data_8N9 # _chem_comp.id 8N9 _chem_comp.name "2-[(2E)-3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-2-[1,2-bis(oxidanyl)ethylidene]-4-methyl-1,3-thiazol-5-yl]ethyl phosphono hydrogen phosphate" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C14 H22 N4 O9 P2 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms "(E)-2(3-((4-amino-2-methylpyrimidin-5-yl)methyl)-2-(1,2-dihydroxyethylidene)-4-methyl-2,3-dihydrothiazol-5-yl)ethyl trihydrogen diphosphate" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-08-09 _chem_comp.pdbx_modified_date 2021-03-13 _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 484.358 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 8N9 _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 5XU9 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBJ # # 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 8N9 "C4'" C1 C 0 1 Y N N -12.844 -33.237 -26.002 -5.364 -0.976 0.348 "C4'" 8N9 1 8N9 "C5'" C2 C 0 1 Y N N -12.935 -33.388 -27.398 -4.515 -1.211 -0.736 "C5'" 8N9 2 8N9 "C6'" C3 C 0 1 Y N N -11.749 -33.452 -28.063 -4.310 -2.517 -1.136 "C6'" 8N9 3 8N9 "N1'" N1 N 0 1 Y N N -10.597 -33.433 -27.398 -4.920 -3.497 -0.484 "N1'" 8N9 4 8N9 "N3'" N2 N 0 1 Y N N -11.668 -33.215 -25.336 -5.939 -2.012 0.951 "N3'" 8N9 5 8N9 "C2'" C4 C 0 1 Y N N -10.595 -33.275 -26.083 -5.714 -3.242 0.535 "C2'" 8N9 6 8N9 C9 C5 C 0 1 N N N -17.973 -33.294 -25.440 -3.911 3.868 0.721 C9 8N9 7 8N9 C8 C6 C 0 1 N N N -16.807 -33.236 -26.405 -3.904 2.621 -0.125 C8 8N9 8 8N9 CM2 C7 C 0 1 N N N -9.227 -33.204 -25.415 -6.386 -4.390 1.245 CM2 8N9 9 8N9 "C7'" C8 C 0 1 N N N -14.257 -33.342 -28.183 -3.841 -0.069 -1.451 "C7'" 8N9 10 8N9 C7 C9 C 0 1 N N N -15.603 -39.041 -27.154 1.705 0.234 -0.084 C7 8N9 11 8N9 C6 C10 C 0 1 N N N -15.900 -38.126 -28.282 0.606 -0.258 0.860 C6 8N9 12 8N9 C5 C11 C 0 1 N N N -15.942 -36.601 -27.975 -0.715 0.335 0.444 C5 8N9 13 8N9 CM4 C12 C 0 1 N N N -13.947 -35.977 -29.481 -1.427 -1.588 -0.911 CM4 8N9 14 8N9 C4 C13 C 0 1 N N N -14.815 -35.790 -28.375 -1.637 -0.213 -0.331 C4 8N9 15 8N9 C2 C14 C 0 1 N N N -16.132 -34.449 -26.720 -2.897 1.750 -0.022 C2 8N9 16 8N9 "N4'" N3 N 0 1 N N N -13.974 -33.108 -25.174 -5.597 0.315 0.792 "N4'" 8N9 17 8N9 N3 N4 N 0 1 N N N -15.145 -34.446 -27.943 -2.785 0.485 -0.600 N3 8N9 18 8N9 O9 O1 O 0 1 N N N -17.014 -33.193 -24.431 -3.801 5.016 -0.122 O9 8N9 19 8N9 O8 O2 O 0 1 N N N -16.519 -31.957 -26.913 -4.927 2.382 -0.996 O8 8N9 20 8N9 OB1 O3 O 0 1 N N N -19.122 -41.705 -27.795 7.629 -0.220 -1.028 OB1 8N9 21 8N9 OB2 O4 O 0 1 N N N -19.996 -40.945 -25.700 7.498 0.779 1.287 OB2 8N9 22 8N9 OA3 O5 O 0 1 N N N -17.593 -41.050 -25.933 5.559 -0.715 0.328 OA3 8N9 23 8N9 OA2 O6 O 0 1 N N N -15.994 -42.747 -26.944 4.259 -0.624 -1.955 OA2 8N9 24 8N9 OB3 O7 O 0 1 N N N -18.919 -43.213 -25.891 7.879 -1.797 0.927 OB3 8N9 25 8N9 O7 O8 O 0 1 N N N -15.890 -40.369 -27.667 2.958 -0.329 0.311 O7 8N9 26 8N9 OA1 O9 O 0 1 N N N -15.204 -41.055 -25.257 4.556 1.436 -0.529 OA1 8N9 27 8N9 PB P1 P 0 1 N N N -18.955 -41.798 -26.236 7.152 -0.482 0.348 PB 8N9 28 8N9 PA1 P2 P 0 1 N N N -16.090 -41.378 -26.412 4.338 -0.026 -0.463 PA1 8N9 29 8N9 S1 S1 S 0 1 N N N -16.842 -35.993 -26.678 -1.381 1.920 0.893 S1 8N9 30 8N9 H1 H1 H 0 1 N N N -11.743 -33.519 -29.141 -3.660 -2.737 -1.971 H1 8N9 31 8N9 H2 H2 H 0 1 N N N -18.672 -32.447 -25.504 -4.842 3.919 1.285 H2 8N9 32 8N9 H3 H3 H 0 1 N N N -18.539 -34.237 -25.451 -3.069 3.843 1.413 H3 8N9 33 8N9 H5 H5 H 0 1 N N N -8.440 -33.301 -26.178 -5.748 -4.738 2.057 H5 8N9 34 8N9 H6 H6 H 0 1 N N N -9.121 -32.238 -24.899 -7.341 -4.057 1.650 H6 8N9 35 8N9 H7 H7 H 0 1 N N N -9.133 -34.022 -24.685 -6.553 -5.205 0.541 H7 8N9 36 8N9 H8 H8 H 0 1 N N N -14.016 -33.325 -29.256 -3.405 -0.430 -2.382 H8 8N9 37 8N9 H9 H9 H 0 1 N N N -14.783 -32.415 -27.911 -4.575 0.707 -1.670 H9 8N9 38 8N9 H10 H10 H 0 1 N N N -14.547 -38.960 -26.857 1.474 -0.075 -1.103 H10 8N9 39 8N9 H11 H11 H 0 1 N N N -16.245 -38.812 -26.290 1.765 1.321 -0.038 H11 8N9 40 8N9 H12 H12 H 0 1 N N N -16.883 -38.408 -28.686 0.547 -1.345 0.814 H12 8N9 41 8N9 H13 H13 H 0 1 N N N -15.128 -38.287 -29.049 0.838 0.051 1.879 H13 8N9 42 8N9 H15 H15 H 0 1 N N N -13.193 -35.176 -29.495 -0.424 -1.936 -0.666 H15 8N9 43 8N9 H16 H16 H 0 1 N N N -13.445 -36.952 -29.392 -2.163 -2.275 -0.493 H16 8N9 44 8N9 H17 H17 H 0 1 N N N -14.530 -35.948 -30.413 -1.543 -1.547 -1.994 H17 8N9 45 8N9 H20 H20 H 0 1 N N N -13.682 -33.022 -24.222 -6.271 0.480 1.470 H20 8N9 46 8N9 H21 H21 H 0 1 N N N -14.490 -32.293 -25.439 -5.088 1.054 0.424 H21 8N9 47 8N9 H23 H23 H 0 1 N N N -17.443 -33.200 -23.584 -3.799 5.857 0.356 H23 8N9 48 8N9 H24 H24 H 0 1 N N N -17.121 -31.324 -26.539 -5.645 3.027 -0.946 H24 8N9 49 8N9 H25 H25 H 0 1 N N N -20.493 -40.564 -26.414 7.213 0.676 2.205 H25 8N9 50 8N9 H26 H26 H 0 1 N N N -19.004 -43.734 -26.681 8.843 -1.728 0.968 H26 8N9 51 8N9 H4 H4 H 0 1 N N N -15.351 -43.237 -26.445 4.117 -1.580 -1.988 H4 8N9 52 # # 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 8N9 CM4 C4 SING N N 1 8N9 C4 C5 DOUB N N 2 8N9 C4 N3 SING N N 3 8N9 C6 C5 SING N N 4 8N9 C6 C7 SING N N 5 8N9 "C7'" N3 SING N N 6 8N9 "C7'" "C5'" SING N N 7 8N9 "C6'" "C5'" DOUB Y N 8 8N9 "C6'" "N1'" SING Y N 9 8N9 C5 S1 SING N N 10 8N9 N3 C2 SING N N 11 8N9 OB1 PB DOUB N N 12 8N9 O7 C7 SING N N 13 8N9 O7 PA1 SING N N 14 8N9 "C5'" "C4'" SING Y N 15 8N9 "N1'" "C2'" DOUB Y N 16 8N9 OA2 PA1 SING N N 17 8N9 O8 C8 SING N N 18 8N9 C2 S1 SING N N 19 8N9 C2 C8 DOUB N E 20 8N9 PA1 OA3 SING N N 21 8N9 PA1 OA1 DOUB N N 22 8N9 C8 C9 SING N N 23 8N9 PB OA3 SING N N 24 8N9 PB OB3 SING N N 25 8N9 PB OB2 SING N N 26 8N9 "C2'" CM2 SING N N 27 8N9 "C2'" "N3'" SING Y N 28 8N9 "C4'" "N3'" DOUB Y N 29 8N9 "C4'" "N4'" SING N N 30 8N9 C9 O9 SING N N 31 8N9 "C6'" H1 SING N N 32 8N9 C9 H2 SING N N 33 8N9 C9 H3 SING N N 34 8N9 CM2 H5 SING N N 35 8N9 CM2 H6 SING N N 36 8N9 CM2 H7 SING N N 37 8N9 "C7'" H8 SING N N 38 8N9 "C7'" H9 SING N N 39 8N9 C7 H10 SING N N 40 8N9 C7 H11 SING N N 41 8N9 C6 H12 SING N N 42 8N9 C6 H13 SING N N 43 8N9 CM4 H15 SING N N 44 8N9 CM4 H16 SING N N 45 8N9 CM4 H17 SING N N 46 8N9 "N4'" H20 SING N N 47 8N9 "N4'" H21 SING N N 48 8N9 O9 H23 SING N N 49 8N9 O8 H24 SING N N 50 8N9 OB2 H25 SING N N 51 8N9 OB3 H26 SING N N 52 8N9 OA2 H4 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 8N9 InChI InChI 1.03 "InChI=1S/C14H22N4O9P2S/c1-8-12(3-4-26-29(24,25)27-28(21,22)23)30-14(11(20)7-19)18(8)6-10-5-16-9(2)17-13(10)15/h5,19-20H,3-4,6-7H2,1-2H3,(H,24,25)(H2,15,16,17)(H2,21,22,23)/b14-11+" 8N9 InChIKey InChI 1.03 LXZUEFPJZTWGEL-SDNWHVSQSA-N 8N9 SMILES_CANONICAL CACTVS 3.385 "Cc1ncc(CN\2C(=C(CCO[P](O)(=O)O[P](O)(O)=O)SC\2=C(O)\CO)C)c(N)n1" 8N9 SMILES CACTVS 3.385 "Cc1ncc(CN2C(=C(CCO[P](O)(=O)O[P](O)(O)=O)SC2=C(O)CO)C)c(N)n1" 8N9 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "Cc1ncc(c(n1)N)CN\2C(=C(S/C2=C(\CO)/O)CCOP(=O)(O)OP(=O)(O)O)C" 8N9 SMILES "OpenEye OEToolkits" 2.0.6 "Cc1ncc(c(n1)N)CN2C(=C(SC2=C(CO)O)CCOP(=O)(O)OP(=O)(O)O)C" # _pdbx_chem_comp_identifier.comp_id 8N9 _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.6 _pdbx_chem_comp_identifier.identifier "2-[(2~{E})-3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-2-[1,2-bis(oxidanyl)ethylidene]-4-methyl-1,3-thiazol-5-yl]ethyl phosphono 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 8N9 "Create component" 2017-08-09 PDBJ 8N9 "Modify name" 2017-08-25 PDBJ 8N9 "Initial release" 2018-06-27 RCSB 8N9 "Modify synonyms" 2021-03-13 RCSB # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id 8N9 _pdbx_chem_comp_synonyms.name "(E)-2(3-((4-amino-2-methylpyrimidin-5-yl)methyl)-2-(1,2-dihydroxyethylidene)-4-methyl-2,3-dihydrothiazol-5-yl)ethyl trihydrogen diphosphate" _pdbx_chem_comp_synonyms.provenance PDB _pdbx_chem_comp_synonyms.type ? ##