data_UPE
# 
_chem_comp.id                                    UPE 
_chem_comp.name                                  
;2'-deoxy-5-[(2-phenylethyl)carbamoyl]uridine 5'-(dihydrogen phosphate)
;
_chem_comp.type                                  "DNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C18 H22 N3 O9 P" 
_chem_comp.mon_nstd_parent_comp_id               DU 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2012-11-07 
_chem_comp.pdbx_modified_date                    2012-11-16 
_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                        455.356 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     UPE 
_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        4HQU 
_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 
UPE P      P      P 0 1 N N N 2.319  -3.351  12.059 -6.729 1.974  -0.098 P      UPE 1  
UPE N1     N1     N 0 1 N N N 7.501  -5.274  9.853  -0.736 -1.078 0.044  N1     UPE 2  
UPE C2     C2     C 0 1 N N N 8.729  -5.482  9.181  -0.856 -1.031 1.380  C2     UPE 3  
UPE O2     O2     O 0 1 N N N 8.758  -5.510  7.938  -1.955 -1.184 1.877  O2     UPE 4  
UPE N3     N3     N 0 1 N N N 9.882  -5.659  9.843  0.198  -0.820 2.186  N3     UPE 5  
UPE C4     C4     C 0 1 N N N 9.918  -5.646  11.179 1.432  -0.647 1.666  C4     UPE 6  
UPE O4     O4     O 0 1 N N N 11.009 -5.810  11.763 2.391  -0.456 2.391  O4     UPE 7  
UPE C5     C5     C 0 1 N N N 8.647  -5.424  11.923 1.592  -0.694 0.204  C5     UPE 8  
UPE C6     C6     C 0 1 N N N 7.479  -5.248  11.187 0.467  -0.914 -0.566 C6     UPE 9  
UPE "C1'"  "C1'"  C 0 1 N N R 6.244  -5.068  9.118  -1.927 -1.317 -0.774 "C1'"  UPE 10 
UPE "C2'"  "C2'"  C 0 1 N N N 5.686  -6.337  8.490  -2.541 -2.695 -0.440 "C2'"  UPE 11 
UPE C21    C21    C 0 1 N N N 8.539  -5.363  13.423 2.911  -0.512 -0.419 C21    UPE 12 
UPE O22    O22    O 0 1 N N N 7.412  -5.212  13.898 3.042  -0.656 -1.620 O22    UPE 13 
UPE N23    N23    N 0 1 N N N 9.609  -5.436  14.222 3.976  -0.185 0.340  N23    UPE 14 
UPE C24    C24    C 0 1 N N N 9.450  -5.354  15.675 5.265  0.106  -0.292 C24    UPE 15 
UPE C25    C25    C 0 1 N N N 10.612 -6.081  16.327 6.297  0.445  0.786  C25    UPE 16 
UPE C26    C26    C 0 1 Y N N 10.468 -7.580  16.365 7.623  0.744  0.136  C26    UPE 17 
UPE C27    C27    C 0 1 Y N N 11.609 -8.335  16.683 7.932  2.038  -0.241 C27    UPE 18 
UPE C28    C28    C 0 1 Y N N 11.549 -9.727  16.722 9.148  2.312  -0.837 C28    UPE 19 
UPE C29    C29    C 0 1 Y N N 10.337 -10.357 16.446 10.056 1.293  -1.057 C29    UPE 20 
UPE "C3'"  "C3'"  C 0 1 N N S 4.188  -6.135  8.505  -4.065 -2.458 -0.528 "C3'"  UPE 21 
UPE "O3'"  "O3'"  O 0 1 N N N 3.805  -5.607  7.234  -4.642 -3.282 -1.544 "O3'"  UPE 22 
UPE C30    C30    C 0 1 Y N N 9.204  -9.597  16.120 9.747  -0.001 -0.681 C30    UPE 23 
UPE C31    C31    C 0 1 Y N N 9.259  -8.203  16.086 8.532  -0.274 -0.079 C31    UPE 24 
UPE "C4'"  "C4'"  C 0 1 N N R 3.933  -5.048  9.534  -4.192 -0.966 -0.905 "C4'"  UPE 25 
UPE "O4'"  "O4'"  O 0 1 N N N 5.221  -4.605  9.998  -2.962 -0.364 -0.447 "O4'"  UPE 26 
UPE "C5'"  "C5'"  C 0 1 N N N 3.022  -5.512  10.672 -5.390 -0.336 -0.191 "C5'"  UPE 27 
UPE "O5'"  "O5'"  O 0 1 N N N 3.203  -4.682  11.818 -5.560 1.009  -0.640 "O5'"  UPE 28 
UPE OP1    OP1    O 0 1 N N N 1.279  -3.231  10.965 -8.041 1.317  -0.291 OP1    UPE 29 
UPE OP2    OP2    O 0 1 N N N 1.850  -3.306  13.495 -6.500 2.266  1.469  OP2    UPE 30 
UPE OP3    OP3    O 0 1 N Y N 3.349  -2.163  11.868 -6.699 3.363  -0.912 OP3    UPE 31 
UPE HN3    HN3    H 0 1 N N N 10.728 -5.803  9.329  0.072  -0.792 3.147  HN3    UPE 32 
UPE H6     H6     H 0 1 N N N 6.543  -5.088  11.702 0.542  -0.956 -1.643 H6     UPE 33 
UPE "H1'"  "H1'"  H 0 1 N N N 6.410  -4.329  8.320  -1.677 -1.258 -1.833 "H1'"  UPE 34 
UPE "H2'"  "H2'"  H 0 1 N N N 6.053  -6.455  7.460  -2.227 -3.440 -1.172 "H2'"  UPE 35 
UPE "H2'A" "H2'A" H 0 0 N N N 5.966  -7.220  9.083  -2.260 -3.005 0.566  "H2'A" UPE 36 
UPE HN23   HN23   H 0 0 N N N 10.520 -5.547  13.826 3.888  -0.143 1.306  HN23   UPE 37 
UPE H24    H24    H 0 1 N N N 9.448  -4.300  15.989 5.600  -0.767 -0.853 H24    UPE 38 
UPE H24A   H24A   H 0 0 N N N 8.502  -5.827  15.972 5.155  0.953  -0.969 H24A   UPE 39 
UPE H25    H25    H 0 1 N N N 11.527 -5.838  15.767 5.962  1.318  1.347  H25    UPE 40 
UPE H25A   H25A   H 0 0 N N N 10.707 -5.719  17.361 6.407  -0.402 1.463  H25A   UPE 41 
UPE H27    H27    H 0 1 N N N 12.540 -7.833  16.899 7.223  2.834  -0.069 H27    UPE 42 
UPE H28    H28    H 0 1 N N N 12.427 -10.308 16.962 9.390  3.323  -1.131 H28    UPE 43 
UPE H29    H29    H 0 1 N N N 10.270 -11.434 16.483 11.006 1.507  -1.524 H29    UPE 44 
UPE "H3'"  "H3'"  H 0 1 N N N 3.657  -7.064  8.760  -4.538 -2.651 0.435  "H3'"  UPE 45 
UPE "HO3'" "HO3'" H 0 0 N N N 2.865  -5.471  7.217  -4.537 -4.230 -1.388 "HO3'" UPE 46 
UPE H30    H30    H 0 1 N N N 8.275  -10.098 15.892 10.455 -0.798 -0.854 H30    UPE 47 
UPE H31    H31    H 0 1 N N N 8.381  -7.622  15.848 8.293  -1.284 0.219  H31    UPE 48 
UPE "H4'"  "H4'"  H 0 1 N N N 3.432  -4.212  9.024  -4.291 -0.854 -1.984 "H4'"  UPE 49 
UPE "H5'"  "H5'"  H 0 1 N N N 1.974  -5.455  10.344 -6.289 -0.911 -0.415 "H5'"  UPE 50 
UPE "H5'A" "H5'A" H 0 0 N N N 3.268  -6.552  10.934 -5.215 -0.341 0.885  "H5'A" UPE 51 
UPE HOP2   HOP2   H 0 0 N N N 0.906  -3.202  13.517 -5.658 2.697  1.670  HOP2   UPE 52 
UPE HOP3   HOP3   H 0 0 N Y N 3.094  -1.639  11.118 -7.378 3.995  -0.637 HOP3   UPE 53 
# 
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 
UPE OP1   P      DOUB N N 1  
UPE "O5'" P      SING N N 2  
UPE OP3   P      SING N N 3  
UPE P     OP2    SING N N 4  
UPE "C1'" N1     SING N N 5  
UPE C2    N1     SING N N 6  
UPE N1    C6     SING N N 7  
UPE O2    C2     DOUB N N 8  
UPE C2    N3     SING N N 9  
UPE N3    C4     SING N N 10 
UPE N3    HN3    SING N N 11 
UPE C4    O4     DOUB N N 12 
UPE C4    C5     SING N N 13 
UPE C6    C5     DOUB N N 14 
UPE C5    C21    SING N N 15 
UPE C6    H6     SING N N 16 
UPE "C2'" "C1'"  SING N N 17 
UPE "C1'" "O4'"  SING N N 18 
UPE "C1'" "H1'"  SING N N 19 
UPE "C2'" "C3'"  SING N N 20 
UPE "C2'" "H2'"  SING N N 21 
UPE "C2'" "H2'A" SING N N 22 
UPE C21   O22    DOUB N N 23 
UPE C21   N23    SING N N 24 
UPE N23   C24    SING N N 25 
UPE N23   HN23   SING N N 26 
UPE C24   C25    SING N N 27 
UPE C24   H24    SING N N 28 
UPE C24   H24A   SING N N 29 
UPE C25   C26    SING N N 30 
UPE C25   H25    SING N N 31 
UPE C25   H25A   SING N N 32 
UPE C31   C26    DOUB Y N 33 
UPE C26   C27    SING Y N 34 
UPE C27   C28    DOUB Y N 35 
UPE C27   H27    SING N N 36 
UPE C29   C28    SING Y N 37 
UPE C28   H28    SING N N 38 
UPE C30   C29    DOUB Y N 39 
UPE C29   H29    SING N N 40 
UPE "O3'" "C3'"  SING N N 41 
UPE "C3'" "C4'"  SING N N 42 
UPE "C3'" "H3'"  SING N N 43 
UPE "O3'" "HO3'" SING N N 44 
UPE C31   C30    SING Y N 45 
UPE C30   H30    SING N N 46 
UPE C31   H31    SING N N 47 
UPE "C4'" "O4'"  SING N N 48 
UPE "C4'" "C5'"  SING N N 49 
UPE "C4'" "H4'"  SING N N 50 
UPE "C5'" "O5'"  SING N N 51 
UPE "C5'" "H5'"  SING N N 52 
UPE "C5'" "H5'A" SING N N 53 
UPE OP2   HOP2   SING N N 54 
UPE OP3   HOP3   SING N N 55 
# 
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 
UPE SMILES           ACDLabs              12.01 "O=P(O)(O)OCC3OC(N2C(=O)NC(=O)C(C(=O)NCCc1ccccc1)=C2)CC3O"                                                                                                                                           
UPE InChI            InChI                1.03  "InChI=1S/C18H22N3O9P/c22-13-8-15(30-14(13)10-29-31(26,27)28)21-9-12(17(24)20-18(21)25)16(23)19-7-6-11-4-2-1-3-5-11/h1-5,9,13-15,22H,6-8,10H2,(H,19,23)(H,20,24,25)(H2,26,27,28)/t13-,14+,15+/m0/s1" 
UPE InChIKey         InChI                1.03  CBTXGTWTWUZPNV-RRFJBIMHSA-N                                                                                                                                                                          
UPE SMILES_CANONICAL CACTVS               3.370 "O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=C(C(=O)NCCc3ccccc3)C(=O)NC2=O"                                                                                                                             
UPE SMILES           CACTVS               3.370 "O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=C(C(=O)NCCc3ccccc3)C(=O)NC2=O"                                                                                                                                  
UPE SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "c1ccc(cc1)CCNC(=O)C2=CN(C(=O)NC2=O)[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O"                                                                                                                            
UPE SMILES           "OpenEye OEToolkits" 1.7.6 "c1ccc(cc1)CCNC(=O)C2=CN(C(=O)NC2=O)C3CC(C(O3)COP(=O)(O)O)O"                                                                                                                                         
# 
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 
UPE "SYSTEMATIC NAME" ACDLabs              12.01 
;2'-deoxy-5-[(2-phenylethyl)carbamoyl]uridine 5'-(dihydrogen phosphate)
;
UPE "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "[(2R,3S,5R)-5-[2,4-bis(oxidanylidene)-5-(2-phenylethylcarbamoyl)pyrimidin-1-yl]-3-oxidanyl-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 
UPE "Create component" 2012-11-07 RCSB 
UPE "Initial release"  2012-11-16 RCSB 
# 
