data_DU3
# 
_chem_comp.id                                    DU3 
_chem_comp.name                                  "2',5'-dideoxy-5'-[(diphenylmethyl)amino]uridine" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C22 H23 N3 O4" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2011-08-18 
_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                        393.436 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     DU3 
_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        3T64 
_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 
DU3 N1     N1     N 0 1 N N N 17.694 21.937 -0.113 3.562  -0.382 -0.309 N1     DU3 1  
DU3 C2     C2     C 0 1 N N N 18.513 22.893 -0.745 4.486  -0.350 -1.287 C2     DU3 2  
DU3 O2     O2     O 0 1 N N N 19.742 22.821 -0.751 4.502  -1.230 -2.125 O2     DU3 3  
DU3 N3     N3     N 0 1 N N N 17.915 23.963 -1.403 5.392  0.643  -1.350 N3     DU3 4  
DU3 C4     C4     C 0 1 N N N 16.504 24.056 -1.447 5.387  1.627  -0.428 C4     DU3 5  
DU3 O4     O4     O 0 1 N N N 16.005 25.020 -2.057 6.206  2.527  -0.484 O4     DU3 6  
DU3 C5     C5     C 0 1 N N N 15.700 23.098 -0.817 4.420  1.605  0.606  C5     DU3 7  
DU3 C6     C6     C 0 1 N N N 16.300 22.025 -0.156 3.520  0.600  0.642  C6     DU3 8  
DU3 "C1'"  "C1'"  C 0 1 N N R 18.356 20.790 0.567  2.589  -1.477 -0.266 "C1'"  DU3 9  
DU3 C17    C17    C 0 1 N N N 18.179 18.371 -4.125 -2.917 -0.219 0.606  C17    DU3 10 
DU3 C18    C18    C 0 1 Y N N 19.309 17.880 -5.049 -2.676 1.268  0.658  C18    DU3 11 
DU3 C19    C19    C 0 1 Y N N 19.238 16.580 -5.538 -3.145 2.008  1.727  C19    DU3 12 
DU3 "C2'"  "C2'"  C 0 1 N N N 17.452 20.039 1.548  2.808  -2.324 1.002  "C2'"  DU3 13 
DU3 C20    C20    C 0 1 Y N N 20.235 16.102 -6.377 -2.924 3.371  1.774  C20    DU3 14 
DU3 C21    C21    C 0 1 Y N N 21.301 16.917 -6.732 -2.233 3.995  0.752  C21    DU3 15 
DU3 C22    C22    C 0 1 Y N N 21.368 18.214 -6.250 -1.763 3.255  -0.317 C22    DU3 16 
DU3 C23    C23    C 0 1 Y N N 20.374 18.700 -5.406 -1.979 1.890  -0.361 C23    DU3 17 
DU3 C24    C24    C 0 1 Y N N 17.735 19.801 -4.479 -4.081 -0.507 -0.307 C24    DU3 18 
DU3 C25    C25    C 0 1 Y N N 16.752 19.926 -5.469 -3.896 -0.530 -1.676 C25    DU3 19 
DU3 C26    C26    C 0 1 Y N N 16.293 21.191 -5.825 -4.964 -0.794 -2.514 C26    DU3 20 
DU3 C27    C27    C 0 1 Y N N 16.765 22.332 -5.185 -6.216 -1.036 -1.982 C27    DU3 21 
DU3 C28    C28    C 0 1 Y N N 17.752 22.212 -4.202 -6.401 -1.014 -0.612 C28    DU3 22 
DU3 C29    C29    C 0 1 Y N N 18.223 20.946 -3.838 -5.333 -0.754 0.226  C29    DU3 23 
DU3 "C3'"  "C3'"  C 0 1 N N S 16.857 18.937 0.681  1.453  -2.248 1.747  "C3'"  DU3 24 
DU3 "O3'"  "O3'"  O 0 1 N N N 16.721 17.778 1.492  1.103  -3.519 2.299  "O3'"  DU3 25 
DU3 "C4'"  "C4'"  C 0 1 N N R 17.921 18.684 -0.381 0.478  -1.852 0.610  "C4'"  DU3 26 
DU3 "O4'"  "O4'"  O 0 1 N N N 18.675 19.915 -0.539 1.256  -0.942 -0.199 "O4'"  DU3 27 
DU3 "C5'"  "C5'"  C 0 1 N N N 17.366 18.288 -1.784 -0.757 -1.150 1.179  "C5'"  DU3 28 
DU3 "N5'"  "N5'"  N 0 1 N N N 18.524 18.201 -2.695 -1.716 -0.893 0.096  "N5'"  DU3 29 
DU3 H5     H5     H 0 1 N N N 14.624 23.189 -0.842 4.401  2.385  1.354  H5     DU3 30 
DU3 H6     H6     H 0 1 N N N 15.692 21.269 0.318  2.774  0.567  1.424  H6     DU3 31 
DU3 "H1'"  "H1'"  H 0 1 N N N 19.208 21.130 1.174  2.695  -2.102 -1.153 "H1'"  DU3 32 
DU3 H17    H17    H 0 1 N N N 17.302 17.730 -4.300 -3.142 -0.586 1.608  H17    DU3 33 
DU3 H19    H19    H 0 1 N N N 18.409 15.944 -5.265 -3.686 1.520  2.525  H19    DU3 34 
DU3 "H2'"  "H2'"  H 0 1 N N N 18.021 19.629 2.395  3.040  -3.355 0.737  "H2'"  DU3 35 
DU3 "H2'A" "H2'A" H 0 0 N N N 16.674 20.693 1.968  3.605  -1.898 1.612  "H2'A" DU3 36 
DU3 H20    H20    H 0 1 N N N 20.181 15.092 -6.755 -3.291 3.950  2.609  H20    DU3 37 
DU3 H21    H21    H 0 1 N N N 22.077 16.541 -7.383 -2.061 5.061  0.788  H21    DU3 38 
DU3 H22    H22    H 0 1 N N N 22.195 18.850 -6.530 -1.223 3.742  -1.115 H22    DU3 39 
DU3 H23    H23    H 0 1 N N N 20.429 19.711 -5.029 -1.612 1.312  -1.196 H23    DU3 40 
DU3 H25    H25    H 0 1 N N N 16.353 19.047 -5.953 -2.917 -0.341 -2.092 H25    DU3 41 
DU3 H26    H26    H 0 1 N N N 15.559 21.288 -6.611 -4.819 -0.811 -3.584 H26    DU3 42 
DU3 H27    H27    H 0 1 N N N 16.372 23.304 -5.445 -7.051 -1.241 -2.636 H27    DU3 43 
DU3 H28    H28    H 0 1 N N N 18.150 23.095 -3.725 -7.380 -1.202 -0.196 H28    DU3 44 
DU3 H29    H29    H 0 1 N N N 18.966 20.852 -3.060 -5.477 -0.741 1.296  H29    DU3 45 
DU3 "H3'"  "H3'"  H 0 1 N N N 15.880 19.191 0.245  1.478  -1.483 2.523  "H3'"  DU3 46 
DU3 "HO3'" "HO3'" H 0 0 N N N 16.351 17.071 0.976  1.734  -3.852 2.952  "HO3'" DU3 47 
DU3 "H4'"  "H4'"  H 0 1 N N N 18.521 17.831 -0.031 0.188  -2.728 0.030  "H4'"  DU3 48 
DU3 "H5'"  "H5'"  H 0 1 N N N 16.848 17.319 -1.731 -1.221 -1.786 1.932  "H5'"  DU3 49 
DU3 "H5'A" "H5'A" H 0 0 N N N 16.654 19.047 -2.142 -0.461 -0.205 1.634  "H5'A" DU3 50 
DU3 "HN5'" "HN5'" H 0 0 N N N 18.938 17.298 -2.582 -1.957 -1.747 -0.384 "HN5'" DU3 51 
DU3 HN3    HN3    H 0 1 N N N 18.479 24.662 -1.842 6.051  0.651  -2.061 HN3    DU3 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 
DU3 C2    N1     SING N N 1  
DU3 C6    N1     SING N N 2  
DU3 N1    "C1'"  SING N N 3  
DU3 N3    C2     SING N N 4  
DU3 O2    C2     DOUB N N 5  
DU3 C4    N3     SING N N 6  
DU3 O4    C4     DOUB N N 7  
DU3 C4    C5     SING N N 8  
DU3 C5    C6     DOUB N N 9  
DU3 C5    H5     SING N N 10 
DU3 C6    H6     SING N N 11 
DU3 "O4'" "C1'"  SING N N 12 
DU3 "C1'" "C2'"  SING N N 13 
DU3 "C1'" "H1'"  SING N N 14 
DU3 C18   C17    SING N N 15 
DU3 C24   C17    SING N N 16 
DU3 C17   "N5'"  SING N N 17 
DU3 C17   H17    SING N N 18 
DU3 C19   C18    DOUB Y N 19 
DU3 C23   C18    SING Y N 20 
DU3 C20   C19    SING Y N 21 
DU3 C19   H19    SING N N 22 
DU3 "C3'" "C2'"  SING N N 23 
DU3 "C2'" "H2'"  SING N N 24 
DU3 "C2'" "H2'A" SING N N 25 
DU3 C21   C20    DOUB Y N 26 
DU3 C20   H20    SING N N 27 
DU3 C21   C22    SING Y N 28 
DU3 C21   H21    SING N N 29 
DU3 C22   C23    DOUB Y N 30 
DU3 C22   H22    SING N N 31 
DU3 C23   H23    SING N N 32 
DU3 C25   C24    DOUB Y N 33 
DU3 C24   C29    SING Y N 34 
DU3 C26   C25    SING Y N 35 
DU3 C25   H25    SING N N 36 
DU3 C26   C27    DOUB Y N 37 
DU3 C26   H26    SING N N 38 
DU3 C27   C28    SING Y N 39 
DU3 C27   H27    SING N N 40 
DU3 C28   C29    DOUB Y N 41 
DU3 C28   H28    SING N N 42 
DU3 C29   H29    SING N N 43 
DU3 "C4'" "C3'"  SING N N 44 
DU3 "C3'" "O3'"  SING N N 45 
DU3 "C3'" "H3'"  SING N N 46 
DU3 "O3'" "HO3'" SING N N 47 
DU3 "C5'" "C4'"  SING N N 48 
DU3 "O4'" "C4'"  SING N N 49 
DU3 "C4'" "H4'"  SING N N 50 
DU3 "N5'" "C5'"  SING N N 51 
DU3 "C5'" "H5'"  SING N N 52 
DU3 "C5'" "H5'A" SING N N 53 
DU3 "N5'" "HN5'" SING N N 54 
DU3 N3    HN3    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 
DU3 SMILES           ACDLabs              12.01 "O=C1NC(=O)N(C=C1)C2OC(C(O)C2)CNC(c3ccccc3)c4ccccc4"                                                                                                                              
DU3 InChI            InChI                1.03  "InChI=1S/C22H23N3O4/c26-17-13-20(25-12-11-19(27)24-22(25)28)29-18(17)14-23-21(15-7-3-1-4-8-15)16-9-5-2-6-10-16/h1-12,17-18,20-21,23,26H,13-14H2,(H,24,27,28)/t17-,18+,20+/m0/s1" 
DU3 InChIKey         InChI                1.03  JJVBLAPDVHVENR-NLWGTHIKSA-N                                                                                                                                                       
DU3 SMILES_CANONICAL CACTVS               3.370 "O[C@H]1C[C@@H](O[C@@H]1CNC(c2ccccc2)c3ccccc3)N4C=CC(=O)NC4=O"                                                                                                                    
DU3 SMILES           CACTVS               3.370 "O[CH]1C[CH](O[CH]1CNC(c2ccccc2)c3ccccc3)N4C=CC(=O)NC4=O"                                                                                                                         
DU3 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.2 "c1ccc(cc1)C(c2ccccc2)NC[C@@H]3[C@H](C[C@@H](O3)N4C=CC(=O)NC4=O)O"                                                                                                                
DU3 SMILES           "OpenEye OEToolkits" 1.7.2 "c1ccc(cc1)C(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 
DU3 "SYSTEMATIC NAME" ACDLabs              12.01 "2',5'-dideoxy-5'-[(diphenylmethyl)amino]uridine"                                             
DU3 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.2 "1-[(2R,4S,5R)-5-[[(diphenylmethyl)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 
DU3 "Create component" 2011-08-18 RCSB 
DU3 "Initial release"  2012-08-24 RCSB 
# 
