data_DU2
# 
_chem_comp.id                                    DU2 
_chem_comp.name                                  "2',5'-dideoxy-5'-{[(R)-(1-methyl-1H-imidazol-2-yl)(phenyl)methyl]amino}uridine" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C20 H23 N5 O4" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2011-11-10 
_chem_comp.pdbx_modified_date                    2012-08-24 
_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                        397.428 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     DU2 
_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        3T6Y 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBJ 
# 
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 
DU2 N1     N1     N 0 1 N N N 17.713 21.750 -0.341 -3.648 -0.360 0.283  N1     DU2 1  
DU2 C2     C2     C 0 1 N N N 18.465 22.717 -0.838 -4.596 -0.402 1.237  C2     DU2 2  
DU2 O2     O2     O 0 1 N N N 19.675 22.573 -0.786 -4.636 -1.347 2.001  O2     DU2 3  
DU2 N3     N3     N 0 1 N N N 17.922 23.820 -1.428 -5.500 0.587  1.357  N3     DU2 4  
DU2 C4     C4     C 0 1 N N N 16.581 23.892 -1.507 -5.469 1.643  0.518  C4     DU2 5  
DU2 O4     O4     O 0 1 N N N 16.070 24.859 -2.069 -6.286 2.539  0.627  O4     DU2 6  
DU2 C5     C5     C 0 1 N N N 15.791 22.902 -0.951 -4.477 1.699  -0.490 C5     DU2 7  
DU2 C6     C6     C 0 1 N N N 16.353 21.823 -0.358 -3.582 0.693  -0.589 C6     DU2 8  
DU2 "C1'"  "C1'"  C 0 1 N N R 18.409 20.651 0.280  -2.674 -1.449 0.180  "C1'"  DU2 9  
DU2 C17    C17    C 0 1 N N R 18.240 18.516 -4.104 2.849  -0.130 -0.455 C17    DU2 10 
DU2 C18    C18    C 0 1 Y N N 17.684 19.738 -4.469 3.991  -0.489 0.461  C18    DU2 11 
DU2 C19    C19    C 0 1 Y N N 18.131 20.903 -3.876 5.256  -0.693 -0.059 C19    DU2 12 
DU2 "C2'"  "C2'"  C 0 1 N N N 17.518 19.961 1.351  -2.861 -2.196 -1.155 "C2'"  DU2 13 
DU2 C20    C20    C 0 1 Y N N 17.595 22.145 -4.257 6.303  -1.022 0.781  C20    DU2 14 
DU2 C21    C21    C 0 1 Y N N 16.599 22.256 -5.244 6.086  -1.147 2.140  C21    DU2 15 
DU2 C22    C22    C 0 1 Y N N 16.170 21.061 -5.831 4.822  -0.943 2.660  C22    DU2 16 
DU2 C23    C23    C 0 1 Y N N 16.689 19.808 -5.464 3.775  -0.609 1.821  C23    DU2 17 
DU2 C24    C24    C 0 1 Y N N 19.149 17.910 -5.002 2.605  1.356  -0.395 C24    DU2 18 
DU2 N25    N25    N 0 1 Y N N 19.760 16.741 -4.801 2.026  1.992  0.586  N25    DU2 19 
DU2 C26    C26    C 0 1 Y N N 20.686 16.362 -5.908 1.980  3.302  0.298  C26    DU2 20 
DU2 C27    C27    C 0 1 Y N N 20.552 17.505 -6.872 2.553  3.483  -0.907 C27    DU2 21 
DU2 N28    N28    N 0 1 Y N N 19.593 18.357 -6.171 2.954  2.250  -1.345 N28    DU2 22 
DU2 C29    C29    C 0 1 N N N 19.168 19.579 -6.748 3.633  1.954  -2.609 C29    DU2 23 
DU2 "C3'"  "C3'"  C 0 1 N N S 16.734 19.018 0.489  -1.488 -2.065 -1.859 "C3'"  DU2 24 
DU2 "C4'"  "C4'"  C 0 1 N N R 17.730 18.586 -0.589 -0.542 -1.759 -0.670 "C4'"  DU2 25 
DU2 "O4'"  "O4'"  O 0 1 N N N 18.636 19.737 -0.788 -1.339 -0.914 0.187  "O4'"  DU2 26 
DU2 O41    O41    O 0 1 N N N 16.487 17.958 1.331  -1.124 -3.290 -2.498 O41    DU2 27 
DU2 "C5'"  "C5'"  C 0 1 N N N 17.009 18.352 -1.929 0.705  -1.014 -1.151 "C5'"  DU2 28 
DU2 "N5'"  "N5'"  N 0 1 N N N 17.965 17.849 -2.948 1.637  -0.843 -0.029 "N5'"  DU2 29 
DU2 HN3    HN3    H 0 1 N N N 18.501 24.551 -1.790 -6.177 0.541  2.050  HN3    DU2 30 
DU2 H5     H5     H 0 1 N N N 14.715 22.991 -0.990 -4.436 2.536  -1.172 H5     DU2 31 
DU2 H6     H6     H 0 1 N N N 15.745 21.048 0.086  -2.818 0.719  -1.352 H6     DU2 32 
DU2 "H1'"  "H1'"  H 0 1 N N N 19.328 20.983 0.785  -2.802 -2.141 1.012  "H1'"  DU2 33 
DU2 H17    H17    H 0 1 N N N 17.637 19.095 -3.389 3.099  -0.416 -1.477 H17    DU2 34 
DU2 H19    H19    H 0 1 N N N 18.897 20.859 -3.115 5.425  -0.595 -1.121 H19    DU2 35 
DU2 "H2'"  "H2'"  H 0 1 N N N 18.108 19.439 2.119  -3.099 -3.244 -0.976 "H2'"  DU2 36 
DU2 "H2'A" "H2'A" H 0 0 N N N 16.876 20.674 1.889  -3.641 -1.722 -1.751 "H2'A" DU2 37 
DU2 H20    H20    H 0 1 N N N 17.959 23.042 -3.777 7.291  -1.182 0.375  H20    DU2 38 
DU2 H21    H21    H 0 1 N N N 16.188 23.212 -5.533 6.904  -1.405 2.796  H21    DU2 39 
DU2 H22    H22    H 0 1 N N N 15.410 21.103 -6.597 4.652  -1.041 3.722  H22    DU2 40 
DU2 H23    H23    H 0 1 N N N 16.329 18.908 -5.940 2.788  -0.445 2.227  H23    DU2 41 
DU2 H26    H26    H 0 1 N N N 21.303 15.480 -5.995 1.558  4.075  0.923  H26    DU2 42 
DU2 H27    H27    H 0 1 N N N 21.034 17.657 -7.826 2.675  4.422  -1.427 H27    DU2 43 
DU2 H29    H29    H 0 1 N N N 19.677 19.726 -7.712 2.891  1.750  -3.381 H29    DU2 44 
DU2 H29A   H29A   H 0 0 N N N 18.080 19.550 -6.908 4.239  2.811  -2.905 H29A   DU2 45 
DU2 H29B   H29B   H 0 0 N N N 19.417 20.410 -6.072 4.274  1.082  -2.482 H29B   DU2 46 
DU2 "H3'"  "H3'"  H 0 1 N N N 15.810 19.412 0.041  -1.493 -1.242 -2.573 "H3'"  DU2 47 
DU2 "H4'"  "H4'"  H 0 1 N N N 18.244 17.663 -0.284 -0.265 -2.678 -0.153 "H4'"  DU2 48 
DU2 HO41   HO41   H 0 0 N N N 15.987 17.296 0.869  -1.738 -3.570 -3.190 HO41   DU2 49 
DU2 "H5'"  "H5'"  H 0 1 N N N 16.210 17.610 -1.785 1.189  -1.589 -1.941 "H5'"  DU2 50 
DU2 "H5'A" "H5'A" H 0 0 N N N 16.576 19.301 -2.277 0.418  -0.036 -1.538 "H5'A" DU2 51 
DU2 "HN5'" "HN5'" H 0 0 N N N 17.598 16.965 -3.237 1.869  -1.732 0.388  "HN5'" DU2 52 
# 
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 
DU2 N1    C2     SING N N 1  
DU2 N1    C6     SING N N 2  
DU2 N1    "C1'"  SING N N 3  
DU2 C2    O2     DOUB N N 4  
DU2 C2    N3     SING N N 5  
DU2 N3    C4     SING N N 6  
DU2 C4    O4     DOUB N N 7  
DU2 C4    C5     SING N N 8  
DU2 C5    C6     DOUB N N 9  
DU2 "C1'" "C2'"  SING N N 10 
DU2 "C1'" "O4'"  SING N N 11 
DU2 C17   C18    SING N N 12 
DU2 C17   C24    SING N N 13 
DU2 C17   "N5'"  SING N N 14 
DU2 C18   C19    DOUB Y N 15 
DU2 C18   C23    SING Y N 16 
DU2 C19   C20    SING Y N 17 
DU2 "C2'" "C3'"  SING N N 18 
DU2 C20   C21    DOUB Y N 19 
DU2 C21   C22    SING Y N 20 
DU2 C22   C23    DOUB Y N 21 
DU2 C24   N25    DOUB Y N 22 
DU2 C24   N28    SING Y N 23 
DU2 N25   C26    SING Y N 24 
DU2 C26   C27    DOUB Y N 25 
DU2 C27   N28    SING Y N 26 
DU2 N28   C29    SING N N 27 
DU2 "C3'" "C4'"  SING N N 28 
DU2 "C3'" O41    SING N N 29 
DU2 "C4'" "O4'"  SING N N 30 
DU2 "C4'" "C5'"  SING N N 31 
DU2 "C5'" "N5'"  SING N N 32 
DU2 N3    HN3    SING N N 33 
DU2 C5    H5     SING N N 34 
DU2 C6    H6     SING N N 35 
DU2 "C1'" "H1'"  SING N N 36 
DU2 C17   H17    SING N N 37 
DU2 C19   H19    SING N N 38 
DU2 "C2'" "H2'"  SING N N 39 
DU2 "C2'" "H2'A" SING N N 40 
DU2 C20   H20    SING N N 41 
DU2 C21   H21    SING N N 42 
DU2 C22   H22    SING N N 43 
DU2 C23   H23    SING N N 44 
DU2 C26   H26    SING N N 45 
DU2 C27   H27    SING N N 46 
DU2 C29   H29    SING N N 47 
DU2 C29   H29A   SING N N 48 
DU2 C29   H29B   SING N N 49 
DU2 "C3'" "H3'"  SING N N 50 
DU2 "C4'" "H4'"  SING N N 51 
DU2 O41   HO41   SING N N 52 
DU2 "C5'" "H5'"  SING N N 53 
DU2 "C5'" "H5'A" SING N N 54 
DU2 "N5'" "HN5'" 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 
DU2 SMILES           ACDLabs              12.01 "O=C1NC(=O)N(C=C1)C2OC(C(O)C2)CNC(c3ccccc3)c4nccn4C"                                                                                                                                      
DU2 InChI            InChI                1.03  "InChI=1S/C20H23N5O4/c1-24-10-8-21-19(24)18(13-5-3-2-4-6-13)22-12-15-14(26)11-17(29-15)25-9-7-16(27)23-20(25)28/h2-10,14-15,17-18,22,26H,11-12H2,1H3,(H,23,27,28)/t14-,15+,17+,18?/m0/s1" 
DU2 InChIKey         InChI                1.03  KPWKGDCQLFIJMC-URHIDPGUSA-N                                                                                                                                                               
DU2 SMILES_CANONICAL CACTVS               3.370 "Cn1ccnc1[C@H](NC[C@H]2O[C@H](C[C@@H]2O)N3C=CC(=O)NC3=O)c4ccccc4"                                                                                                                         
DU2 SMILES           CACTVS               3.370 "Cn1ccnc1[CH](NC[CH]2O[CH](C[CH]2O)N3C=CC(=O)NC3=O)c4ccccc4"                                                                                                                              
DU2 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.2 "Cn1ccnc1C(c2ccccc2)NC[C@@H]3[C@H](C[C@@H](O3)N4C=CC(=O)NC4=O)O"                                                                                                                          
DU2 SMILES           "OpenEye OEToolkits" 1.7.2 "Cn1ccnc1C(c2ccccc2)NCC3C(CC(O3)N4C=CC(=O)NC4=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 
DU2 "SYSTEMATIC NAME" ACDLabs              12.01 "2',5'-dideoxy-5'-{[(R)-(1-methyl-1H-imidazol-2-yl)(phenyl)methyl]amino}uridine"                                     
DU2 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.2 "1-[(2R,4S,5R)-5-[[[(1-methylimidazol-2-yl)-phenyl-methyl]amino]methyl]-4-oxidanyl-oxolan-2-yl]pyrimidine-2,4-dione" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
DU2 "Create component" 2011-11-10 PDBJ 
DU2 "Modify name"      2012-08-20 PDBJ 
DU2 "Modify formula"   2012-08-20 PDBJ 
DU2 "Modify name"      2012-08-21 PDBJ 
DU2 "Modify formula"   2012-08-21 PDBJ 
DU2 "Initial release"  2012-08-24 RCSB 
# 
