data_DU4
# 
_chem_comp.id                                    DU4 
_chem_comp.name                                  "2',5'-dideoxy-5'-[(diphenylmethyl)(methyl)amino]uridine" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C23 H25 N3 O4" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2011-11-10 
_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                        407.462 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     DU4 
_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        3T70 
_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 
DU4 N1     N1     N 0 1 N N N 17.504 21.747 -0.241 3.408  -0.315 -0.404 N1     DU4 1  
DU4 C2     C2     C 0 1 N N N 18.329 22.730 -0.831 4.306  -0.265 -1.404 C2     DU4 2  
DU4 O2     O2     O 0 1 N N N 19.561 22.661 -0.823 4.369  -1.181 -2.200 O2     DU4 3  
DU4 N3     N3     N 0 1 N N N 17.731 23.819 -1.452 5.137  0.786  -1.536 N3     DU4 4  
DU4 C4     C4     C 0 1 N N N 16.335 23.943 -1.507 5.081  1.811  -0.661 C4     DU4 5  
DU4 O4     O4     O 0 1 N N N 15.852 24.925 -2.066 5.831  2.762  -0.780 O4     DU4 6  
DU4 C5     C5     C 0 1 N N N 15.510 22.973 -0.927 4.140  1.771  0.396  C5     DU4 7  
DU4 C6     C6     C 0 1 N N N 16.098 21.881 -0.288 3.318  0.705  0.505  C6     DU4 8  
DU4 "C1'"  "C1'"  C 0 1 N N R 18.139 20.573 0.408  2.513  -1.469 -0.290 "C1'"  DU4 9  
DU4 C17    C17    C 0 1 N N N 18.031 18.244 -4.406 -2.944 -0.333 0.593  C17    DU4 10 
DU4 C18    C18    C 0 1 Y N N 19.188 17.939 -5.397 -2.443 1.024  1.014  C18    DU4 11 
DU4 C19    C19    C 0 1 Y N N 19.011 16.949 -6.366 -2.909 1.602  2.180  C19    DU4 12 
DU4 "C2'"  "C2'"  C 0 1 N N N 17.284 19.723 1.354  2.816  -2.241 1.009  "C2'"  DU4 13 
DU4 C20    C20    C 0 1 Y N N 20.035 16.651 -7.271 -2.449 2.847  2.566  C20    DU4 14 
DU4 C21    C21    C 0 1 Y N N 21.242 17.352 -7.211 -1.523 3.514  1.787  C21    DU4 15 
DU4 C22    C22    C 0 1 Y N N 21.422 18.344 -6.250 -1.056 2.936  0.621  C22    DU4 16 
DU4 C23    C23    C 0 1 Y N N 20.398 18.640 -5.343 -1.512 1.689  0.237  C23    DU4 17 
DU4 C24    C24    C 0 1 Y N N 17.572 19.691 -4.663 -3.925 -0.177 -0.540 C24    DU4 18 
DU4 C25    C25    C 0 1 Y N N 16.583 19.903 -5.627 -5.278 -0.353 -0.312 C25    DU4 19 
DU4 C26    C26    C 0 1 Y N N 16.139 21.195 -5.910 -6.178 -0.209 -1.352 C26    DU4 20 
DU4 C27    C27    C 0 1 Y N N 16.684 22.280 -5.224 -5.726 0.110  -2.618 C27    DU4 21 
DU4 C28    C28    C 0 1 Y N N 17.681 22.073 -4.269 -4.374 0.286  -2.846 C28    DU4 22 
DU4 C29    C29    C 0 1 Y N N 18.128 20.783 -3.987 -3.474 0.147  -1.806 C29    DU4 23 
DU4 "C3'"  "C3'"  C 0 1 N N S 16.721 18.646 0.437  1.475  -2.224 1.783  "C3'"  DU4 24 
DU4 "O3'"  "O3'"  O 0 1 N N N 16.544 17.437 1.180  1.225  -3.489 2.398  "O3'"  DU4 25 
DU4 "C4'"  "C4'"  C 0 1 N N R 17.815 18.456 -0.619 0.452  -1.946 0.652  "C4'"  DU4 26 
DU4 "O4'"  "O4'"  O 0 1 N N N 18.488 19.728 -0.734 1.148  -1.024 -0.213 "O4'"  DU4 27 
DU4 C41    C41    C 0 1 N N N 18.912 16.573 -2.851 -2.270 -2.471 -0.321 C41    DU4 28 
DU4 "C5'"  "C5'"  C 0 1 N N N 17.274 18.089 -2.036 -0.814 -1.300 1.219  "C5'"  DU4 29 
DU4 "N5'"  "N5'"  N 0 1 N N N 18.400 17.956 -2.990 -1.812 -1.158 0.150  "N5'"  DU4 30 
DU4 HN3    HN3    H 0 1 N N N 18.305 24.526 -1.866 5.779  0.806  -2.262 HN3    DU4 31 
DU4 H5     H5     H 0 1 N N N 14.435 23.068 -0.973 4.080  2.582  1.107  H5     DU4 32 
DU4 H6     H6     H 0 1 N N N 15.473 21.132 0.175  2.594  0.657  1.304  H6     DU4 33 
DU4 "H1'"  "H1'"  H 0 1 N N N 18.947 20.942 1.057  2.643  -2.125 -1.150 "H1'"  DU4 34 
DU4 H17    H17    H 0 1 N N N 17.180 17.569 -4.583 -3.437 -0.816 1.437  H17    DU4 35 
DU4 H19    H19    H 0 1 N N N 18.077 16.410 -6.417 -3.633 1.081  2.789  H19    DU4 36 
DU4 "H2'"  "H2'"  H 0 1 N N N 17.886 19.290 2.167  3.113  -3.265 0.783  "H2'"  DU4 37 
DU4 "H2'A" "H2'A" H 0 0 N N N 16.485 20.316 1.822  3.593  -1.735 1.581  "H2'A" DU4 38 
DU4 H20    H20    H 0 1 N N N 19.893 15.881 -8.015 -2.814 3.299  3.477  H20    DU4 39 
DU4 H21    H21    H 0 1 N N N 22.034 17.125 -7.909 -1.164 4.487  2.088  H21    DU4 40 
DU4 H22    H22    H 0 1 N N N 22.355 18.887 -6.205 -0.332 3.457  0.012  H22    DU4 41 
DU4 H23    H23    H 0 1 N N N 20.542 19.411 -4.600 -1.145 1.235  -0.671 H23    DU4 42 
DU4 H25    H25    H 0 1 N N N 16.160 19.062 -6.156 -5.631 -0.602 0.677  H25    DU4 43 
DU4 H26    H26    H 0 1 N N N 15.376 21.354 -6.658 -7.234 -0.347 -1.174 H26    DU4 44 
DU4 H27    H27    H 0 1 N N N 16.335 23.281 -5.432 -6.429 0.221  -3.431 H27    DU4 45 
DU4 H28    H28    H 0 1 N N N 18.108 22.916 -3.746 -4.021 0.535  -3.836 H28    DU4 46 
DU4 H29    H29    H 0 1 N N N 18.901 20.627 -3.249 -2.418 0.289  -1.982 H29    DU4 47 
DU4 "H3'"  "H3'"  H 0 1 N N N 15.748 18.912 -0.002 1.464  -1.424 2.523  "H3'"  DU4 48 
DU4 "HO3'" "HO3'" H 0 0 N N N 16.193 16.763 0.610  1.891  -3.748 3.049  "HO3'" DU4 49 
DU4 "H4'"  "H4'"  H 0 1 N N N 18.458 17.624 -0.296 0.210  -2.865 0.119  "H4'"  DU4 50 
DU4 H41    H41    H 0 1 N N N 19.177 16.384 -1.800 -3.032 -2.336 -1.089 H41    DU4 51 
DU4 H41A   H41A   H 0 0 N N N 18.135 15.861 -3.167 -1.427 -3.022 -0.739 H41A   DU4 52 
DU4 H41B   H41B   H 0 0 N N N 19.804 16.447 -3.483 -2.690 -3.031 0.514  H41B   DU4 53 
DU4 "H5'"  "H5'"  H 0 1 N N N 16.730 17.135 -1.981 -1.219 -1.929 2.012  "H5'"  DU4 54 
DU4 "H5'A" "H5'A" H 0 0 N N N 16.596 18.883 -2.383 -0.572 -0.317 1.623  "H5'A" DU4 55 
# 
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 
DU4 N1    C2     SING N N 1  
DU4 N1    C6     SING N N 2  
DU4 N1    "C1'"  SING N N 3  
DU4 C2    O2     DOUB N N 4  
DU4 C2    N3     SING N N 5  
DU4 N3    C4     SING N N 6  
DU4 C4    O4     DOUB N N 7  
DU4 C4    C5     SING N N 8  
DU4 C5    C6     DOUB N N 9  
DU4 "C1'" "C2'"  SING N N 10 
DU4 "C1'" "O4'"  SING N N 11 
DU4 C17   C18    SING N N 12 
DU4 C17   C24    SING N N 13 
DU4 C17   "N5'"  SING N N 14 
DU4 C18   C19    DOUB Y N 15 
DU4 C18   C23    SING Y N 16 
DU4 C19   C20    SING Y N 17 
DU4 "C2'" "C3'"  SING N N 18 
DU4 C20   C21    DOUB Y N 19 
DU4 C21   C22    SING Y N 20 
DU4 C22   C23    DOUB Y N 21 
DU4 C24   C25    DOUB Y N 22 
DU4 C24   C29    SING Y N 23 
DU4 C25   C26    SING Y N 24 
DU4 C26   C27    DOUB Y N 25 
DU4 C27   C28    SING Y N 26 
DU4 C28   C29    DOUB Y N 27 
DU4 "C3'" "O3'"  SING N N 28 
DU4 "C3'" "C4'"  SING N N 29 
DU4 "C4'" "O4'"  SING N N 30 
DU4 "C4'" "C5'"  SING N N 31 
DU4 C41   "N5'"  SING N N 32 
DU4 "C5'" "N5'"  SING N N 33 
DU4 N3    HN3    SING N N 34 
DU4 C5    H5     SING N N 35 
DU4 C6    H6     SING N N 36 
DU4 "C1'" "H1'"  SING N N 37 
DU4 C17   H17    SING N N 38 
DU4 C19   H19    SING N N 39 
DU4 "C2'" "H2'"  SING N N 40 
DU4 "C2'" "H2'A" SING N N 41 
DU4 C20   H20    SING N N 42 
DU4 C21   H21    SING N N 43 
DU4 C22   H22    SING N N 44 
DU4 C23   H23    SING N N 45 
DU4 C25   H25    SING N N 46 
DU4 C26   H26    SING N N 47 
DU4 C27   H27    SING N N 48 
DU4 C28   H28    SING N N 49 
DU4 C29   H29    SING N N 50 
DU4 "C3'" "H3'"  SING N N 51 
DU4 "O3'" "HO3'" SING N N 52 
DU4 "C4'" "H4'"  SING N N 53 
DU4 C41   H41    SING N N 54 
DU4 C41   H41A   SING N N 55 
DU4 C41   H41B   SING N N 56 
DU4 "C5'" "H5'"  SING N N 57 
DU4 "C5'" "H5'A" SING N N 58 
# 
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 
DU4 SMILES           ACDLabs              12.01 "O=C1NC(=O)N(C=C1)C2OC(C(O)C2)CN(C(c3ccccc3)c4ccccc4)C"                                                                                                                               
DU4 InChI            InChI                1.03  "InChI=1S/C23H25N3O4/c1-25(22(16-8-4-2-5-9-16)17-10-6-3-7-11-17)15-19-18(27)14-21(30-19)26-13-12-20(28)24-23(26)29/h2-13,18-19,21-22,27H,14-15H2,1H3,(H,24,28,29)/t18-,19+,21+/m0/s1" 
DU4 InChIKey         InChI                1.03  GMULPQZINUAVEX-QKNQBKEWSA-N                                                                                                                                                           
DU4 SMILES_CANONICAL CACTVS               3.370 "CN(C[C@H]1O[C@H](C[C@@H]1O)N2C=CC(=O)NC2=O)C(c3ccccc3)c4ccccc4"                                                                                                                      
DU4 SMILES           CACTVS               3.370 "CN(C[CH]1O[CH](C[CH]1O)N2C=CC(=O)NC2=O)C(c3ccccc3)c4ccccc4"                                                                                                                          
DU4 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.2 "C[N@](C[C@@H]1[C@H](C[C@@H](O1)N2C=CC(=O)NC2=O)O)C(c3ccccc3)c4ccccc4"                                                                                                                
DU4 SMILES           "OpenEye OEToolkits" 1.7.2 "CN(CC1C(CC(O1)N2C=CC(=O)NC2=O)O)C(c3ccccc3)c4ccccc4"                                                                                                                                 
# 
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 
DU4 "SYSTEMATIC NAME" ACDLabs              12.01 "2',5'-dideoxy-5'-[(diphenylmethyl)(methyl)amino]uridine"                                             
DU4 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.2 "1-[(2R,4S,5R)-5-[[(diphenylmethyl)-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 
DU4 "Create component" 2011-11-10 PDBJ 
DU4 "Initial release"  2012-08-24 RCSB 
# 
