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 #