data_8DT
# 
_chem_comp.id                                    8DT 
_chem_comp.name                                  
; 5-(3-(acetamide-N-yl)-1-propen-1-yl)-2'-deoxyuridine
;
_chem_comp.type                                  "DNA linking" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C14 H20 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                     2016-09-12 
_chem_comp.pdbx_modified_date                    2016-09-16 
_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                        405.297 
_chem_comp.one_letter_code                       U 
_chem_comp.three_letter_code                     8DT 
_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        5LUY 
_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 
8DT OP1   O1  O 0 1 N N N 63.943 -41.715 24.822 -6.906 1.375  0.041  OP1   8DT 1  
8DT P     P1  P 0 1 N N N 64.098 -41.211 26.238 -5.571 2.011  -0.016 P     8DT 2  
8DT OP2   O2  O 0 1 N N N 65.407 -41.748 26.809 -5.123 2.450  1.467  OP2   8DT 3  
8DT "O5'" O3  O 0 1 N N N 64.582 -39.689 25.895 -4.503 0.965  -0.612 "O5'" 8DT 4  
8DT "C5'" C1  C 0 1 N N N 63.650 -38.895 25.149 -4.292 -0.334 -0.055 "C5'" 8DT 5  
8DT "C4'" C2  C 0 1 N N R 64.211 -37.632 24.578 -3.213 -1.064 -0.858 "C4'" 8DT 6  
8DT "C3'" C3  C 0 1 N N S 65.563 -37.707 23.956 -2.972 -2.483 -0.284 "C3'" 8DT 7  
8DT "O3'" O4  O 0 1 N N N 65.696 -36.741 22.898 -3.889 -3.424 -0.847 "O3'" 8DT 8  
8DT "C2'" C4  C 0 1 N N N 66.485 -37.223 25.058 -1.524 -2.778 -0.746 "C2'" 8DT 9  
8DT "O4'" O5  O 0 1 N N N 64.302 -36.663 25.643 -1.934 -0.414 -0.700 "O4'" 8DT 10 
8DT "C1'" C5  C 0 1 N N R 65.619 -36.170 25.758 -0.926 -1.386 -1.027 "C1'" 8DT 11 
8DT N1    N1  N 0 1 N N N 65.922 -35.968 27.158 0.259  -1.175 -0.193 N1    8DT 12 
8DT C6    C6  C 0 1 N N N 65.694 -36.960 28.024 1.480  -1.039 -0.788 C6    8DT 13 
8DT C2    C7  C 0 1 N N N 66.348 -34.745 27.596 0.121  -1.114 1.141  C2    8DT 14 
8DT O2    O6  O 0 1 N N N 66.473 -33.851 26.738 -0.987 -1.237 1.627  O2    8DT 15 
8DT N3    N2  N 0 1 N N N 66.593 -34.525 28.929 1.173  -0.922 1.957  N3    8DT 16 
8DT C4    C8  C 0 1 N N N 66.407 -35.558 29.808 2.414  -0.783 1.446  C4    8DT 17 
8DT O4    O7  O 0 1 N N N 66.617 -35.374 31.035 3.371  -0.610 2.178  O4    8DT 18 
8DT C5    C9  C 0 1 N N N 65.968 -36.790 29.373 2.587  -0.842 -0.013 C5    8DT 19 
8DT C7    C10 C 0 1 N N N 65.719 -37.973 30.242 3.923  -0.692 -0.625 C7    8DT 20 
8DT C1    C11 C 0 1 N N N 65.838 -37.962 31.568 4.969  -0.390 0.133  C1    8DT 21 
8DT C3    C12 C 0 1 N N N 65.515 -39.153 32.442 6.309  -0.125 -0.504 C3    8DT 22 
8DT N9    N3  N 0 1 N N N 65.863 -38.634 33.761 6.801  1.187  -0.077 N9    8DT 23 
8DT C32   C13 C 0 1 N N N 65.022 -38.224 34.734 7.990  1.639  -0.523 C32   8DT 24 
8DT O34   O8  O 0 1 N N N 63.772 -38.432 34.695 8.652  0.960  -1.279 O34   8DT 25 
8DT C33   C14 C 0 1 N N N 65.778 -37.467 35.847 8.496  2.989  -0.084 C33   8DT 26 
8DT H2    H2  H 0 1 N N N 65.843 -42.282 26.155 -4.255 2.875  1.506  H2    8DT 27 
8DT H3    H3  H 0 1 N N N 62.818 -38.627 25.817 -3.969 -0.236 0.982  H3    8DT 28 
8DT H4    H4  H 0 1 N N N 63.270 -39.506 24.317 -5.221 -0.902 -0.094 H4    8DT 29 
8DT H5    H5  H 0 1 N N N 63.507 -37.258 23.820 -3.490 -1.116 -1.911 H5    8DT 30 
8DT H6    H6  H 0 1 N N N 65.814 -38.729 23.636 -3.040 -2.479 0.804  H6    8DT 31 
8DT H7    H7  H 0 1 N N N 66.564 -36.806 22.516 -3.777 -4.327 -0.518 H7    8DT 32 
8DT H8    H8  H 0 1 N N N 66.752 -38.041 25.744 -0.966 -3.280 0.044  H8    8DT 33 
8DT H9    H9  H 0 1 N N N 67.402 -36.776 24.645 -1.529 -3.382 -1.654 H9    8DT 34 
8DT H10   H10 H 0 1 N N N 65.718 -35.218 25.216 -0.660 -1.303 -2.081 H10   8DT 35 
8DT H11   H11 H 0 1 N N N 65.294 -37.899 27.671 1.569  -1.087 -1.863 H11   8DT 36 
8DT H12   H12 H 0 1 N N N 66.901 -33.630 29.251 1.039  -0.883 2.916  H12   8DT 37 
8DT H13   H13 H 0 1 N N N 65.424 -38.897 29.767 4.048  -0.827 -1.689 H13   8DT 38 
8DT H14   H14 H 0 1 N N N 66.183 -37.056 32.044 4.861  -0.335 1.206  H14   8DT 39 
8DT H15   H15 H 0 1 N N N 64.450 -39.421 32.382 7.016  -0.896 -0.197 H15   8DT 40 
8DT H16   H16 H 0 1 N N N 66.129 -40.027 32.177 6.205  -0.138 -1.589 H16   8DT 41 
8DT H17   H17 H 0 1 N N N 66.840 -38.575 33.968 6.272  1.731  0.528  H17   8DT 42 
8DT H18   H18 H 0 1 N N N 65.063 -37.130 36.612 8.600  3.002  1.001  H18   8DT 43 
8DT H19   H19 H 0 1 N N N 66.519 -38.137 36.308 9.465  3.181  -0.545 H19   8DT 44 
8DT H20   H20 H 0 1 N N N 66.291 -36.595 35.414 7.789  3.760  -0.391 H20   8DT 45 
8DT OP3   OP3 O 0 1 N Y N 63.019 -41.101 27.334 -5.636 3.311  -0.964 OP3   8DT 46 
8DT H1    H1  H 0 1 N N N 62.187 -41.408 26.992 -6.261 3.986  -0.664 H1    8DT 47 
# 
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 
8DT "O3'" "C3'" SING N N 1  
8DT "C3'" "C4'" SING N N 2  
8DT "C3'" "C2'" SING N N 3  
8DT "C4'" "C5'" SING N N 4  
8DT "C4'" "O4'" SING N N 5  
8DT OP1   P     DOUB N N 6  
8DT "C2'" "C1'" SING N N 7  
8DT "C5'" "O5'" SING N N 8  
8DT "O4'" "C1'" SING N N 9  
8DT "C1'" N1    SING N N 10 
8DT "O5'" P     SING N N 11 
8DT P     OP2   SING N N 12 
8DT O2    C2    DOUB N N 13 
8DT N1    C2    SING N N 14 
8DT N1    C6    SING N N 15 
8DT C2    N3    SING N N 16 
8DT C6    C5    DOUB N N 17 
8DT N3    C4    SING N N 18 
8DT C5    C4    SING N N 19 
8DT C5    C7    SING N N 20 
8DT C4    O4    DOUB N N 21 
8DT C7    C1    DOUB N E 22 
8DT C1    C3    SING N N 23 
8DT C3    N9    SING N N 24 
8DT N9    C32   SING N N 25 
8DT O34   C32   DOUB N N 26 
8DT C32   C33   SING N N 27 
8DT OP2   H2    SING N N 28 
8DT "C5'" H3    SING N N 29 
8DT "C5'" H4    SING N N 30 
8DT "C4'" H5    SING N N 31 
8DT "C3'" H6    SING N N 32 
8DT "O3'" H7    SING N N 33 
8DT "C2'" H8    SING N N 34 
8DT "C2'" H9    SING N N 35 
8DT "C1'" H10   SING N N 36 
8DT C6    H11   SING N N 37 
8DT N3    H12   SING N N 38 
8DT C7    H13   SING N N 39 
8DT C1    H14   SING N N 40 
8DT C3    H15   SING N N 41 
8DT C3    H16   SING N N 42 
8DT N9    H17   SING N N 43 
8DT C33   H18   SING N N 44 
8DT C33   H19   SING N N 45 
8DT C33   H20   SING N N 46 
8DT P     OP3   SING N N 47 
8DT OP3   H1    SING N N 48 
# 
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 
8DT InChI            InChI                1.03  "InChI=1S/C14H20N3O9P/c1-8(18)15-4-2-3-9-6-17(14(21)16-13(9)20)12-5-10(19)11(26-12)7-25-27(22,23)24/h2-3,6,10-12,19H,4-5,7H2,1H3,(H,15,18)(H,16,20,21)(H2,22,23,24)/b3-2+/t10-,11+,12+/m0/s1" 
8DT InChIKey         InChI                1.03  JBKMBEZUJCTZND-FBUKTIRESA-N                                                                                                                                                                   
8DT SMILES_CANONICAL CACTVS               3.385 "CC(=O)NC/C=C/C1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O"                                                                                                                        
8DT SMILES           CACTVS               3.385 "CC(=O)NCC=CC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O"                                                                                                                              
8DT SMILES_CANONICAL "OpenEye OEToolkits" 2.0.5 "CC(=O)NC/C=C/C1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O"                                                                                                                          
8DT SMILES           "OpenEye OEToolkits" 2.0.5 "CC(=O)NCC=CC1=CN(C(=O)NC1=O)C2CC(C(O2)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 
8DT "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.5 "[(2~{R},3~{S},5~{R})-5-[5-[(~{E})-3-acetamidoprop-1-enyl]-2,4-bis(oxidanylidene)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 
8DT "Create component"   2016-09-12 EBI  
8DT "Other modification" 2016-09-13 EBI  
8DT "Initial release"    2016-09-21 RCSB 
# 
