data_PDU
# 
_chem_comp.id                                    PDU 
_chem_comp.name                                  "5(1-PROPYNYL)-2'-DEOXYURIDINE-5-MONOPHOSPHATE" 
_chem_comp.type                                  "DNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C12 H19 N2 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                     1999-07-08 
_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                        350.262 
_chem_comp.one_letter_code                       U 
_chem_comp.three_letter_code                     PDU 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        ? 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        1P3X 
_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 
PDU OP3    O3P  O 0 1 N Y N -0.326 11.391 3.961 2.738  -0.521 -4.968 OP3    PDU 1  
PDU P      P    P 0 1 N N N 1.020  11.691 3.054 1.345  0.126  -4.487 P      PDU 2  
PDU OP1    O1P  O 0 1 N N N 1.721  12.834 3.687 1.573  1.524  -4.057 OP1    PDU 3  
PDU OP2    O2P  O 0 1 N N N 0.582  11.825 1.647 0.294  0.104  -5.706 OP2    PDU 4  
PDU "O5'"  O5*  O 0 1 N N N 2.048  10.406 3.133 0.755  -0.724 -3.254 "O5'"  PDU 5  
PDU "C5'"  C5*  C 0 1 N N N 1.591  9.163  3.678 -0.474 -0.103 -2.874 "C5'"  PDU 6  
PDU "C4'"  C4*  C 0 1 N N R 2.528  8.011  4.010 -1.090 -0.866 -1.700 "C4'"  PDU 7  
PDU "O4'"  O4*  O 0 1 N N N 1.717  6.998  4.676 -0.260 -0.754 -0.523 "O4'"  PDU 8  
PDU "C3'"  C3*  C 0 1 N N S 3.183  7.373  2.808 -2.428 -0.214 -1.267 "C3'"  PDU 9  
PDU "O3'"  O3*  O 0 1 N N N 4.540  6.989  3.080 -3.517 -0.718 -2.043 "O3'"  PDU 10 
PDU "C2'"  C2*  C 0 1 N N N 2.318  6.165  2.681 -2.545 -0.666 0.208  "C2'"  PDU 11 
PDU "C1'"  C1*  C 0 1 N N R 1.906  5.711  4.066 -1.102 -1.028 0.609  "C1'"  PDU 12 
PDU N1     N1   N 0 1 N N N 0.664  4.890  3.874 -0.682 -0.212 1.751  N1     PDU 13 
PDU C2     C2   C 0 1 N N N 0.597  3.545  4.294 -0.666 1.128  1.642  C2     PDU 14 
PDU O2     O2   O 0 1 N N N 1.535  2.975  4.847 -1.001 1.648  0.596  O2     PDU 15 
PDU N3     N3   N 0 1 N N N -0.614 2.875  4.049 -0.286 1.901  2.676  N3     PDU 16 
PDU C4     C4   C 0 1 N N N -1.721 3.433  3.440 0.083  1.340  3.845  C4     PDU 17 
PDU O4     O4   O 0 1 N N N -2.740 2.768  3.262 0.427  2.039  4.781  O4     PDU 18 
PDU C5     C5   C 0 1 N N N -1.557 4.817  3.050 0.075  -0.070 3.971  C5     PDU 19 
PDU C5A    C5A  C 0 1 N N N -2.658 5.457  2.396 0.488  -0.722 5.265  C5A    PDU 20 
PDU C5B    C5B  C 0 1 N N N -3.619 5.948  1.895 1.993  -0.998 5.241  C5B    PDU 21 
PDU C5M    C5M  C 0 1 N N N -4.841 6.513  1.336 2.411  -1.661 6.555  C5M    PDU 22 
PDU C6     C6   C 0 1 N N N -0.405 5.489  3.266 -0.310 -0.821 2.919  C6     PDU 23 
PDU HOP3   3HOP H 0 0 N N N -0.775 10.658 3.555 3.057  0.017  -5.705 HOP3   PDU 24 
PDU HOP2   2HOP H 0 0 N N N 1.356  11.997 1.125 0.174  -0.822 -5.954 HOP2   PDU 25 
PDU "H5'"  1H5* H 0 1 N N N 0.862  8.733  2.987 -1.163 -0.116 -3.718 "H5'"  PDU 26 
PDU "H5''" 2H5* H 0 0 N N N 1.239  9.437  4.670 -0.283 0.928  -2.577 "H5''" PDU 27 
PDU "H4'"  H4*  H 0 1 N N N 3.318  8.305  4.688 -1.241 -1.914 -1.962 "H4'"  PDU 28 
PDU "H3'"  H3*  H 0 1 N N N 2.998  8.026  1.941 -2.372 0.871  -1.338 "H3'"  PDU 29 
PDU "HO3'" H3T  H 0 0 N Y N 4.952  6.587  2.323 -4.325 -0.346 -1.664 "HO3'" PDU 30 
PDU "H2''" 2H2* H 0 0 N N N 2.752  5.310  2.243 -2.920 0.148  0.828  "H2''" PDU 31 
PDU "H2'"  1H2* H 0 1 N N N 1.547  6.514  2.019 -3.194 -1.538 0.290  "H2'"  PDU 32 
PDU "H1'"  H1*  H 0 1 N N N 2.703  5.189  4.621 -1.043 -2.085 0.867  "H1'"  PDU 33 
PDU H3     H3   H 0 1 N N N -0.727 1.897  4.326 -0.280 2.866  2.581  H3     PDU 34 
PDU H5A1   1H5A H 0 0 N N N -2.258 6.463  2.663 -0.051 -1.662 5.386  H5A1   PDU 35 
PDU H5A2   2H5A H 0 0 N N N -2.266 5.155  1.396 0.253  -0.059 6.098  H5A2   PDU 36 
PDU H5B1   1H5B H 0 0 N N N -3.175 6.965  2.000 2.532  -0.059 5.120  H5B1   PDU 37 
PDU H5B2   2H5B H 0 0 N N N -3.340 5.522  0.902 2.227  -1.661 4.408  H5B2   PDU 38 
PDU H71    1H5M H 0 1 N N N -5.204 7.298  2.001 3.483  -1.857 6.537  H71    PDU 39 
PDU H72    2H5M H 0 1 N N N -5.598 5.731  1.286 2.177  -0.997 7.387  H72    PDU 40 
PDU H73    3H5M H 0 1 N N N -4.651 6.911  0.340 1.872  -2.600 6.676  H73    PDU 41 
PDU H6     H6   H 0 1 N N N -0.290 6.533  2.946 -0.326 -1.898 2.998  H6     PDU 42 
# 
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 
PDU OP3   P      SING N N 1  
PDU OP3   HOP3   SING N N 2  
PDU P     OP1    DOUB N N 3  
PDU P     OP2    SING N N 4  
PDU P     "O5'"  SING N N 5  
PDU OP2   HOP2   SING N N 6  
PDU "O5'" "C5'"  SING N N 7  
PDU "C5'" "C4'"  SING N N 8  
PDU "C5'" "H5'"  SING N N 9  
PDU "C5'" "H5''" SING N N 10 
PDU "C4'" "O4'"  SING N N 11 
PDU "C4'" "C3'"  SING N N 12 
PDU "C4'" "H4'"  SING N N 13 
PDU "O4'" "C1'"  SING N N 14 
PDU "C3'" "O3'"  SING N N 15 
PDU "C3'" "C2'"  SING N N 16 
PDU "C3'" "H3'"  SING N N 17 
PDU "O3'" "HO3'" SING N N 18 
PDU "C2'" "C1'"  SING N N 19 
PDU "C2'" "H2''" SING N N 20 
PDU "C2'" "H2'"  SING N N 21 
PDU "C1'" N1     SING N N 22 
PDU "C1'" "H1'"  SING N N 23 
PDU N1    C2     SING N N 24 
PDU N1    C6     SING N N 25 
PDU C2    O2     DOUB N N 26 
PDU C2    N3     SING N N 27 
PDU N3    C4     SING N N 28 
PDU N3    H3     SING N N 29 
PDU C4    O4     DOUB N N 30 
PDU C4    C5     SING N N 31 
PDU C5    C5A    SING N N 32 
PDU C5    C6     DOUB N N 33 
PDU C5A   C5B    SING N N 34 
PDU C5A   H5A1   SING N N 35 
PDU C5A   H5A2   SING N N 36 
PDU C5B   C5M    SING N N 37 
PDU C5B   H5B1   SING N N 38 
PDU C5B   H5B2   SING N N 39 
PDU C5M   H71    SING N N 40 
PDU C5M   H72    SING N N 41 
PDU C5M   H73    SING N N 42 
PDU C6    H6     SING N N 43 
# 
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 
PDU SMILES           ACDLabs              10.04 "O=C1NC(=O)N(C=C1CCC)C2OC(C(O)C2)COP(=O)(O)O"                                                                                                                           
PDU InChI            InChI                1.02b "InChI=1/C12H19N2O8P/c1-2-3-7-5-14(12(17)13-11(7)16)10-4-8(15)9(22-10)6-21-23(18,19)20/h5,8-10,15H,2-4,6H2,1H3,(H,13,16,17)(H2,18,19,20)/t8-,9+,10+/m0/s1/f/h13,18-19H" 
PDU InChIKey         InChI                1.02b MCQFLTGFZQKDHC-BRWMURASDY                                                                                                                                               
PDU SMILES_CANONICAL CACTVS               3.341 "CCCC1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O"                                                                                                            
PDU SMILES           CACTVS               3.341 "CCCC1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O"                                                                                                                
PDU SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CCCC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O"                                                                                                              
PDU SMILES           "OpenEye OEToolkits" 1.5.0 "CCCC1=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 
PDU "SYSTEMATIC NAME" ACDLabs              10.04 
;2'-deoxy-5-propyluridine 5'-(dihydrogen phosphate)
;
PDU "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(2R,3S,5R)-5-(2,4-dioxo-5-propyl-pyrimidin-1-yl)-3-hydroxy-oxolan-2-yl]methyl dihydrogen phosphate" 
# 
