data_ZP4 # _chem_comp.id ZP4 _chem_comp.name "[[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl] [(2S,3S,5R)-3-azido-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl hydrogen phosphate" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C20 H28 N10 O19 P4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2008-10-15 _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 836.387 _chem_comp.one_letter_code ? _chem_comp.three_letter_code ZP4 _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag N _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 3E4J _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 ZP4 "O5'" "O5'" O 0 1 N N N -28.514 -34.411 55.129 4.224 -1.107 -1.052 O1 ZP4 1 ZP4 "N3'" "N3'" N 0 1 N N N -27.607 -31.452 57.111 5.780 2.637 -3.325 N1 ZP4 2 ZP4 N3A N3A N 1 1 N N N -28.417 -31.178 57.992 6.443 3.207 -4.031 N2 ZP4 3 ZP4 N3B N3B N -1 1 N N N -29.049 -30.913 58.899 7.105 3.778 -4.737 N3 ZP4 4 ZP4 N1 N1 N 0 1 N N N -29.317 -31.285 52.826 6.962 2.745 1.134 N4 ZP4 5 ZP4 C6 C6 C 0 1 N N N -29.749 -32.574 52.651 6.850 3.910 1.843 C1 ZP4 6 ZP4 C2 C2 C 0 1 N N N -30.051 -30.225 52.381 7.731 1.738 1.587 C2 ZP4 7 ZP4 O2 O2 O 0 1 N N N -29.650 -29.070 52.435 7.811 0.709 0.943 O2 ZP4 8 ZP4 N3 N3 N 0 1 N N N -31.276 -30.561 51.867 8.412 1.853 2.741 N5 ZP4 9 ZP4 C4 C4 C 0 1 N N N -31.807 -31.820 51.743 8.333 2.987 3.467 C3 ZP4 10 ZP4 O4 O4 O 0 1 N N N -32.959 -31.959 51.349 8.950 3.092 4.512 O3 ZP4 11 ZP4 C5 C5 C 0 1 N N N -30.930 -32.890 52.131 7.523 4.052 3.005 C4 ZP4 12 ZP4 C5A C5A C 0 1 N N N -31.373 -34.301 51.938 7.418 5.330 3.796 C5 ZP4 13 ZP4 "C2'" "C2'" C 0 1 N N N -28.210 -30.501 54.965 7.217 2.465 -1.316 C6 ZP4 14 ZP4 "C5'" "C5'" C 0 1 N N N -27.150 -34.041 55.092 5.320 -0.495 -1.734 C7 ZP4 15 ZP4 "C4'" "C4'" C 0 1 N N S -27.056 -32.547 54.958 5.265 1.021 -1.529 C8 ZP4 16 ZP4 "O4'" "O4'" O 0 1 N N N -27.341 -32.219 53.600 5.516 1.336 -0.149 O4 ZP4 17 ZP4 "C1'" "C1'" C 0 1 N N R -28.062 -31.002 53.533 6.232 2.590 -0.127 C9 ZP4 18 ZP4 "C3'" "C3'" C 0 1 N N S -28.062 -31.770 55.769 6.368 1.702 -2.362 C10 ZP4 19 ZP4 PA PA P 0 1 N N R -28.939 -35.853 55.596 3.968 -2.697 -1.053 P1 ZP4 20 ZP4 O1A O1A O 0 1 N N N -27.720 -36.704 55.727 5.178 -3.435 -0.289 O5 ZP4 21 ZP4 O2A O2A O 0 1 N N N -30.060 -36.365 54.715 3.896 -3.184 -2.449 O6 ZP4 22 ZP4 O3A O3A O 0 1 N N N -29.568 -35.528 57.037 2.582 -3.018 -0.301 O7 ZP4 23 ZP4 PB PB P 0 1 N N R -28.799 -34.962 58.321 1.624 -4.310 -0.224 P2 ZP4 24 ZP4 O1B O1B O 0 1 N N N -29.505 -33.677 58.615 2.229 -5.364 0.832 O8 ZP4 25 ZP4 O2B O2B O 0 1 N N N -27.317 -34.918 58.116 1.541 -4.942 -1.559 O9 ZP4 26 ZP4 O3B O3B O 0 1 N N N -29.143 -35.896 59.596 0.153 -3.860 0.250 O10 ZP4 27 ZP4 PG PG P 0 1 N N S -29.601 -37.414 59.571 -1.293 -4.568 0.233 P3 ZP4 28 ZP4 O1G O1G O 0 1 N N N -28.774 -38.176 58.594 -1.463 -5.313 -1.034 O11 ZP4 29 ZP4 O2G O2G O 0 1 N N N -29.676 -37.963 60.973 -1.406 -5.588 1.474 O12 ZP4 30 ZP4 O3G O3G O 0 1 N N N -31.043 -37.368 58.902 -2.442 -3.447 0.354 O13 ZP4 31 ZP4 PD PD P 0 1 N N R -32.392 -38.048 59.481 -4.031 -3.441 0.097 P4 ZP4 32 ZP4 O1D O1D O 0 1 N N N -32.624 -37.775 60.966 -4.319 -3.435 -1.487 O14 ZP4 33 ZP4 O2D O2D O 0 1 N N N -33.503 -37.719 58.486 -4.633 -4.649 0.704 O15 ZP4 34 ZP4 O51 O51 O 0 1 N N N -32.014 -39.590 59.270 -4.678 -2.126 0.765 O16 ZP4 35 ZP4 C51 C51 C 0 1 N N N -32.461 -40.289 58.149 -6.086 -1.884 0.800 C11 ZP4 36 ZP4 C41 C41 C 0 1 N N R -31.381 -40.163 57.071 -6.356 -0.552 1.503 C12 ZP4 37 ZP4 O41 O41 O 0 1 N N N -30.376 -41.186 57.101 -5.838 0.531 0.713 O17 ZP4 38 ZP4 C11 C11 C 0 1 N N R -29.912 -41.525 55.762 -6.728 1.653 0.900 C13 ZP4 39 ZP4 C21 C21 C 0 1 N N R -30.800 -40.695 54.793 -8.135 1.002 0.899 C14 ZP4 40 ZP4 O21 O21 O 0 1 N N N -30.150 -39.708 53.948 -9.071 1.810 1.614 O18 ZP4 41 ZP4 C31 C31 C 0 1 N N S -31.965 -40.156 55.662 -7.875 -0.332 1.641 C15 ZP4 42 ZP4 O31 O31 O 0 1 N N N -32.211 -38.754 55.362 -8.241 -0.217 3.018 O19 ZP4 43 ZP4 N9R N9R N 0 1 Y N N -30.021 -43.041 55.586 -6.596 2.605 -0.205 N6 ZP4 44 ZP4 C8R C8R C 0 1 Y N N -31.107 -43.813 55.905 -6.141 2.328 -1.459 C16 ZP4 45 ZP4 N7R N7R N 0 1 Y N N -30.889 -45.128 55.656 -6.156 3.407 -2.187 N7 ZP4 46 ZP4 C5R C5R C 0 1 Y N N -29.641 -45.243 55.165 -6.621 4.442 -1.448 C17 ZP4 47 ZP4 C6R C6R C 0 1 Y N N -28.763 -46.362 54.697 -6.852 5.806 -1.694 C18 ZP4 48 ZP4 N6R N6R N 0 1 N N N -29.213 -47.643 54.722 -6.588 6.357 -2.935 N8 ZP4 49 ZP4 N1R N1R N 0 1 Y N N -27.491 -46.051 54.243 -7.331 6.556 -0.706 N9 ZP4 50 ZP4 C2R C2R C 0 1 Y N N -27.008 -44.764 54.210 -7.587 6.039 0.482 C19 ZP4 51 ZP4 N3R N3R N 0 1 Y N N -27.758 -43.701 54.632 -7.386 4.767 0.758 N10 ZP4 52 ZP4 C4R C4R C 0 1 Y N N -29.061 -43.866 55.107 -6.915 3.940 -0.169 C20 ZP4 53 ZP4 H6 H6 H 0 1 N N N -29.093 -33.377 52.953 6.228 4.712 1.475 H1 ZP4 54 ZP4 HN3 HN3 H 0 1 N N N -31.846 -29.805 51.547 8.962 1.118 3.053 H2 ZP4 55 ZP4 H5A H5A H 0 1 N N N -31.482 -34.508 50.863 8.032 5.254 4.694 H3 ZP4 56 ZP4 H5AA H5AA H 0 0 N N N -30.624 -34.982 52.368 7.766 6.165 3.188 H4 ZP4 57 ZP4 H5AB H5AB H 0 0 N N N -32.340 -34.453 52.440 6.379 5.497 4.081 H5 ZP4 58 ZP4 "H2'" "H2'" H 0 1 N N N -29.185 -30.020 55.133 7.503 3.448 -1.690 H6 ZP4 59 ZP4 "H2'A" "H2'A" H 0 0 N N N -27.478 -29.725 55.234 8.097 1.887 -1.034 H7 ZP4 60 ZP4 "H5'" "H5'" H 0 1 N N N -26.654 -34.362 56.020 6.258 -0.882 -1.336 H8 ZP4 61 ZP4 "H5'A" "H5'A" H 0 0 N N N -26.655 -34.524 54.236 5.256 -0.720 -2.799 H9 ZP4 62 ZP4 "H4'" "H4'" H 0 1 N N N -26.049 -32.278 55.310 4.288 1.400 -1.827 H10 ZP4 63 ZP4 "H1'" "H1'" H 0 1 N N N -27.569 -30.196 52.970 5.550 3.427 -0.280 H11 ZP4 64 ZP4 "H3'" "H3'" H 0 1 N N N -28.989 -32.342 55.923 6.975 0.956 -2.875 H12 ZP4 65 ZP4 HO1A HO1A H 0 0 N N N -27.365 -36.885 54.864 5.284 -3.164 0.633 H13 ZP4 66 ZP4 HO1B HO1B H 0 0 N N N -29.655 -33.604 59.550 2.312 -5.017 1.731 H14 ZP4 67 ZP4 HO2G HO2G H 0 0 N N N -29.692 -38.912 60.941 -1.304 -5.167 2.339 H15 ZP4 68 ZP4 HO1D HO1D H 0 0 N N N -32.672 -38.599 61.436 -3.952 -2.670 -1.950 H16 ZP4 69 ZP4 H51 H51 H 0 1 N N N -32.623 -41.347 58.402 -6.473 -1.843 -0.218 H17 ZP4 70 ZP4 H51A H51A H 0 0 N N N -33.416 -39.877 57.791 -6.580 -2.689 1.344 H18 ZP4 71 ZP4 H41 H41 H 0 1 N N N -30.909 -39.199 57.313 -5.888 -0.551 2.487 H19 ZP4 72 ZP4 H11 H11 H 0 1 N N N -28.858 -41.279 55.564 -6.533 2.143 1.854 H20 ZP4 73 ZP4 H21 H21 H 0 1 N N N -31.157 -41.354 53.988 -8.478 0.819 -0.119 H21 ZP4 74 ZP4 HO21 HO21 H 0 0 N N N -30.008 -38.910 54.444 -9.966 1.444 1.642 H22 ZP4 75 ZP4 H31 H31 H 0 1 N N N -32.886 -40.739 55.512 -8.424 -1.146 1.167 H23 ZP4 76 ZP4 HO31 HO31 H 0 0 N N N -32.265 -38.261 56.172 -9.176 -0.020 3.162 H24 ZP4 77 ZP4 H8R H8R H 0 1 N N N -32.029 -43.420 56.308 -5.815 1.356 -1.799 H25 ZP4 78 ZP4 HN6R HN6R H 0 0 N N N -29.324 -47.976 53.786 -6.239 5.800 -3.649 H26 ZP4 79 ZP4 HN6A HN6A H 0 0 N N N -28.553 -48.219 55.205 -6.751 7.300 -3.093 H27 ZP4 80 ZP4 H2R H2R H 0 1 N N N -26.009 -44.588 53.841 -7.975 6.683 1.257 H28 ZP4 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 ZP4 "O5'" PA SING N N 1 ZP4 "N3'" N3A DOUB N N 2 ZP4 N3A N3B DOUB N N 3 ZP4 N1 "C1'" SING N N 4 ZP4 C6 N1 SING N N 5 ZP4 C6 H6 SING N N 6 ZP4 C2 N1 SING N N 7 ZP4 C2 O2 DOUB N N 8 ZP4 N3 C2 SING N N 9 ZP4 N3 HN3 SING N N 10 ZP4 C4 N3 SING N N 11 ZP4 C4 C5 SING N N 12 ZP4 O4 C4 DOUB N N 13 ZP4 C5 C6 DOUB N N 14 ZP4 C5A C5 SING N N 15 ZP4 C5A H5A SING N N 16 ZP4 C5A H5AA SING N N 17 ZP4 C5A H5AB SING N N 18 ZP4 "C2'" "C3'" SING N N 19 ZP4 "C2'" "H2'" SING N N 20 ZP4 "C2'" "H2'A" SING N N 21 ZP4 "C5'" "O5'" SING N N 22 ZP4 "C5'" "H5'" SING N N 23 ZP4 "C5'" "H5'A" SING N N 24 ZP4 "C4'" "C5'" SING N N 25 ZP4 "C4'" "C3'" SING N N 26 ZP4 "C4'" "H4'" SING N N 27 ZP4 "O4'" "C4'" SING N N 28 ZP4 "C1'" "C2'" SING N N 29 ZP4 "C1'" "O4'" SING N N 30 ZP4 "C1'" "H1'" SING N N 31 ZP4 "C3'" "N3'" SING N N 32 ZP4 "C3'" "H3'" SING N N 33 ZP4 PA O1A SING N N 34 ZP4 PA O3A SING N N 35 ZP4 O1A HO1A SING N N 36 ZP4 O2A PA DOUB N N 37 ZP4 O3A PB SING N N 38 ZP4 PB O1B SING N N 39 ZP4 PB O3B SING N N 40 ZP4 O1B HO1B SING N N 41 ZP4 O2B PB DOUB N N 42 ZP4 PG O3B SING N N 43 ZP4 PG O2G SING N N 44 ZP4 O1G PG DOUB N N 45 ZP4 O2G HO2G SING N N 46 ZP4 O3G PG SING N N 47 ZP4 O3G PD SING N N 48 ZP4 PD O1D SING N N 49 ZP4 O1D HO1D SING N N 50 ZP4 O2D PD DOUB N N 51 ZP4 O51 PD SING N N 52 ZP4 C51 O51 SING N N 53 ZP4 C51 H51 SING N N 54 ZP4 C51 H51A SING N N 55 ZP4 C41 C51 SING N N 56 ZP4 C41 O41 SING N N 57 ZP4 C41 H41 SING N N 58 ZP4 C11 O41 SING N N 59 ZP4 C11 H11 SING N N 60 ZP4 C21 C11 SING N N 61 ZP4 C21 C31 SING N N 62 ZP4 C21 H21 SING N N 63 ZP4 O21 C21 SING N N 64 ZP4 O21 HO21 SING N N 65 ZP4 C31 C41 SING N N 66 ZP4 C31 H31 SING N N 67 ZP4 O31 C31 SING N N 68 ZP4 O31 HO31 SING N N 69 ZP4 N9R C11 SING N N 70 ZP4 N9R C8R SING Y N 71 ZP4 C8R H8R SING N N 72 ZP4 N7R C8R DOUB Y N 73 ZP4 C5R N7R SING Y N 74 ZP4 C6R C5R DOUB Y N 75 ZP4 C6R N6R SING N N 76 ZP4 N6R HN6R SING N N 77 ZP4 N6R HN6A SING N N 78 ZP4 N1R C6R SING Y N 79 ZP4 C2R N1R DOUB Y N 80 ZP4 C2R N3R SING Y N 81 ZP4 C2R H2R SING N N 82 ZP4 N3R C4R DOUB Y N 83 ZP4 C4R N9R SING Y N 84 ZP4 C4R C5R 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 ZP4 SMILES_CANONICAL CACTVS 3.341 "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)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)O2)C(=O)NC1=O" ZP4 SMILES CACTVS 3.341 "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)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)O2)C(=O)NC1=O" ZP4 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@@](=O)(O)O[P@@](=O)(O)O[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)N=[N+]=[N-]" ZP4 SMILES "OpenEye OEToolkits" 1.5.0 "CC1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)N=[N+]=[N-]" ZP4 InChI InChI 1.03 ;InChI=1S/C20H28N10O19P4/c1-8-3-29(20(34)26-18(8)33)12-2-9(27-28-22)10(45-12)4-43-50(35,36)47-52(39,40)49-53(41,42)48-51(37,38)44-5-11-14(31)15(32)19(46-11)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)(H2,21,23,24)(H,26,33,34)/t9-,10+,11+,12+,14+,15+,19+/m0/s1 ; ZP4 InChIKey InChI 1.03 NHJROJSMKQZWCP-SLFMBYJQSA-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 ZP4 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "[[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl] [(2S,3S,5R)-3-azido-5-(5-methyl-2,4-dioxo-pyrimidin-1-yl)oxolan-2-yl]methyl hydrogen 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 ZP4 "Create component" 2008-10-15 RCSB ZP4 "Modify descriptor" 2011-06-04 RCSB #