data_Z5A
# 
_chem_comp.id                                    Z5A 
_chem_comp.name                                  "P1-(5'-ADENOSYL)P5-(5'-(3'AZIDO-3'-DEOXYTHYMIDYL))PENTAPHOSPHATE" 
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C20 H24 N10 O22 P5" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    -5 
_chem_comp.pdbx_initial_date                     1999-07-08 
_chem_comp.pdbx_modified_date                    2011-06-07 
_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                        911.327 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     Z5A 
_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        1E9A 
_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 
Z5A N1T    N1T    N 0  1 N N N 13.437 77.844 24.153 10.417 -1.193  -5.663 N1T    Z5A 1  
Z5A C2T    C2T    C 0  1 N N N 13.859 79.128 23.755 11.182 -2.292  -6.115 C2T    Z5A 2  
Z5A O2T    O2T    O 0  1 N N N 14.546 79.867 24.454 11.347 -2.567  -7.306 O2T    Z5A 3  
Z5A N3T    N3T    N 0  1 N N N 13.417 79.508 22.521 11.760 -3.072  -5.107 N3T    Z5A 4  
Z5A C4T    C4T    C 0  1 N N N 12.652 78.695 21.706 11.656 -2.875  -3.738 C4T    Z5A 5  
Z5A O4T    O4T    O 0  1 N N N 12.255 79.114 20.469 12.192 -3.601  -2.905 O4T    Z5A 6  
Z5A C5T    C5T    C 0  1 N N N 12.283 77.349 22.189 10.836 -1.701  -3.337 C5T    Z5A 7  
Z5A C6T    C6T    C 0  1 N N N 12.718 76.946 23.430 10.283 -0.953  -4.299 C6T    Z5A 8  
Z5A C7T    C7T    C 0  1 N N N 11.451 76.450 21.327 10.676 -1.421  -1.877 C7T    Z5A 9  
Z5A "C5'"  "C5'"  C 0  1 N N N 14.814 73.906 26.376 7.775  1.729   -4.858 "C5'"  Z5A 10 
Z5A "O5'"  "O5'"  O 0  1 N N N 13.454 73.467 26.164 8.547  2.622   -4.072 "O5'"  Z5A 11 
Z5A "C4'"  "C4'"  C 0  1 N N S 14.800 75.461 26.462 8.429  1.580   -6.226 "C4'"  Z5A 12 
Z5A "O4'"  "O4'"  O 0  1 N N N 14.661 76.206 25.240 9.739  1.016   -6.033 "O4'"  Z5A 13 
Z5A "C3'"  "C3'"  C 0  1 N N S 13.736 75.955 27.396 7.668  0.625   -7.138 "C3'"  Z5A 14 
Z5A "C2'"  "C2'"  C 0  1 N N N 12.850 76.894 26.518 8.329  -0.705  -6.862 "C2'"  Z5A 15 
Z5A "C1'"  "C1'"  C 0  1 N N R 13.876 77.348 25.455 9.767  -0.307  -6.584 "C1'"  Z5A 16 
Z5A NA3    NA3    N 0  1 N N N 14.377 76.766 28.515 7.908  1.004   -8.536 NA3    Z5A 17 
Z5A N3B    N3B    N 1  1 N N N 13.745 76.718 29.577 7.060  1.758   -9.042 N3B    Z5A 18 
Z5A N3C    N3C    N -1 1 N N N 13.435 76.637 30.685 6.287  2.450   -9.516 N3C    Z5A 19 
Z5A PA     PA     P 0  1 N N N 12.947 72.036 26.724 8.061  2.958   -2.547 PA     Z5A 20 
Z5A O1P    O1P    O 0  1 N N N 11.635 71.922 26.018 7.698  1.671   -1.838 O1P    Z5A 21 
Z5A O2P    O2P    O -1 1 N N N 14.020 71.055 26.126 9.051  3.926   -1.936 O2P    Z5A 22 
Z5A OPA    OPA    O 0  1 N N N 12.956 72.010 28.196 6.689  3.777   -2.886 OPA    Z5A 23 
Z5A PB     PB     P 0  1 N N N ?      ?      ?      5.601  4.462   -1.880 PB     Z5A 24 
Z5A O3P    O3P    O 0  1 N N N ?      ?      ?      4.424  4.947   -2.697 O3P    Z5A 25 
Z5A O4P    O4P    O -1 1 N N N ?      ?      ?      6.333  5.394   -0.940 O4P    Z5A 26 
Z5A OPB    OPB    O 0  1 N N N 10.293 72.261 30.415 5.138  3.135   -1.051 OPB    Z5A 27 
Z5A PC     PC     P 0  1 N N N 10.955 70.962 30.387 4.065  2.922   0.161  PC     Z5A 28 
Z5A O5P    O5P    O 0  1 N N N 12.158 70.869 31.255 2.677  3.188   -0.379 O5P    Z5A 29 
Z5A O6P    O6P    O -1 1 N N N 11.265 70.230 29.100 4.571  3.633   1.396  O6P    Z5A 30 
Z5A OPC    OPC    O 0  1 N N N 9.807  70.128 31.157 4.240  1.314   0.371  OPC    Z5A 31 
Z5A PD     PD     P 0  1 N N N 8.384  69.557 30.602 3.506  0.298   1.415  PD     Z5A 32 
Z5A O7P    O7P    O 0  1 N N N 8.705  68.913 29.315 2.041  0.206   1.054  O7P    Z5A 33 
Z5A O8P    O8P    O -1 1 N N N 7.312  70.559 30.704 3.947  0.643   2.820  O8P    Z5A 34 
Z5A OPD    OPD    O 0  1 N N N 8.065  68.418 31.657 4.246  -1.083  0.957  OPD    Z5A 35 
Z5A PE     PE     P 0  1 N N N 8.200  66.833 31.680 4.074  -2.606  1.520  PE     Z5A 36 
Z5A O9P    O9P    O 0  1 N N N 9.553  66.359 31.285 2.682  -3.089  1.176  O9P    Z5A 37 
Z5A OAP    OAP    O -1 1 N N N 7.053  66.288 30.906 4.590  -2.653  2.942  OAP    Z5A 38 
Z5A O5B    O5*    O 0  1 N N N 7.963  66.506 33.174 5.153  -3.341  0.536  O5B    Z5A 39 
Z5A C5B    C5*    C 0  1 N N N 8.915  66.943 34.207 4.857  -3.405  -0.848 C5B    Z5A 40 
Z5A C4B    C4*    C 0  1 N N R 8.883  66.043 35.305 5.986  -4.125  -1.563 C4B    Z5A 41 
Z5A O4B    O4*    O 0  1 N N N 7.664  66.080 36.039 6.091  -5.472  -1.074 O4B    Z5A 42 
Z5A C3B    C3*    C 0  1 N N S 9.074  64.583 34.862 5.767  -4.261  -3.060 C3B    Z5A 43 
Z5A "O3'"  O3*    O 0  1 N N N 9.808  63.856 35.874 6.109  -3.082  -3.757 "O3'"  Z5A 44 
Z5A C2B    C2*    C 0  1 N N R 7.656  64.026 34.841 6.647  -5.446  -3.408 C2B    Z5A 45 
Z5A "O2'"  O2*    O 0  1 N N N 7.479  62.633 35.079 7.999  -5.042  -3.617 "O2'"  Z5A 46 
Z5A C1B    C1*    C 0  1 N N R 7.010  64.794 36.030 6.568  -6.310  -2.148 C1B    Z5A 47 
Z5A N9A    N9A    N 0  1 Y N N 5.573  65.057 35.709 5.689  -7.472  -2.287 N9A    Z5A 48 
Z5A C8A    C8A    C 0  1 Y N N 5.017  65.336 34.463 4.336  -7.492  -2.069 C8A    Z5A 49 
Z5A N7A    N7A    N 0  1 Y N N 3.710  65.561 34.639 3.816  -8.684  -2.274 N7A    Z5A 50 
Z5A C5A    C5A    C 0  1 Y N N 3.424  65.385 35.964 4.878  -9.472  -2.641 C5A    Z5A 51 
Z5A C6A    C6A    C 0  1 Y N N 2.221  65.472 36.700 4.973  -10.817 -2.985 C6A    Z5A 52 
Z5A N6A    N6A    N 0  1 N N N 1.074  65.749 36.099 3.832  -11.638 -2.996 N6A    Z5A 53 
Z5A N1A    N1A    N 0  1 Y N N 2.401  65.240 37.993 6.184  -11.330 -3.310 N1A    Z5A 54 
Z5A C2A    C2A    C 0  1 Y N N 3.560  64.947 38.615 7.247  -10.490 -3.281 C2A    Z5A 55 
Z5A N3A    N3A    N 0  1 Y N N 4.719  64.865 37.959 7.281  -9.177  -2.966 N3A    Z5A 56 
Z5A C4A    C4A    C 0  1 Y N N 4.554  65.070 36.692 6.052  -8.737  -2.656 C4A    Z5A 57 
Z5A H3T    H3T    H 0  1 N N N 13.669 80.440 22.194 12.314 -3.867  -5.411 H3T    Z5A 58 
Z5A H6T    H6T    H 0  1 N N N 12.499 75.942 23.830 9.677  -0.087  -4.049 H6T    Z5A 59 
Z5A H7T1   1H7T   H 0  0 N N N 11.953 76.345 20.337 10.527 -2.356  -1.338 H7T1   Z5A 60 
Z5A H7T2   2H7T   H 0  0 N N N 11.172 75.434 21.692 9.816  -0.772  -1.718 H7T2   Z5A 61 
Z5A H7T3   3H7T   H 0  0 N N N 10.518 76.993 21.046 11.569 -0.925  -1.497 H7T3   Z5A 62 
Z5A "H5'1" "1H5'" H 0  0 N N N 15.520 73.521 25.603 7.727  0.762   -4.348 "H5'1" Z5A 63 
Z5A "H5'2" "2H5'" H 0  0 N N N 15.291 73.427 27.263 6.763  2.133   -4.958 "H5'2" Z5A 64 
Z5A "H4'"  "H4'"  H 0  1 N N N 15.835 75.657 26.828 8.547  2.575   -6.669 "H4'"  Z5A 65 
Z5A "H3'"  "H3'"  H 0  1 N N N 13.155 75.125 27.861 6.589  0.616   -6.959 "H3'"  Z5A 66 
Z5A "H2'1" "1H2'" H 0  0 N N N 12.330 77.714 27.065 7.877  -1.158  -5.970 "H2'1" Z5A 67 
Z5A "H2'2" "2H2'" H 0  0 N N N 11.914 76.437 26.119 8.248  -1.429  -7.679 "H2'2" Z5A 68 
Z5A "H1'"  "H1'"  H 0  1 N N N 14.356 78.261 25.879 10.363 -0.281  -7.502 "H1'"  Z5A 69 
Z5A H5A1   1H5*   H 0  0 N N N 8.735  67.997 34.524 3.913  -3.943  -0.983 H5A1   Z5A 70 
Z5A H5A2   2H5*   H 0  0 N N N 9.945  67.070 33.800 4.747  -2.387  -1.233 H5A2   Z5A 71 
Z5A H4B    H4*    H 0  1 N N N 9.724  66.386 35.952 6.927  -3.605  -1.345 H4B    Z5A 72 
Z5A H3B    H3*    H 0  1 N N N 9.619  64.502 33.893 4.719  -4.508  -3.269 H3B    Z5A 73 
Z5A "HO'3" 3HO*   H 0  0 N N N 9.926  62.954 35.600 5.831  -2.342  -3.196 "HO'3" Z5A 74 
Z5A "H2'"  H2*    H 0  1 N N N 7.232  64.155 33.818 6.323  -5.958  -4.320 "H2'"  Z5A 75 
Z5A "HO'2" 2HO*   H 0  0 N N N 6.595  62.286 35.066 8.510  -5.843  -3.829 "HO'2" Z5A 76 
Z5A H1B    H1*    H 0  1 N N N 7.101  64.230 36.987 7.541  -6.720  -1.859 H1B    Z5A 77 
Z5A H8A    H8A    H 0  1 N N N 5.532  65.373 33.488 3.788  -6.611  -1.763 H8A    Z5A 78 
Z5A H6A1   1H6A   H 0  0 N N N 0.938  65.072 35.348 3.207  -11.624 -2.212 H6A1   Z5A 79 
Z5A H6A2   2H6A   H 0  0 N N N 0.206  65.812 36.630 3.705  -12.295 -3.742 H6A2   Z5A 80 
Z5A H2A    H2A    H 0  1 N N N 3.560  64.767 39.703 8.201  -10.934 -3.546 H2A    Z5A 81 
# 
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 
Z5A N1T   C2T    SING N N 1  
Z5A N1T   C6T    SING N N 2  
Z5A N1T   "C1'"  SING N N 3  
Z5A C2T   O2T    DOUB N N 4  
Z5A C2T   N3T    SING N N 5  
Z5A N3T   C4T    SING N N 6  
Z5A N3T   H3T    SING N N 7  
Z5A C4T   O4T    DOUB N N 8  
Z5A C4T   C5T    SING N N 9  
Z5A C5T   C6T    DOUB N N 10 
Z5A C5T   C7T    SING N N 11 
Z5A C6T   H6T    SING N N 12 
Z5A C7T   H7T1   SING N N 13 
Z5A C7T   H7T2   SING N N 14 
Z5A C7T   H7T3   SING N N 15 
Z5A "C5'" "O5'"  SING N N 16 
Z5A "C5'" "C4'"  SING N N 17 
Z5A "C5'" "H5'1" SING N N 18 
Z5A "C5'" "H5'2" SING N N 19 
Z5A "O5'" PA     SING N N 20 
Z5A "C4'" "O4'"  SING N N 21 
Z5A "C4'" "C3'"  SING N N 22 
Z5A "C4'" "H4'"  SING N N 23 
Z5A "O4'" "C1'"  SING N N 24 
Z5A "C3'" "C2'"  SING N N 25 
Z5A "C3'" NA3    SING N N 26 
Z5A "C3'" "H3'"  SING N N 27 
Z5A "C2'" "C1'"  SING N N 28 
Z5A "C2'" "H2'1" SING N N 29 
Z5A "C2'" "H2'2" SING N N 30 
Z5A "C1'" "H1'"  SING N N 31 
Z5A NA3   N3B    DOUB N N 32 
Z5A N3B   N3C    DOUB N N 33 
Z5A PA    O1P    DOUB N N 34 
Z5A PA    O2P    SING N N 35 
Z5A PA    OPA    SING N N 36 
Z5A OPA   PB     SING N N 37 
Z5A PB    O3P    DOUB N N 38 
Z5A PB    O4P    SING N N 39 
Z5A PB    OPB    SING N N 40 
Z5A OPB   PC     SING N N 41 
Z5A PC    O5P    DOUB N N 42 
Z5A PC    O6P    SING N N 43 
Z5A PC    OPC    SING N N 44 
Z5A OPC   PD     SING N N 45 
Z5A PD    O7P    DOUB N N 46 
Z5A PD    O8P    SING N N 47 
Z5A PD    OPD    SING N N 48 
Z5A OPD   PE     SING N N 49 
Z5A PE    O9P    DOUB N N 50 
Z5A PE    OAP    SING N N 51 
Z5A PE    O5B    SING N N 52 
Z5A O5B   C5B    SING N N 53 
Z5A C5B   C4B    SING N N 54 
Z5A C5B   H5A1   SING N N 55 
Z5A C5B   H5A2   SING N N 56 
Z5A C4B   O4B    SING N N 57 
Z5A C4B   C3B    SING N N 58 
Z5A C4B   H4B    SING N N 59 
Z5A O4B   C1B    SING N N 60 
Z5A C3B   "O3'"  SING N N 61 
Z5A C3B   C2B    SING N N 62 
Z5A C3B   H3B    SING N N 63 
Z5A "O3'" "HO'3" SING N N 64 
Z5A C2B   "O2'"  SING N N 65 
Z5A C2B   C1B    SING N N 66 
Z5A C2B   "H2'"  SING N N 67 
Z5A "O2'" "HO'2" SING N N 68 
Z5A C1B   N9A    SING N N 69 
Z5A C1B   H1B    SING N N 70 
Z5A N9A   C8A    SING Y N 71 
Z5A N9A   C4A    SING Y N 72 
Z5A C8A   N7A    DOUB Y N 73 
Z5A C8A   H8A    SING N N 74 
Z5A N7A   C5A    SING Y N 75 
Z5A C5A   C6A    SING Y N 76 
Z5A C5A   C4A    DOUB Y N 77 
Z5A C6A   N6A    SING N N 78 
Z5A C6A   N1A    DOUB Y N 79 
Z5A N6A   H6A1   SING N N 80 
Z5A N6A   H6A2   SING N N 81 
Z5A N1A   C2A    SING Y N 82 
Z5A C2A   N3A    DOUB Y N 83 
Z5A C2A   H2A    SING N N 84 
Z5A N3A   C4A    SING Y N 85 
# 
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 
Z5A InChI            InChI                1.03  
;InChI=1S/C20H29N10O22P5/c1-8-3-29(20(34)26-18(8)33)12-2-9(27-28-22)10(47-12)4-45-53(35,36)49-55(39,40)51-57(43,44)52-56(41,42)50-54(37,38)46-5-11-14(31)15(32)19(48-11)30-7-25-13-16(21)23-6-24-17(13)30/h3,6-7,9-12,14-15,19,31-32H,2,4-5H2,1H3,(H,35,36)(H,37,38)(H,39,40)(H,41,42)(H,43,44)(H2,21,23,24)(H,26,33,34)/p-5/t9-,10+,11+,12+,14+,15+,19+/m0/s1
;
Z5A InChIKey         InChI                1.03  QNIWSXQXLJIUJW-SLFMBYJQSA-I 
Z5A SMILES_CANONICAL CACTVS               3.370 "CC1=CN([C@H]2C[C@H](N=[N+]=[N-])[C@@H](CO[P]([O-])(=O)O[P]([O-])(=O)O[P]([O-])(=O)O[P]([O-])(=O)O[P]([O-])(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)O2)C(=O)NC1=O" 
Z5A SMILES           CACTVS               3.370 "CC1=CN([CH]2C[CH](N=[N+]=[N-])[CH](CO[P]([O-])(=O)O[P]([O-])(=O)O[P]([O-])(=O)O[P]([O-])(=O)O[P]([O-])(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)O2)C(=O)NC1=O" 
Z5A SMILES_CANONICAL "OpenEye OEToolkits" 1.7.2 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)([O-])OP(=O)([O-])OP(=O)([O-])OP(=O)([O-])OP(=O)([O-])OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)N=[N+]=[N-]" 
Z5A SMILES           "OpenEye OEToolkits" 1.7.2 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)([O-])OP(=O)([O-])OP(=O)([O-])OP(=O)([O-])OP(=O)([O-])OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)N=[N+]=[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 
Z5A "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.2 
;[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanidyl-phosphoryl] [[[[(2S,3S,5R)-3-azido-5-[5-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]oxolan-2-yl]methoxy-oxidanidyl-phosphoryl]oxy-oxidanidyl-phosphoryl]oxy-oxidanidyl-phosphoryl] 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 
Z5A "Create component"  1999-07-08 EBI  
Z5A "Modify descriptor" 2011-06-04 RCSB 
Z5A "Modify descriptor" 2011-06-07 RCSB 
Z5A "Modify identifier" 2011-06-07 RCSB 
# 
