data_ZP1 # _chem_comp.id ZP1 _chem_comp.name "(4~{S})-4-[(2~{R})-3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl(phosphonooxy)phosphoryl]oxyethyl]-2~{H}-1,3-thiazol-2-yl]-4-[ethoxy(oxidanyl)phosphoryl]-4-oxidanyl-butanoic acid" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C18 H31 N4 O13 P3 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2019-03-16 _chem_comp.pdbx_modified_date 2019-09-06 _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 636.444 _chem_comp.one_letter_code ? _chem_comp.three_letter_code ZP1 _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 6R2A _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 ZP1 "N1'" N1 N 0 1 Y N N 39.914 24.626 26.444 -3.585 -4.016 -1.530 "N1'" ZP1 1 ZP1 "C2'" C1 C 0 1 Y N N 39.452 24.527 25.182 -2.789 -5.005 -1.176 "C2'" ZP1 2 ZP1 CM2 C2 C 0 1 N N N 38.125 23.827 24.954 -2.745 -6.249 -2.025 CM2 ZP1 3 ZP1 "N3'" N2 N 0 1 Y N N 40.080 25.013 24.068 -2.032 -4.936 -0.100 "N3'" ZP1 4 ZP1 "C4'" C3 C 0 1 Y N N 41.284 25.655 24.315 -2.046 -3.854 0.672 "C4'" ZP1 5 ZP1 "N4'" N3 N 0 1 N N N 41.829 26.277 23.242 -1.247 -3.785 1.802 "N4'" ZP1 6 ZP1 "C5'" C4 C 0 1 Y N N 41.871 25.760 25.626 -2.878 -2.787 0.325 "C5'" ZP1 7 ZP1 "C6'" C5 C 0 1 Y N N 41.114 25.223 26.647 -3.654 -2.904 -0.811 "C6'" ZP1 8 ZP1 "C7'" C6 C 0 1 N N N 43.225 26.399 25.834 -2.927 -1.540 1.169 "C7'" ZP1 9 ZP1 N3 N4 N 0 1 N N N 44.379 25.716 25.190 -2.029 -0.531 0.603 N3 ZP1 10 ZP1 C2 C7 C 0 1 N N R 44.858 26.089 23.848 -2.428 0.365 -0.496 C2 ZP1 11 ZP1 S1 S1 S 0 1 N N N 46.201 24.927 23.477 -0.917 1.371 -0.743 S1 ZP1 12 ZP1 C5 C8 C 0 1 N N N 45.837 23.870 24.832 0.038 0.580 0.530 C5 ZP1 13 ZP1 C4 C9 C 0 1 N N N 44.818 24.368 25.593 -0.743 -0.339 1.058 C4 ZP1 14 ZP1 CM4 C10 C 0 1 N N N 44.248 23.671 26.806 -0.222 -1.193 2.185 CM4 ZP1 15 ZP1 C6 C11 C 0 1 N N N 46.624 22.630 25.023 1.457 0.898 0.926 C6 ZP1 16 ZP1 C7 C12 C 0 1 N N N 46.307 21.651 23.846 2.423 0.137 0.016 C7 ZP1 17 ZP1 O7 O1 O 0 1 N N N 47.086 20.513 23.919 3.768 0.438 0.391 O7 ZP1 18 ZP1 PA P1 P 0 1 N N N 46.948 19.392 22.676 5.049 -0.189 -0.356 PA ZP1 19 ZP1 O1A O2 O 0 1 N N N 47.805 18.224 23.063 5.079 -1.782 -0.122 O1A ZP1 20 ZP1 O2A O3 O 0 1 N N N 45.497 19.096 22.448 4.962 0.095 -1.806 O2A ZP1 21 ZP1 O3A O4 O 0 1 N N N 47.499 20.203 21.489 6.393 0.466 0.240 O3A ZP1 22 ZP1 PB P2 P 0 1 N N N 49.095 20.768 21.173 7.905 0.602 -0.297 PB ZP1 23 ZP1 O1B O5 O 0 1 N N N 49.315 20.538 19.689 7.888 1.023 -1.716 O1B ZP1 24 ZP1 O2B O6 O 0 1 N N N 49.976 19.866 22.023 8.689 1.700 0.580 O2B ZP1 25 ZP1 O3B O7 O 0 1 N N N 49.111 22.225 21.581 8.649 -0.820 -0.168 O3B ZP1 26 ZP1 C11 C13 C 0 1 N N S 45.007 27.570 23.377 -3.611 1.242 -0.081 C11 ZP1 27 ZP1 P4 P3 P 0 1 N N N 46.311 28.490 24.252 -3.175 2.178 1.422 P4 ZP1 28 ZP1 O5 O8 O 0 1 N N N 46.076 29.948 23.974 -4.202 3.404 1.607 O5 ZP1 29 ZP1 O6 O9 O 0 1 N N N 47.672 27.956 23.885 -1.797 2.703 1.294 O6 ZP1 30 ZP1 O8 O10 O 0 1 N N N 46.023 28.426 25.901 -3.263 1.206 2.703 O8 ZP1 31 ZP1 C12 C14 C 0 1 N N N 45.522 27.538 21.890 -3.942 2.219 -1.212 C12 ZP1 32 ZP1 O11 O11 O 0 1 N N N 43.799 28.334 23.512 -4.747 0.417 0.184 O11 ZP1 33 ZP1 C13 C15 C 0 1 N N N 44.570 27.228 20.763 -4.186 1.439 -2.505 C13 ZP1 34 ZP1 C14 C16 C 0 1 N N N 43.819 28.496 20.279 -4.512 2.401 -3.618 C14 ZP1 35 ZP1 O15 O12 O 0 1 N N N 43.389 28.451 19.109 -4.547 3.588 -3.399 O15 ZP1 36 ZP1 O16 O13 O 0 1 N N N 43.665 29.505 21.026 -4.765 1.938 -4.852 O16 ZP1 37 ZP1 C8 C17 C 0 1 N N N 47.195 28.384 26.682 -2.851 1.605 4.011 C8 ZP1 38 ZP1 C9 C18 C 0 1 N N N 48.016 29.705 26.690 -2.961 0.414 4.966 C9 ZP1 39 ZP1 H1 H1 H 0 1 N N N 37.887 23.832 23.880 -1.976 -6.140 -2.789 H1 ZP1 40 ZP1 H2 H2 H 0 1 N N N 38.193 22.788 25.309 -2.513 -7.110 -1.397 H2 ZP1 41 ZP1 H3 H3 H 0 1 N N N 37.333 24.353 25.508 -3.714 -6.398 -2.502 H3 ZP1 42 ZP1 H4 H4 H 0 1 N N N 41.237 26.150 22.446 -0.558 -4.451 1.951 H4 ZP1 43 ZP1 H5 H5 H 0 1 N N N 41.923 27.254 23.435 -1.377 -3.070 2.445 H5 ZP1 44 ZP1 H6 H6 H 0 1 N N N 41.496 25.281 27.656 -4.309 -2.100 -1.110 H6 ZP1 45 ZP1 H7 H7 H 0 1 N N N 43.417 26.434 26.917 -3.946 -1.151 1.185 H7 ZP1 46 ZP1 H8 H8 H 0 1 N N N 43.177 27.424 25.437 -2.613 -1.776 2.186 H8 ZP1 47 ZP1 H9 H9 H 0 1 N N N 44.068 25.707 23.184 -2.666 -0.205 -1.395 H9 ZP1 48 ZP1 H10 H10 H 0 1 N N N 43.440 24.282 27.235 0.248 -2.088 1.776 H10 ZP1 49 ZP1 H11 H11 H 0 1 N N N 43.848 22.690 26.511 0.512 -0.628 2.760 H11 ZP1 50 ZP1 H12 H12 H 0 1 N N N 45.041 23.533 27.556 -1.048 -1.482 2.835 H12 ZP1 51 ZP1 H13 H13 H 0 1 N N N 46.350 22.161 25.979 1.630 1.969 0.826 H13 ZP1 52 ZP1 H14 H14 H 0 1 N N N 47.698 22.869 25.027 1.621 0.598 1.962 H14 ZP1 53 ZP1 H15 H15 H 0 1 N N N 46.505 22.161 22.892 2.249 -0.934 0.116 H15 ZP1 54 ZP1 H16 H16 H 0 1 N N N 45.246 21.363 23.894 2.259 0.437 -1.019 H16 ZP1 55 ZP1 H17 H17 H 0 1 N N N 47.271 17.439 23.106 5.135 -2.042 0.808 H17 ZP1 56 ZP1 H18 H18 H 0 1 N N N 50.508 19.318 21.458 9.609 1.834 0.312 H18 ZP1 57 ZP1 H19 H19 H 0 1 N N N 49.261 22.767 20.815 8.697 -1.158 0.736 H19 ZP1 58 ZP1 H20 H20 H 0 1 N N N 46.858 30.328 23.591 -5.126 3.134 1.697 H20 ZP1 59 ZP1 H21 H21 H 0 1 N N N 46.319 26.781 21.848 -4.838 2.783 -0.953 H21 ZP1 60 ZP1 H22 H22 H 0 1 N N N 45.947 28.531 21.681 -3.109 2.907 -1.354 H22 ZP1 61 ZP1 H23 H23 H 0 1 N N N 43.521 28.330 24.420 -5.554 0.911 0.380 H23 ZP1 62 ZP1 H24 H24 H 0 1 N N N 43.833 26.489 21.112 -3.290 0.875 -2.763 H24 ZP1 63 ZP1 H25 H25 H 0 1 N N N 45.140 26.808 19.921 -5.019 0.751 -2.362 H25 ZP1 64 ZP1 H26 H26 H 0 1 N N N 43.189 30.179 20.555 -4.970 2.593 -5.534 H26 ZP1 65 ZP1 H27 H27 H 0 1 N N N 46.908 28.152 27.718 -1.817 1.949 3.978 H27 ZP1 66 ZP1 H28 H28 H 0 1 N N N 47.839 27.582 26.291 -3.491 2.414 4.364 H28 ZP1 67 ZP1 H29 H29 H 0 1 N N N 48.908 29.579 27.322 -2.255 -0.360 4.665 H29 ZP1 68 ZP1 H30 H30 H 0 1 N N N 48.326 29.950 25.663 -2.733 0.739 5.981 H30 ZP1 69 ZP1 H31 H31 H 0 1 N N N 47.395 30.520 27.090 -3.975 0.014 4.932 H31 ZP1 70 # # 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 ZP1 O15 C14 DOUB N N 1 ZP1 O1B PB DOUB N N 2 ZP1 C14 C13 SING N N 3 ZP1 C14 O16 SING N N 4 ZP1 C13 C12 SING N N 5 ZP1 PB O3A SING N N 6 ZP1 PB O3B SING N N 7 ZP1 PB O2B SING N N 8 ZP1 O3A PA SING N N 9 ZP1 C12 C11 SING N N 10 ZP1 O2A PA DOUB N N 11 ZP1 PA O1A SING N N 12 ZP1 PA O7 SING N N 13 ZP1 "N4'" "C4'" SING N N 14 ZP1 C11 O11 SING N N 15 ZP1 C11 C2 SING N N 16 ZP1 C11 P4 SING N N 17 ZP1 S1 C2 SING N N 18 ZP1 S1 C5 SING N N 19 ZP1 C7 O7 SING N N 20 ZP1 C7 C6 SING N N 21 ZP1 C2 N3 SING N N 22 ZP1 O6 P4 DOUB N N 23 ZP1 O5 P4 SING N N 24 ZP1 "N3'" "C4'" DOUB Y N 25 ZP1 "N3'" "C2'" SING Y N 26 ZP1 P4 O8 SING N N 27 ZP1 "C4'" "C5'" SING Y N 28 ZP1 C5 C6 SING N N 29 ZP1 C5 C4 DOUB N N 30 ZP1 CM2 "C2'" SING N N 31 ZP1 "C2'" "N1'" DOUB Y N 32 ZP1 N3 C4 SING N N 33 ZP1 N3 "C7'" SING N N 34 ZP1 C4 CM4 SING N N 35 ZP1 "C5'" "C7'" SING N N 36 ZP1 "C5'" "C6'" DOUB Y N 37 ZP1 O8 C8 SING N N 38 ZP1 "N1'" "C6'" SING Y N 39 ZP1 C8 C9 SING N N 40 ZP1 CM2 H1 SING N N 41 ZP1 CM2 H2 SING N N 42 ZP1 CM2 H3 SING N N 43 ZP1 "N4'" H4 SING N N 44 ZP1 "N4'" H5 SING N N 45 ZP1 "C6'" H6 SING N N 46 ZP1 "C7'" H7 SING N N 47 ZP1 "C7'" H8 SING N N 48 ZP1 C2 H9 SING N N 49 ZP1 CM4 H10 SING N N 50 ZP1 CM4 H11 SING N N 51 ZP1 CM4 H12 SING N N 52 ZP1 C6 H13 SING N N 53 ZP1 C6 H14 SING N N 54 ZP1 C7 H15 SING N N 55 ZP1 C7 H16 SING N N 56 ZP1 O1A H17 SING N N 57 ZP1 O2B H18 SING N N 58 ZP1 O3B H19 SING N N 59 ZP1 O5 H20 SING N N 60 ZP1 C12 H21 SING N N 61 ZP1 C12 H22 SING N N 62 ZP1 O11 H23 SING N N 63 ZP1 C13 H24 SING N N 64 ZP1 C13 H25 SING N N 65 ZP1 O16 H26 SING N N 66 ZP1 C8 H27 SING N N 67 ZP1 C8 H28 SING N N 68 ZP1 C9 H29 SING N N 69 ZP1 C9 H30 SING N N 70 ZP1 C9 H31 SING N N 71 # # 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 ZP1 InChI InChI 1.03 "InChI=1S/C18H31N4O13P3S/c1-4-33-36(26,27)18(25,7-5-15(23)24)17-22(10-13-9-20-12(3)21-16(13)19)11(2)14(39-17)6-8-34-38(31,32)35-37(28,29)30/h9,17,25H,4-8,10H2,1-3H3,(H,23,24)(H,26,27)(H,31,32)(H2,19,20,21)(H2,28,29,30)/t17-,18+/m1/s1" ZP1 InChIKey InChI 1.03 XUQXUYTXDQCESE-MSOLQXFVSA-N ZP1 SMILES_CANONICAL CACTVS 3.385 "CCO[P](O)(=O)[C@@](O)(CCC(O)=O)[C@H]1SC(=C(C)N1Cc2cnc(C)nc2N)CCO[P](O)(=O)O[P](O)(O)=O" ZP1 SMILES CACTVS 3.385 "CCO[P](O)(=O)[C](O)(CCC(O)=O)[CH]1SC(=C(C)N1Cc2cnc(C)nc2N)CCO[P](O)(=O)O[P](O)(O)=O" ZP1 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CCOP(=O)([C@@](CCC(=O)O)([C@@H]1N(C(=C(S1)CCOP(=O)(O)OP(=O)(O)O)C)Cc2cnc(nc2N)C)O)O" ZP1 SMILES "OpenEye OEToolkits" 2.0.7 "CCOP(=O)(C(CCC(=O)O)(C1N(C(=C(S1)CCOP(=O)(O)OP(=O)(O)O)C)Cc2cnc(nc2N)C)O)O" # _pdbx_chem_comp_identifier.comp_id ZP1 _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "(4~{S})-4-[(2~{R})-3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-5-[2-[oxidanyl(phosphonooxy)phosphoryl]oxyethyl]-2~{H}-1,3-thiazol-2-yl]-4-[ethoxy(oxidanyl)phosphoryl]-4-oxidanyl-butanoic acid" # # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site ZP1 "Create component" 2019-03-16 RCSB ZP1 "Initial release" 2019-09-11 RCSB ##