data_SDE
# 
_chem_comp.id                                    SDE 
_chem_comp.name                                  "(S,S)-N6,N6-(2,3-dihydroxy-1,4-butadiyl)-2'-deoxyadenosine-5'-monophosphate" 
_chem_comp.type                                  "DNA LINKING" 
_chem_comp.pdbx_type                             ATOMN 
_chem_comp.formula                               "C14 H22 N5 O8 P" 
_chem_comp.mon_nstd_parent_comp_id               DA 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2014-01-07 
_chem_comp.pdbx_modified_date                    2014-05-23 
_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                        419.327 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     SDE 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   Y 
_chem_comp.pdbx_ideal_coordinates_details        Corina 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        2MHZ 
_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 
SDE P      P      P 0 1 N N N 3.988  -7.952 17.163 5.996  -1.769 -0.375 P      SDE 1  
SDE O1P    O1P    O 0 1 N N N 4.613  -8.781 18.225 7.206  -0.636 -0.831 O1P    SDE 2  
SDE O2P    O2P    O 0 1 N N N 4.404  -8.158 15.754 6.625  -1.796 1.226  O2P    SDE 3  
SDE "O5'"  "O5'"  O 0 1 N N N 2.374  -8.095 17.247 4.774  -0.635 -0.799 "O5'"  SDE 4  
SDE "C5'"  "C5'"  C 0 1 N N N 1.681  -8.175 18.487 4.378  0.221  0.274  "C5'"  SDE 5  
SDE "C4'"  "C4'"  C 0 1 N N R 0.181  -7.843 18.382 3.335  1.221  -0.230 "C4'"  SDE 6  
SDE "O4'"  "O4'"  O 0 1 N N N -0.012 -6.431 18.394 2.113  0.542  -0.592 "O4'"  SDE 7  
SDE "C1'"  "C1'"  C 0 1 N N R -0.477 -5.991 17.126 1.062  1.523  -0.558 "C1'"  SDE 8  
SDE N9     N9     N 0 1 Y N N 0.409  -4.897 16.664 -0.187 0.899  -0.114 N9     SDE 9  
SDE C8     C8     C 0 1 Y N N 1.673  -4.974 16.127 -0.301 -0.232 0.637  C8     SDE 10 
SDE N7     N7     N 0 1 Y N N 2.250  -3.819 15.930 -1.556 -0.499 0.852  N7     SDE 11 
SDE C5     C5     C 0 1 Y N N 1.280  -2.907 16.349 -2.326 0.442  0.254  C5     SDE 12 
SDE C6     C6     C 0 1 Y N N 1.234  -1.498 16.436 -3.709 0.667  0.149  C6     SDE 13 
SDE N6     N6     N 0 1 N N N 2.271  -0.688 16.162 -4.614 -0.193 0.746  N6     SDE 14 
SDE CA     CA     C 0 1 N N N 2.899  0.177  17.160 -6.000 0.245  0.501  CA     SDE 15 
SDE CB     CB     C 0 1 N N S 4.155  0.657  16.429 -6.736 -0.929 -0.178 CB     SDE 16 
SDE OB     OB     O 0 1 N N N 4.562  1.923  16.938 -8.071 -1.044 0.321  OB     SDE 17 
SDE CG     CG     C 0 1 N N S 3.689  0.733  14.966 -5.888 -2.160 0.235  CG     SDE 18 
SDE OG     OG     O 0 1 N N N 4.804  0.778  14.080 -6.012 -3.213 -0.723 OG     SDE 19 
SDE CD     CD     C 0 1 N N N 2.881  -0.560 14.832 -4.456 -1.569 0.230  CD     SDE 20 
SDE N1     N1     N 0 1 Y N N 0.119  -0.901 16.901 -4.128 1.726  -0.537 N1     SDE 21 
SDE C2     C2     C 0 1 Y N N -0.916 -1.661 17.248 -3.272 2.553  -1.109 C2     SDE 22 
SDE N3     N3     N 0 1 Y N N -1.009 -2.984 17.216 -1.968 2.381  -1.037 N3     SDE 23 
SDE C4     C4     C 0 1 Y N N 0.143  -3.553 16.769 -1.456 1.351  -0.373 C4     SDE 24 
SDE "C3'"  "C3'"  C 0 1 N N S -0.519 -8.409 17.135 2.895  2.173  0.911  "C3'"  SDE 25 
SDE "C2'"  "C2'"  C 0 1 N N N -0.517 -7.206 16.192 1.489  2.617  0.440  "C2'"  SDE 26 
SDE "O3'"  "O3'"  O 0 1 N N N -1.813 -8.869 17.501 3.778  3.293  1.009  "O3'"  SDE 27 
SDE H1     H1     H 0 1 N N N 4.251  -8.540 19.070 7.765  -0.930 -1.563 H1     SDE 28 
SDE H3     H3     H 0 1 N N N 5.348  -8.077 15.687 6.147  -2.385 1.827  H3     SDE 29 
SDE "H5'2" "H5'2" H 0 0 N N N 1.783  -9.199 18.876 3.948  -0.378 1.077  "H5'2" SDE 30 
SDE "H5'1" "H5'1" H 0 0 N N N 2.145  -7.467 19.190 5.247  0.761  0.648  "H5'1" SDE 31 
SDE "H4'"  "H4'"  H 0 1 N N N -0.314 -8.277 19.263 3.725  1.786  -1.077 "H4'"  SDE 32 
SDE "H1'"  "H1'"  H 0 1 N N N -1.501 -5.600 17.223 0.928  1.957  -1.549 "H1'"  SDE 33 
SDE H8     H8     H 0 1 N N N 2.150  -5.913 15.888 0.529  -0.821 1.001  H8     SDE 34 
SDE HA2    HA2    H 0 1 N N N 2.245  1.021  17.425 -6.484 0.490  1.446  HA2    SDE 35 
SDE HA1    HA1    H 0 1 N N N 3.157  -0.386 18.069 -6.003 1.116  -0.154 HA1    SDE 36 
SDE HB     HB     H 0 1 N N N 4.955  -0.092 16.527 -6.741 -0.807 -1.261 HB     SDE 37 
SDE HOB    HOB    H 0 1 N N N 4.840  1.827  17.841 -8.621 -0.267 0.155  HOB    SDE 38 
SDE HG     HG     H 0 1 N N N 3.030  1.603  14.829 -6.163 -2.507 1.231  HG     SDE 39 
SDE HOG    HOG    H 0 1 N N N 5.272  1.596  14.200 -5.499 -4.003 -0.507 HOG    SDE 40 
SDE HD1    HD1    H 0 1 N N N 2.114  -0.471 14.049 -4.057 -1.551 -0.784 HD1    SDE 41 
SDE HD2    HD2    H 0 1 N N N 3.534  -1.417 14.609 -3.804 -2.148 0.885  HD2    SDE 42 
SDE H2     H2     H 0 1 N N N -1.791 -1.135 17.600 -3.655 3.400  -1.657 H2     SDE 43 
SDE "H3'"  "H3'"  H 0 1 N N N 0.088  -9.220 16.706 2.838  1.641  1.861  "H3'"  SDE 44 
SDE "H2'2" "H2'2" H 0 0 N N N -1.428 -7.193 15.575 1.541  3.586  -0.056 "H2'2" SDE 45 
SDE "H2'1" "H2'1" H 0 0 N N N 0.368  -7.225 15.539 0.799  2.655  1.282  "H2'1" SDE 46 
SDE H4     H4     H 0 1 N N N -1.731 -9.614 18.085 3.544  3.918  1.709  H4     SDE 47 
SDE O3P    O3P    O 0 1 N Y N ?      ?      ?      4.785  -2.903 0.082  O3P    SDE 48 
SDE H5     H5     H 0 1 N N N ?      ?      ?      6.502  -2.715 -1.380 H5     SDE 49 
SDE H6     H6     H 0 1 N N N ?      ?      ?      5.136  -3.744 0.405  H6     SDE 50 
# 
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 
SDE OG    CG     SING N N 1  
SDE CD    CG     SING N N 2  
SDE CD    N6     SING N N 3  
SDE CG    CB     SING N N 4  
SDE O2P   P      SING N N 5  
SDE N7    C8     DOUB Y N 6  
SDE N7    C5     SING Y N 7  
SDE C8    N9     SING Y N 8  
SDE N6    C6     SING N N 9  
SDE N6    CA     SING N N 10 
SDE "C2'" "C1'"  SING N N 11 
SDE "C2'" "C3'"  SING N N 12 
SDE C5    C6     DOUB Y N 13 
SDE C5    C4     SING Y N 14 
SDE CB    OB     SING N N 15 
SDE CB    CA     SING N N 16 
SDE C6    N1     SING Y N 17 
SDE N9    C4     SING Y N 18 
SDE N9    "C1'"  SING N N 19 
SDE C4    N3     DOUB Y N 20 
SDE N1    C2     DOUB Y N 21 
SDE "C1'" "O4'"  SING N N 22 
SDE "C3'" "O3'"  SING N N 23 
SDE "C3'" "C4'"  SING N N 24 
SDE P     "O5'"  SING N N 25 
SDE P     O1P    SING N N 26 
SDE N3    C2     SING Y N 27 
SDE "O5'" "C5'"  SING N N 28 
SDE "C4'" "O4'"  SING N N 29 
SDE "C4'" "C5'"  SING N N 30 
SDE O1P   H1     SING N N 31 
SDE O2P   H3     SING N N 32 
SDE "C5'" "H5'2" SING N N 33 
SDE "C5'" "H5'1" SING N N 34 
SDE "C4'" "H4'"  SING N N 35 
SDE "C1'" "H1'"  SING N N 36 
SDE C8    H8     SING N N 37 
SDE CA    HA2    SING N N 38 
SDE CA    HA1    SING N N 39 
SDE CB    HB     SING N N 40 
SDE OB    HOB    SING N N 41 
SDE CG    HG     SING N N 42 
SDE OG    HOG    SING N N 43 
SDE CD    HD1    SING N N 44 
SDE CD    HD2    SING N N 45 
SDE C2    H2     SING N N 46 
SDE "C3'" "H3'"  SING N N 47 
SDE "C2'" "H2'2" SING N N 48 
SDE "C2'" "H2'1" SING N N 49 
SDE "O3'" H4     SING N N 50 
SDE P     O3P    SING N N 51 
SDE P     H5     SING N N 52 
SDE O3P   H6     SING N N 53 
# 
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 
SDE SMILES           ACDLabs              12.01 "n3c1c(ncnc1N2CC(O)C(O)C2)n(c3)C4OC(C(O)C4)COP(O)(O)O"                                                                                                      
SDE InChI            InChI                1.03  "InChI=1S/C14H22N5O8P/c20-7-1-11(27-10(7)4-26-28(23,24)25)19-6-17-12-13(15-5-16-14(12)19)18-2-8(21)9(22)3-18/h5-11,20-25,28H,1-4H2/t7-,8-,9-,10+,11+/m0/s1" 
SDE InChIKey         InChI                1.03  AFIPVZHEZSDVQA-LADJIXMOSA-N                                                                                                                                 
SDE SMILES_CANONICAL CACTVS               3.385 "O[C@H]1C[C@@H](O[C@@H]1CO[PH](O)(O)O)n2cnc3c(ncnc23)N4C[C@H](O)[C@@H](O)C4"                                                                                
SDE SMILES           CACTVS               3.385 "O[CH]1C[CH](O[CH]1CO[PH](O)(O)O)n2cnc3c(ncnc23)N4C[CH](O)[CH](O)C4"                                                                                        
SDE SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "c1nc2c(c(n1)N3C[C@@H]([C@H](C3)O)O)ncn2[C@H]4C[C@@H]([C@H](O4)COP(O)(O)O)O"                                                                                
SDE SMILES           "OpenEye OEToolkits" 1.7.6 "c1nc2c(c(n1)N3CC(C(C3)O)O)ncn2C4CC(C(O4)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 
SDE "SYSTEMATIC NAME" ACDLabs              12.01 "(3S,4S)-1-{9-[(2R,4S,5R)-4-hydroxy-5-{[(trihydroxy-lambda~5~-phosphanyl)oxy]methyl}tetrahydrofuran-2-yl]-9H-purin-6-yl}pyrrolidine-3,4-diol (non-preferred name)" 
SDE "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(3S,4S)-1-[9-[(2R,4S,5R)-4-oxidanyl-5-[[tris(oxidanyl)-$l^{5}-phosphanyl]oxymethyl]oxolan-2-yl]purin-6-yl]pyrrolidine-3,4-diol"                                   
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
SDE "Create component" 2014-01-07 RCSB 
SDE "Initial release"  2014-05-28 RCSB 
# 
