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                    2008-10-14 
_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 InChI            InChI                1.02b InChI=1/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/f/h16,22H 
N3E InChIKey         InChI                1.02b IBEGWFLXVPJKRI-OQNCIFOKDG                                                                                                                                                             
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                                                                                                                                         
# 
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" 
# 
