data_ZDU
# 
_chem_comp.id                                    ZDU 
_chem_comp.name                                  "5-(3-AMINOPROPYL)-2'-DEOXYURIDINE-5'-MONOPHOSPHATE" 
_chem_comp.type                                  "DNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C12 H20 N3 O8 P" 
_chem_comp.mon_nstd_parent_comp_id               DU 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2005-04-08 
_chem_comp.pdbx_modified_date                    2009-01-07 
_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                        365.276 
_chem_comp.one_letter_code                       U 
_chem_comp.three_letter_code                     ZDU 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   Y 
_chem_comp.pdbx_ideal_coordinates_details        ? 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        1Z5T 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  EBI 
# 
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 
ZDU P      P    P 0 1 N N N 3.248  -12.692 45.584 -3.968 -1.665 3.118  P      ZDU 1  
ZDU OP1    O1P  O 0 1 N N N 2.650  -11.716 44.693 -4.406 -2.599 4.208  OP1    ZDU 2  
ZDU OP2    O2P  O 0 1 N N N 4.484  -12.387 46.320 -3.912 -2.311 1.636  OP2    ZDU 3  
ZDU "O5'"  O5*  O 0 1 N N N 3.476  -14.042 44.773 -2.493 -1.028 3.315  "O5'"  ZDU 4  
ZDU N1     N1   N 0 1 N N N 0.941  -17.102 42.324 1.164  -2.047 0.989  N1     ZDU 5  
ZDU C6     C6   C 0 1 N N N 0.285  -15.887 42.306 -0.013 -2.784 0.958  C6     ZDU 6  
ZDU C2     C2   C 0 1 N N N 0.306  -18.265 41.929 2.333  -2.544 0.374  C2     ZDU 7  
ZDU O2     O2   O 0 1 N N N 0.878  -19.347 41.885 3.410  -1.945 0.363  O2     ZDU 8  
ZDU N3     N3   N 0 1 N N N -1.029 -18.102 41.581 2.194  -3.793 -0.240 N3     ZDU 9  
ZDU C4     C4   C 0 1 N N N -1.766 -16.897 41.579 1.047  -4.570 -0.300 C4     ZDU 10 
ZDU O4     O4   O 0 1 N N N -2.976 -16.899 41.258 0.995  -5.663 -0.857 O4     ZDU 11 
ZDU C5     C5   C 0 1 N N N -1.003 -15.717 41.973 -0.143 -3.980 0.369  C5     ZDU 12 
ZDU C5A    C5A  C 0 1 N N N -1.650 -14.354 41.988 -1.420 -4.757 0.347  C5A    ZDU 13 
ZDU C5B    C5B  C 0 1 N N N -1.910 -13.795 40.570 -2.254 -4.400 -0.880 C5B    ZDU 14 
ZDU C5G    C5G  C 0 1 N N N -2.747 -12.545 40.656 -3.558 -5.188 -0.993 C5G    ZDU 15 
ZDU N5D    N5D  N 0 1 N N N -2.852 -11.826 39.340 -4.335 -4.808 -2.141 N5D    ZDU 16 
ZDU "C2'"  C2*  C 0 1 N N N 3.446  -16.434 42.118 0.710  0.360  0.754  "C2'"  ZDU 17 
ZDU "C5'"  C5*  C 0 1 N N N 3.788  -15.226 45.465 -2.005 -0.136 2.327  "C5'"  ZDU 18 
ZDU "C4'"  C4*  C 0 1 N N R 3.680  -16.407 44.535 -0.611 0.328  2.728  "C4'"  ZDU 19 
ZDU "O4'"  O4*  O 0 1 N N N 2.320  -16.611 44.133 0.247  -0.829 2.764  "O4'"  ZDU 20 
ZDU "C1'"  C1*  C 0 1 N N R 2.329  -17.182 42.841 1.157  -0.778 1.657  "C1'"  ZDU 21 
ZDU "C3'"  C3*  C 0 1 N N S 4.464  -16.232 43.245 0.008  1.286  1.720  "C3'"  ZDU 22 
ZDU "O3'"  O3*  O 0 1 N N N 5.469  -17.239 43.239 0.965  2.121  2.368  "O3'"  ZDU 23 
ZDU OP3    O3P  O 0 1 N Y N ?      ?       ?      -4.901 -0.360 2.920  OP3    ZDU 24 
ZDU HOP2   2HOP H 0 0 N N N 4.875  -13.026 46.903 -4.684 -2.823 1.313  HOP2   ZDU 25 
ZDU H6     H6   H 0 1 N N N 0.837  -14.973 42.581 -0.857 -2.318 1.458  H6     ZDU 26 
ZDU HN3    HN3  H 0 1 N N N -1.516 -18.952 41.298 3.023  -4.171 -0.689 HN3    ZDU 27 
ZDU H5A1   1H5A H 0 0 N N N -2.588 -14.364 42.590 -1.153 -5.818 0.312  H5A1   ZDU 28 
ZDU H5A2   2H5A H 0 0 N N N -1.052 -13.635 42.596 -1.963 -4.568 1.277  H5A2   ZDU 29 
ZDU H5B1   1H5B H 0 0 N N N -0.962 -13.626 40.006 -2.493 -3.329 -0.861 H5B1   ZDU 30 
ZDU H5B2   2H5B H 0 0 N N N -2.365 -14.558 39.896 -1.647 -4.578 -1.776 H5B2   ZDU 31 
ZDU H5G1   1H5G H 0 0 N N N -3.757 -12.767 41.071 -3.373 -6.264 -1.056 H5G1   ZDU 32 
ZDU H5G2   2H5G H 0 0 N N N -2.369 -11.864 41.454 -4.181 -5.003 -0.112 H5G2   ZDU 33 
ZDU H5D1   1H5D H 0 0 N N N -3.418 -10.979 39.398 -5.310 -4.580 -2.022 H5D1   ZDU 34 
ZDU H5D2   2H5D H 0 0 N N N -3.197 -12.448 38.609 -3.961 -4.969 -3.063 H5D2   ZDU 35 
ZDU "H2'"  1H2* H 0 1 N N N 3.841  -16.938 41.205 -0.003 -0.001 0.003  "H2'"  ZDU 36 
ZDU "H2''" 2H2* H 0 0 N N N 3.130  -15.503 41.591 1.556  0.818  0.232  "H2''" ZDU 37 
ZDU "H5'"  1H5* H 0 1 N N N 4.786  -15.171 45.958 -1.971 -0.654 1.366  "H5'"  ZDU 38 
ZDU "H5''" 2H5* H 0 0 N N N 3.162  -15.354 46.378 -2.683 0.718  2.254  "H5''" ZDU 39 
ZDU "H4'"  H4*  H 0 1 N N N 4.090  -17.265 45.116 -0.644 0.753  3.736  "H4'"  ZDU 40 
ZDU "H1'"  H1*  H 0 1 N N N 2.569  -18.265 42.735 2.163  -0.604 2.054  "H1'"  ZDU 41 
ZDU "H3'"  H3*  H 0 1 N N N 4.957  -15.238 43.131 -0.722 1.941  1.236  "H3'"  ZDU 42 
ZDU "HO3'" H3T  H 0 0 N Y N 6.100  -17.113 43.937 0.743  3.042  2.146  "HO3'" ZDU 43 
ZDU HOP3   3HOP H 0 0 N N N 0.391  -0.639  0.583  -5.874 -0.475 2.871  HOP3   ZDU 44 
# 
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 
ZDU P     OP1    DOUB N N 1  
ZDU P     OP2    SING N N 2  
ZDU P     "O5'"  SING N N 3  
ZDU P     OP3    SING N N 4  
ZDU OP2   HOP2   SING N N 5  
ZDU "O5'" "C5'"  SING N N 6  
ZDU N1    C6     SING N N 7  
ZDU N1    C2     SING N N 8  
ZDU N1    "C1'"  SING N N 9  
ZDU C6    C5     DOUB N N 10 
ZDU C6    H6     SING N N 11 
ZDU C2    O2     DOUB N N 12 
ZDU C2    N3     SING N N 13 
ZDU N3    C4     SING N N 14 
ZDU N3    HN3    SING N N 15 
ZDU C4    O4     DOUB N N 16 
ZDU C4    C5     SING N N 17 
ZDU C5    C5A    SING N N 18 
ZDU C5A   C5B    SING N N 19 
ZDU C5A   H5A1   SING N N 20 
ZDU C5A   H5A2   SING N N 21 
ZDU C5B   C5G    SING N N 22 
ZDU C5B   H5B1   SING N N 23 
ZDU C5B   H5B2   SING N N 24 
ZDU C5G   N5D    SING N N 25 
ZDU C5G   H5G1   SING N N 26 
ZDU C5G   H5G2   SING N N 27 
ZDU N5D   H5D1   SING N N 28 
ZDU N5D   H5D2   SING N N 29 
ZDU "C2'" "C1'"  SING N N 30 
ZDU "C2'" "C3'"  SING N N 31 
ZDU "C2'" "H2'"  SING N N 32 
ZDU "C2'" "H2''" SING N N 33 
ZDU "C5'" "C4'"  SING N N 34 
ZDU "C5'" "H5'"  SING N N 35 
ZDU "C5'" "H5''" SING N N 36 
ZDU "C4'" "O4'"  SING N N 37 
ZDU "C4'" "C3'"  SING N N 38 
ZDU "C4'" "H4'"  SING N N 39 
ZDU "O4'" "C1'"  SING N N 40 
ZDU "C1'" "H1'"  SING N N 41 
ZDU "C3'" "O3'"  SING N N 42 
ZDU "C3'" "H3'"  SING N N 43 
ZDU "O3'" "HO3'" SING N N 44 
ZDU OP3   HOP3   SING N N 45 
# 
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 
ZDU SMILES           ACDLabs              10.04 "O=C1NC(=O)N(C=C1CCCN)C2OC(C(O)C2)COP(=O)(O)O"                                                                                                                            
ZDU InChI            InChI                1.02b "InChI=1/C12H20N3O8P/c13-3-1-2-7-5-15(12(18)14-11(7)17)10-4-8(16)9(23-10)6-22-24(19,20)21/h5,8-10,16H,1-4,6,13H2,(H,14,17,18)(H2,19,20,21)/t8-,9+,10+/m0/s1/f/h14,19-20H" 
ZDU InChIKey         InChI                1.02b DPQBGKUKUKNQCZ-VULCGYEUDP                                                                                                                                                 
ZDU SMILES_CANONICAL CACTVS               3.341 "NCCCC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O"                                                                                                             
ZDU SMILES           CACTVS               3.341 "NCCCC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O"                                                                                                                 
ZDU SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "C1[C@@H]([C@H](O[C@H]1N2C=C(C(=O)NC2=O)CCCN)COP(=O)(O)O)O"                                                                                                               
ZDU SMILES           "OpenEye OEToolkits" 1.5.0 "C1C(C(OC1N2C=C(C(=O)NC2=O)CCCN)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 
ZDU "SYSTEMATIC NAME" ACDLabs              10.04 
;5-(3-aminopropyl)-2'-deoxyuridine 5'-(dihydrogen phosphate)
;
ZDU "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-5-[5-(3-aminopropyl)-2,4-dioxo-pyrimidin-1-yl]-3-hydroxy-oxolan-2-yl]methyl dihydrogen phosphate" 
# 
