data_SOS
# 
_chem_comp.id                                    SOS 
_chem_comp.name                                  "[(1R,2S,4R)-4-({2-AMINO-5-[BENZYL(FORMYL)AMINO]-6-OXO-1,6-DIHYDROPYRIMIDIN-4-YL}AMINO)-2-HYDROXYCYCLOPENTYL]METHYL DIHYDROGEN PHOSPHATE" 
_chem_comp.type                                  "DNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C18 H24 N5 O7 P" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2007-01-23 
_chem_comp.pdbx_modified_date                    2011-06-04 
_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                        453.386 
_chem_comp.one_letter_code                       N 
_chem_comp.three_letter_code                     SOS 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   N 
_chem_comp.pdbx_ideal_coordinates_details        "OpenEye OEToolkits" 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        ? 
_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 
SOS OP3    O3P  O 0 1 N Y N -4.738 21.868 46.925 3.912  4.663  -3.442 OP3    SOS 1  
SOS C15    C15  C 0 1 Y N N -6.141 16.440 45.164 0.691  -1.131 -0.937 C15    SOS 2  
SOS C14    C14  C 0 1 Y N N -6.550 17.729 45.568 1.783  -0.732 -1.707 C14    SOS 3  
SOS C13    C13  C 0 1 Y N N -5.660 18.799 45.449 3.076  -0.845 -1.197 C13    SOS 4  
SOS C12    C12  C 0 1 Y N N -4.363 18.604 44.949 3.277  -1.358 0.085  C12    SOS 5  
SOS C11    C11  C 0 1 Y N N -3.969 17.321 44.529 2.185  -1.757 0.856  C11    SOS 6  
SOS C10    C10  C 0 1 Y N N -4.866 16.258 44.634 0.900  -1.641 0.339  C10    SOS 7  
SOS C9     C9   C 0 1 N N N -4.450 14.863 44.174 -0.275 -2.071 1.169  C9     SOS 8  
SOS N7     N7   N 0 1 N N N -3.799 14.097 45.248 -0.796 -0.979 1.984  N7     SOS 9  
SOS C8     C8   C 0 1 N N N -2.531 13.678 45.004 -0.305 -0.764 3.268  C8     SOS 10 
SOS O8     O8   O 0 1 N N N -1.841 13.019 45.786 0.563  -1.403 3.855  O8     SOS 11 
SOS C5     C5   C 0 1 N N N -4.370 13.782 46.440 -1.773 -0.163 1.484  C5     SOS 12 
SOS C6     C6   C 0 1 N N N -5.305 12.745 46.529 -3.048 -0.828 1.104  C6     SOS 13 
SOS O6     O6   O 0 1 N N N -5.638 12.158 45.503 -3.218 -2.037 1.230  O6     SOS 14 
SOS N1     N1   N 0 1 N N N -5.879 12.387 47.758 -3.996 0.036  0.606  N1     SOS 15 
SOS C2     C2   C 0 1 N N N -5.517 13.026 48.910 -3.786 1.396  0.473  C2     SOS 16 
SOS N2     N2   N 0 1 N N N -6.056 12.718 50.111 -4.836 2.112  -0.040 N2     SOS 17 
SOS N3     N3   N 0 1 N N N -4.612 14.015 48.801 -2.661 1.954  0.813  N3     SOS 18 
SOS C4     C4   C 0 1 N N N -4.034 14.418 47.642 -1.633 1.176  1.327  C4     SOS 19 
SOS N9     N9   N 0 1 N N N -3.129 15.427 47.664 -0.496 1.770  1.666  N9     SOS 20 
SOS "C1'"  C1*  C 0 1 N N R -3.010 16.350 48.815 -0.289 3.191  1.521  "C1'"  SOS 21 
SOS "C6'"  C6*  C 0 1 N N N -4.397 17.017 49.191 0.092  3.545  0.075  "C6'"  SOS 22 
SOS "C2'"  C2*  C 0 1 N N N -2.070 17.567 48.537 0.876  3.672  2.386  "C2'"  SOS 23 
SOS "C3'"  C3*  C 0 1 N N S -2.566 18.220 49.755 2.076  3.601  1.451  "C3'"  SOS 24 
SOS "O3'"  O3*  O 0 1 N N N -1.964 17.860 50.990 3.142  4.408  1.914  "O3'"  SOS 25 
SOS "C4'"  C4*  C 0 1 N N R -4.048 18.455 49.686 1.505  4.141  0.142  "C4'"  SOS 26 
SOS "C5'"  C5*  C 0 1 N N N -4.558 19.437 48.625 2.359  3.795  -1.069 "C5'"  SOS 27 
SOS "O5'"  O5*  O 0 1 N N N -4.149 20.738 48.955 1.720  4.291  -2.233 "O5'"  SOS 28 
SOS P      P    P 0 1 N N N -4.930 22.068 48.552 2.432  4.051  -3.667 P      SOS 29 
SOS OP2    O2P  O 0 1 N N N -4.163 23.265 48.726 2.691  2.455  -3.704 OP2    SOS 30 
SOS OP1    O1P  O 0 1 N N N -6.399 21.971 48.536 1.688  4.608  -4.845 OP1    SOS 31 
SOS H15    H15  H 0 1 N N N -6.812 15.600 45.265 -0.313 -1.039 -1.343 H15    SOS 32 
SOS H14    H14  H 0 1 N N N -7.542 17.887 45.965 1.626  -0.333 -2.705 H14    SOS 33 
SOS H13    H13  H 0 1 N N N -5.974 19.789 45.745 3.926  -0.534 -1.797 H13    SOS 34 
SOS H12    H12  H 0 1 N N N -3.673 19.433 44.887 4.284  -1.446 0.482  H12    SOS 35 
SOS H11    H11  H 0 1 N N N -2.979 17.160 44.128 2.352  -2.155 1.853  H11    SOS 36 
SOS H91    1H9  H 0 1 N N N -5.349 14.318 43.849 -1.088 -2.432 0.529  H91    SOS 37 
SOS H92    2H9  H 0 1 N N N -3.728 14.977 43.352 -0.002 -2.891 1.842  H92    SOS 38 
SOS H8     H8   H 0 1 N N N -2.093 13.942 44.053 -0.793 0.094  3.760  H8     SOS 39 
SOS HN1    HN1  H 0 1 N N N -6.561 11.656 47.791 -4.894 -0.343 0.324  HN1    SOS 40 
SOS HN21   1HN2 H 0 0 N N N -6.713 11.973 49.999 -4.646 2.991  -0.463 HN21   SOS 41 
SOS HN22   2HN2 H 0 0 N N N -5.832 13.166 50.977 -5.749 1.726  0.031  HN22   SOS 42 
SOS HN9    HN9  H 0 1 N N N -2.235 14.986 47.582 0.253  1.191  2.042  HN9    SOS 43 
SOS "H1'"  H1*  H 0 1 N N N -2.615 15.708 49.616 -1.214 3.698  1.814  "H1'"  SOS 44 
SOS "H6'1" 1H6* H 0 0 N N N -5.062 17.056 48.316 -0.602 4.285  -0.340 "H6'1" SOS 45 
SOS "H6'2" 2H6* H 0 0 N N N -4.929 16.440 49.962 0.057  2.666  -0.580 "H6'2" SOS 46 
SOS "H2'"  1H2* H 0 1 N N N -0.991 17.358 48.494 0.712  4.708  2.710  "H2'"  SOS 47 
SOS "H2''" 2H2* H 0 0 N N N -2.112 18.091 47.571 1.029  3.073  3.290  "H2''" SOS 48 
SOS "H3'"  H3*  H 0 1 N N N -2.144 19.236 49.766 2.432  2.570  1.343  "H3'"  SOS 49 
SOS "HO3'" H3T  H 0 0 N Y N -1.025 17.780 50.873 3.059  4.465  2.881  "HO3'" SOS 50 
SOS "H4'"  H4*  H 0 1 N N N -4.462 18.876 50.614 1.438  5.235  0.194  "H4'"  SOS 51 
SOS "H5'"  1H5* H 0 1 N N N -5.657 19.397 48.587 2.469  2.712  -1.155 "H5'"  SOS 52 
SOS "H5''" 2H5* H 0 0 N N N -4.146 19.162 47.643 3.345  4.255  -0.978 "H5''" SOS 53 
SOS HOP2   2HOP H 0 0 N N N -3.993 23.401 49.651 3.060  2.054  -4.520 HOP2   SOS 54 
SOS HOP3   3HOP H 0 0 N N N -4.701 22.718 46.503 4.523  4.721  -4.207 HOP3   SOS 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 
SOS OP3   P      SING N N 1  
SOS OP3   HOP3   SING N N 2  
SOS C15   C10    SING Y N 3  
SOS C15   C14    DOUB Y N 4  
SOS C15   H15    SING N N 5  
SOS C14   C13    SING Y N 6  
SOS C14   H14    SING N N 7  
SOS C13   C12    DOUB Y N 8  
SOS C13   H13    SING N N 9  
SOS C12   C11    SING Y N 10 
SOS C12   H12    SING N N 11 
SOS C11   C10    DOUB Y N 12 
SOS C11   H11    SING N N 13 
SOS C10   C9     SING N N 14 
SOS C9    N7     SING N N 15 
SOS C9    H91    SING N N 16 
SOS C9    H92    SING N N 17 
SOS N7    C8     SING N N 18 
SOS N7    C5     SING N N 19 
SOS C8    O8     DOUB N N 20 
SOS C8    H8     SING N N 21 
SOS C5    C6     SING N N 22 
SOS C5    C4     DOUB N N 23 
SOS C6    O6     DOUB N N 24 
SOS C6    N1     SING N N 25 
SOS N1    C2     SING N N 26 
SOS N1    HN1    SING N N 27 
SOS C2    N3     DOUB N N 28 
SOS C2    N2     SING N N 29 
SOS N2    HN21   SING N N 30 
SOS N2    HN22   SING N N 31 
SOS N3    C4     SING N N 32 
SOS C4    N9     SING N N 33 
SOS N9    "C1'"  SING N N 34 
SOS N9    HN9    SING N N 35 
SOS "C1'" "C2'"  SING N N 36 
SOS "C1'" "C6'"  SING N N 37 
SOS "C1'" "H1'"  SING N N 38 
SOS "C6'" "C4'"  SING N N 39 
SOS "C6'" "H6'1" SING N N 40 
SOS "C6'" "H6'2" SING N N 41 
SOS "C2'" "C3'"  SING N N 42 
SOS "C2'" "H2'"  SING N N 43 
SOS "C2'" "H2''" SING N N 44 
SOS "C3'" "C4'"  SING N N 45 
SOS "C3'" "O3'"  SING N N 46 
SOS "C3'" "H3'"  SING N N 47 
SOS "O3'" "HO3'" SING N N 48 
SOS "C4'" "C5'"  SING N N 49 
SOS "C4'" "H4'"  SING N N 50 
SOS "C5'" "O5'"  SING N N 51 
SOS "C5'" "H5'"  SING N N 52 
SOS "C5'" "H5''" SING N N 53 
SOS "O5'" P      SING N N 54 
SOS P     OP1    DOUB N N 55 
SOS P     OP2    SING N N 56 
SOS OP2   HOP2   SING N N 57 
# 
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 
SOS SMILES           ACDLabs              10.04 "O=C2C(N(C=O)Cc1ccccc1)=C(N=C(N)N2)NC3CC(COP(=O)(O)O)C(O)C3"                                                                                                                                     
SOS SMILES_CANONICAL CACTVS               3.341 "NC1=NC(=C(N(Cc2ccccc2)C=O)C(=O)N1)N[C@H]3C[C@H](O)[C@@H](CO[P](O)(O)=O)C3"                                                                                                                      
SOS SMILES           CACTVS               3.341 "NC1=NC(=C(N(Cc2ccccc2)C=O)C(=O)N1)N[CH]3C[CH](O)[CH](CO[P](O)(O)=O)C3"                                                                                                                          
SOS SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "c1ccc(cc1)CN(C=O)C2=C(N=C(NC2=O)N)N[C@@H]3C[C@@H]([C@H](C3)O)COP(=O)(O)O"                                                                                                                       
SOS SMILES           "OpenEye OEToolkits" 1.5.0 "c1ccc(cc1)CN(C=O)C2=C(N=C(NC2=O)N)NC3CC(C(C3)O)COP(=O)(O)O"                                                                                                                                     
SOS InChI            InChI                1.03  "InChI=1S/C18H24N5O7P/c19-18-21-16(20-13-6-12(14(25)7-13)9-30-31(27,28)29)15(17(26)22-18)23(10-24)8-11-4-2-1-3-5-11/h1-5,10,12-14,25H,6-9H2,(H2,27,28,29)(H4,19,20,21,22,26)/t12-,13-,14+/m1/s1" 
SOS InChIKey         InChI                1.03  ULUAJGLRYKCHQG-MCIONIFRSA-N                                                                                                                                                                      
# 
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 
SOS "SYSTEMATIC NAME" ACDLabs              10.04 "[(1R,2S,4R)-4-({2-amino-5-[benzyl(formyl)amino]-6-oxo-1,6-dihydropyrimidin-4-yl}amino)-2-hydroxycyclopentyl]methyl dihydrogen phosphate"    
SOS "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[(1R,2S,4R)-4-[[2-amino-5-(methanoyl-(phenylmethyl)amino)-6-oxo-1H-pyrimidin-4-yl]amino]-2-hydroxy-cyclopentyl]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 
SOS "Create component"  2007-01-23 RCSB 
SOS "Modify descriptor" 2011-06-04 RCSB 
# 
