3H)-dione"  
N3E  "SYSTEMATIC NAME"  "OpenEye OEToolkits"  1.5.0  "1-[(2S,3S,4S,5R)-5-(2,4-dioxopyrimidin-1-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl]piperidine-4-carboxylic 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
N3E  "Create component"   2006-03-17  RCSB  
N3E  "Modify descriptor"  2011-06-04  RCSB  
N3E  "Modify synonyms"    2021-03-01  PDBE  
#
_pdbx_chem_comp_synonyms.ordinal     1
_pdbx_chem_comp_synonyms.comp_id     N3E
_pdbx_chem_comp_synonyms.name        3-N-PIPERIDINE-4-CARBOXYL-3-DEOXY-ARA-URIDINE
_pdbx_chem_comp_synonyms.provenance  ?
_pdbx_chem_comp_synonyms.type        ?
##
