data_A1EL3 # _chem_comp.id A1EL3 _chem_comp.name "[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-4-oxidanyl-oxolan-2-yl]methyl-[(3~{S})-3-azanyl-4-oxidanyl-4-oxidanylidene-butyl]-methyl-sulfanium" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C25 H35 N11 O11 P S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 1 _chem_comp.pdbx_initial_date 2025-02-14 _chem_comp.pdbx_modified_date 2025-11-21 _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 728.651 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1EL3 _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 9LQA _chem_comp.pdbx_subcomponent_list "SAM AMP" _chem_comp.pdbx_processing_site PDBC _chem_comp.pdbx_pcm ? # 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.pdbx_n_terminal_atom_flag _chem_comp_atom.pdbx_backbone_atom_flag _chem_comp_atom.pdbx_c_terminal_atom_flag _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 A1EL3 N23 N5 N 0 1 N N N N N N 35.755 6.496 7.066 -8.123 4.717 -0.649 N SAM 1 A1EL3 C22 C12 C 0 1 N N S N N N 34.981 7.427 6.226 -8.743 3.441 -0.266 CA SAM 2 A1EL3 C24 C13 C 0 1 N N N N N N 33.617 7.544 6.842 -9.973 3.709 0.562 C SAM 3 A1EL3 O25 O3 O 0 1 N N N N N N 33.527 7.439 8.046 -10.915 2.762 0.690 O SAM 4 A1EL3 O26 O4 O 0 1 N N N N N N 32.516 7.775 6.133 -10.112 4.777 1.110 OXT SAM 5 A1EL3 C21 C2 C 0 1 N N N N N N 35.043 6.941 4.772 -7.747 2.616 0.551 CB SAM 6 A1EL3 C20 C11 C 0 1 N N N N N N 34.596 7.925 3.680 -6.554 2.239 -0.329 CG SAM 7 A1EL3 S17 S1 S 1 1 N N R N N N 34.770 7.321 2.129 -5.374 1.260 0.641 SD SAM 8 A1EL3 C18 C10 C 0 1 N N N N N N 35.189 8.537 1.090 -6.208 -0.343 0.802 CE SAM 9 A1EL3 C16 C9 C 0 1 N N N N N N 36.069 6.338 2.452 -4.053 0.914 -0.553 "C5'" SAM 10 A1EL3 C14 C8 C 0 1 N N S N N N 36.741 5.685 1.267 -2.960 0.082 0.122 "C4'" SAM 11 A1EL3 O15 O1 O 0 1 N N N N N N 38.062 5.374 1.700 -3.473 -1.218 0.457 "O4'" SAM 12 A1EL3 C13 C7 C 0 1 N N S N N N 36.101 4.351 0.920 -1.784 -0.126 -0.851 "C3'" SAM 13 A1EL3 O27 O5 O 0 1 N N N N N N 36.348 4.175 -0.458 -0.582 0.425 -0.309 "O3'" SAM 14 A1EL3 C12 C6 C 0 1 N N R N N N 36.950 3.348 1.671 -1.665 -1.665 -0.979 "C2'" SAM 15 A1EL3 O19 O2 O 0 1 N N N N N N 36.991 2.058 1.081 -0.295 -2.071 -0.983 "O2'" SAM 16 A1EL3 C11 C5 C 0 1 N N R N N N 38.314 3.990 1.563 -2.384 -2.153 0.304 "C1'" SAM 17 A1EL3 N10 N4 N 0 1 Y N N N N N 39.212 3.452 2.598 -2.894 -3.515 0.123 N9 SAM 18 A1EL3 C9 C25 C 0 1 Y N N N N N 40.359 2.800 2.373 -4.154 -3.859 -0.269 C8 SAM 19 A1EL3 N8 N11 N 0 1 Y N N N N N 40.944 2.424 3.528 -4.263 -5.154 -0.326 N7 SAM 20 A1EL3 C7 C24 C 0 1 Y N N N N N 40.152 2.842 4.517 -3.084 -5.722 0.024 C5 SAM 21 A1EL3 C2 C1 C 0 1 Y N N N N N 40.182 2.780 5.985 -2.620 -7.043 0.142 C6 SAM 22 A1EL3 N1 N3 N 0 1 N N N N N N 41.192 2.173 6.637 -3.453 -8.114 -0.133 N6 SAM 23 A1EL3 N3 N1 N 0 1 Y N N N N N 39.159 3.346 6.638 -1.363 -7.241 0.523 N1 SAM 24 A1EL3 C4 C3 C 0 1 Y N N N N N 38.145 3.951 5.999 -0.560 -6.226 0.788 C2 SAM 25 A1EL3 N5 N2 N 0 1 Y N N N N N 38.056 4.047 4.675 -0.951 -4.973 0.691 N3 SAM 26 A1EL3 C6 C4 C 0 1 Y N N N N N 39.011 3.519 3.898 -2.190 -4.677 0.311 C4 SAM 27 A1EL3 P28 P1 P 0 1 N N N N N N 35.268 3.488 -1.393 0.253 1.593 -1.037 P AMP 28 A1EL3 O29 O6 O 0 1 N N N N N N 35.735 3.595 -2.769 0.589 1.174 -2.416 O1P AMP 29 A1EL3 O30 O7 O 0 1 N N N N N N 35.033 1.971 -0.958 -0.634 2.936 -1.086 O2P AMP 30 A1EL3 O31 O8 O 0 1 N N N N N N 33.889 4.273 -1.247 1.609 1.875 -0.216 "O5'" AMP 31 A1EL3 C32 C14 C 0 1 N N N N N N 33.783 5.615 -1.656 2.616 2.785 -0.665 "C5'" AMP 32 A1EL3 C33 C15 C 0 1 N N R N N N 32.558 6.196 -0.981 3.764 2.814 0.346 "C4'" AMP 33 A1EL3 O37 O9 O 0 1 N N N N N N 32.667 7.604 -0.991 4.435 1.543 0.361 "O4'" AMP 34 A1EL3 C34 C16 C 0 1 N N S N N N 31.302 5.847 -1.754 4.799 3.877 -0.067 "C3'" AMP 35 A1EL3 O49 O11 O 0 1 N N N N N N 30.237 5.820 -0.810 4.936 4.866 0.955 "O3'" AMP 36 A1EL3 C35 C17 C 0 1 N N R N N N 31.149 7.017 -2.708 6.117 3.081 -0.230 "C2'" AMP 37 A1EL3 O48 O10 O 0 1 N N N N N N 29.793 7.311 -3.040 7.224 3.809 0.305 "O2'" AMP 38 A1EL3 C36 C18 C 0 1 N N R N N N 31.743 8.156 -1.915 5.832 1.806 0.612 "C1'" AMP 39 A1EL3 N38 N6 N 0 1 Y N N N N N 32.501 9.070 -2.767 6.660 0.689 0.152 N9 AMP 40 A1EL3 C39 C19 C 0 1 Y N N N N N 33.120 8.820 -3.925 6.294 -0.271 -0.744 C8 AMP 41 A1EL3 N40 N7 N 0 1 Y N N N N N 33.721 9.938 -4.385 7.275 -1.106 -0.927 N7 AMP 42 A1EL3 C41 C20 C 0 1 Y N N N N N 33.481 10.912 -3.498 8.330 -0.737 -0.161 C5 AMP 43 A1EL3 C46 C23 C 0 1 Y N N N N N 33.801 12.339 -3.353 9.624 -1.244 0.050 C6 AMP 44 A1EL3 N47 N10 N 0 1 N N N N N N 34.535 12.985 -4.278 10.056 -2.379 -0.613 N6 AMP 45 A1EL3 N45 N9 N 0 1 Y N N N N N 33.336 12.969 -2.265 10.422 -0.607 0.901 N1 AMP 46 A1EL3 C44 C22 C 0 1 Y N N N N N 32.602 12.352 -1.334 10.018 0.477 1.537 C2 AMP 47 A1EL3 N43 N8 N 0 1 Y N N N N N 32.269 11.066 -1.393 8.816 0.987 1.371 N3 AMP 48 A1EL3 C42 C21 C 0 1 Y N N N N N 32.676 10.322 -2.434 7.948 0.419 0.541 C4 AMP 49 A1EL3 H27 H27 H 0 1 N N N N N N 35.724 6.800 8.018 -7.856 5.248 0.166 HN1 SAM 50 A1EL3 H28 H28 H 0 1 N N N N N N 35.362 5.579 6.996 -7.333 4.567 -1.259 HN2 SAM 51 A1EL3 H15 H15 H 0 1 N N N N N N 35.461 8.416 6.269 -9.022 2.889 -1.164 HA SAM 52 A1EL3 H1 H1 H 0 1 N N N N N N 34.404 6.049 4.694 -7.401 3.204 1.402 HB1 SAM 53 A1EL3 H2 H2 H 0 1 N N N N N N 36.086 6.664 4.560 -8.235 1.710 0.911 HB2 SAM 54 A1EL3 H13 H13 H 0 1 N N N N N N 35.200 8.840 3.767 -6.901 1.651 -1.179 HG1 SAM 55 A1EL3 H14 H14 H 0 1 N N N N N N 33.536 8.168 3.843 -6.066 3.145 -0.688 HG2 SAM 56 A1EL3 H10 H10 H 0 1 N N N N N N 34.312 9.171 0.894 -5.498 -1.086 1.166 HE1 SAM 57 A1EL3 H11 H11 H 0 1 N N N N N N 35.988 9.145 1.540 -7.034 -0.253 1.508 HE2 SAM 58 A1EL3 H12 H12 H 0 1 N N N N N N 35.547 8.104 0.144 -6.592 -0.652 -0.170 HE3 SAM 59 A1EL3 H8 H8 H 0 1 N N N N N N 35.722 5.537 3.121 -4.462 0.360 -1.398 "H5'1" SAM 60 A1EL3 H9 H9 H 0 1 N N N N N N 36.825 6.946 2.970 -3.627 1.854 -0.907 "H5'2" SAM 61 A1EL3 H7 H7 H 0 1 N N N N N N 36.737 6.357 0.396 -2.614 0.587 1.023 "H4'" SAM 62 A1EL3 H6 H6 H 0 1 N N N N N N 35.039 4.305 1.202 -2.007 0.321 -1.820 "H3'" SAM 63 A1EL3 H5 H5 H 0 1 N N N N N N 36.636 3.300 2.724 -2.178 -2.022 -1.872 "H2'" SAM 64 A1EL3 H32 H32 H 0 1 N N N N N N 37.540 1.487 1.605 -0.169 -3.027 -1.061 "HO2'" SAM 65 A1EL3 H4 H4 H 0 1 N N N N N N 38.732 3.775 0.568 -1.713 -2.105 1.162 "H1'" SAM 66 A1EL3 H24 H24 H 0 1 N N N N N N 40.764 2.601 1.392 -4.944 -3.159 -0.498 H8 SAM 67 A1EL3 H25 H25 H 0 1 N N N N N N 41.034 2.228 7.623 -4.369 -7.956 -0.411 HN61 SAM 68 A1EL3 H26 H26 H 0 1 N N N N N N 41.239 1.213 6.360 -3.121 -9.021 -0.049 HN62 SAM 69 A1EL3 H3 H3 H 0 1 N N N N N N 37.355 4.385 6.595 0.454 -6.432 1.095 H2 SAM 70 A1EL3 H33 H33 H 0 1 N N N N N N 32.620 7.546 8.307 -11.686 2.980 1.231 H33 SAM 71 A1EL3 H34 H34 H 0 1 N N N N N N 35.243 1.397 -1.685 -0.891 3.270 -0.215 HOP2 AMP 72 A1EL3 H16 H16 H 0 1 N N N N N N 34.681 6.173 -1.352 2.993 2.459 -1.634 "H5'1" AMP 73 A1EL3 H17 H17 H 0 1 N N N N N N 33.671 5.668 -2.749 2.188 3.783 -0.758 "H5'2" AMP 74 A1EL3 H18 H18 H 0 1 N N N N N N 32.481 5.810 0.046 3.377 3.040 1.340 "H4'" AMP 75 A1EL3 H19 H19 H 0 1 N N N N N N 31.416 4.898 -2.298 4.513 4.342 -1.011 "H3'" AMP 76 A1EL3 H36 H36 H 0 1 N N N N N N 30.352 5.082 -0.224 5.576 5.561 0.747 "HO3'" AMP 77 A1EL3 H20 H20 H 0 1 N N N N N N 31.748 6.839 -3.613 6.289 2.826 -1.276 "H2'" AMP 78 A1EL3 H35 H35 H 0 1 N N N N N N 29.425 6.591 -3.539 7.441 4.613 -0.187 "HO2'" AMP 79 A1EL3 H21 H21 H 0 1 N N N N N N 30.942 8.699 -1.392 6.001 2.000 1.671 "H1'" AMP 80 A1EL3 H22 H22 H 0 1 N N N N N N 33.137 7.861 -4.422 5.332 -0.329 -1.232 H8 AMP 81 A1EL3 H30 H30 H 0 1 N N N N N N 34.648 13.941 -4.007 9.464 -2.835 -1.231 HN61 AMP 82 A1EL3 H31 H31 H 0 1 N N N N N N 35.433 12.552 -4.353 10.952 -2.719 -0.459 HN62 AMP 83 A1EL3 H23 H23 H 0 1 N N N N N N 32.261 12.929 -0.488 10.699 0.964 2.220 H2 AMP 84 # 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 A1EL3 N40 C39 DOUB Y N 1 A1EL3 N40 C41 SING Y N 2 A1EL3 N47 C46 SING N N 3 A1EL3 C39 N38 SING Y N 4 A1EL3 C41 C46 DOUB Y N 5 A1EL3 C41 C42 SING Y N 6 A1EL3 C46 N45 SING Y N 7 A1EL3 O48 C35 SING N N 8 A1EL3 O29 P28 DOUB N N 9 A1EL3 N38 C42 SING Y N 10 A1EL3 N38 C36 SING N N 11 A1EL3 C35 C36 SING N N 12 A1EL3 C35 C34 SING N N 13 A1EL3 C42 N43 DOUB Y N 14 A1EL3 N45 C44 DOUB Y N 15 A1EL3 C36 O37 SING N N 16 A1EL3 C34 C33 SING N N 17 A1EL3 C34 O49 SING N N 18 A1EL3 C32 O31 SING N N 19 A1EL3 C32 C33 SING N N 20 A1EL3 P28 O31 SING N N 21 A1EL3 P28 O30 SING N N 22 A1EL3 P28 O27 SING N N 23 A1EL3 N43 C44 SING Y N 24 A1EL3 O37 C33 SING N N 25 A1EL3 O27 C13 SING N N 26 A1EL3 C13 C14 SING N N 27 A1EL3 C13 C12 SING N N 28 A1EL3 O19 C12 SING N N 29 A1EL3 C18 S17 SING N N 30 A1EL3 C14 O15 SING N N 31 A1EL3 C14 C16 SING N N 32 A1EL3 C11 C12 SING N N 33 A1EL3 C11 O15 SING N N 34 A1EL3 C11 N10 SING N N 35 A1EL3 S17 C16 SING N N 36 A1EL3 S17 C20 SING N N 37 A1EL3 C9 N10 SING Y N 38 A1EL3 C9 N8 DOUB Y N 39 A1EL3 N10 C6 SING Y N 40 A1EL3 N8 C7 SING Y N 41 A1EL3 C20 C21 SING N N 42 A1EL3 C6 C7 DOUB Y N 43 A1EL3 C6 N5 SING Y N 44 A1EL3 C7 C2 SING Y N 45 A1EL3 N5 C4 DOUB Y N 46 A1EL3 C21 C22 SING N N 47 A1EL3 C2 N1 SING N N 48 A1EL3 C2 N3 DOUB Y N 49 A1EL3 C4 N3 SING Y N 50 A1EL3 O26 C24 DOUB N N 51 A1EL3 C22 C24 SING N N 52 A1EL3 C22 N23 SING N N 53 A1EL3 C24 O25 SING N N 54 A1EL3 C21 H1 SING N N 55 A1EL3 C21 H2 SING N N 56 A1EL3 C4 H3 SING N N 57 A1EL3 C11 H4 SING N N 58 A1EL3 C12 H5 SING N N 59 A1EL3 C13 H6 SING N N 60 A1EL3 C14 H7 SING N N 61 A1EL3 C16 H8 SING N N 62 A1EL3 C16 H9 SING N N 63 A1EL3 C18 H10 SING N N 64 A1EL3 C18 H11 SING N N 65 A1EL3 C18 H12 SING N N 66 A1EL3 C20 H13 SING N N 67 A1EL3 C20 H14 SING N N 68 A1EL3 C22 H15 SING N N 69 A1EL3 C32 H16 SING N N 70 A1EL3 C32 H17 SING N N 71 A1EL3 C33 H18 SING N N 72 A1EL3 C34 H19 SING N N 73 A1EL3 C35 H20 SING N N 74 A1EL3 C36 H21 SING N N 75 A1EL3 C39 H22 SING N N 76 A1EL3 C44 H23 SING N N 77 A1EL3 C9 H24 SING N N 78 A1EL3 N1 H25 SING N N 79 A1EL3 N1 H26 SING N N 80 A1EL3 N23 H27 SING N N 81 A1EL3 N23 H28 SING N N 82 A1EL3 N47 H30 SING N N 83 A1EL3 N47 H31 SING N N 84 A1EL3 O19 H32 SING N N 85 A1EL3 O25 H33 SING N N 86 A1EL3 O30 H34 SING N N 87 A1EL3 O48 H35 SING N N 88 A1EL3 O49 H36 SING N N 89 # 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 A1EL3 InChI InChI 1.06 "InChI=1S/C25H34N11O11PS/c1-49(3-2-10(26)25(40)41)5-12-18(17(39)24(46-12)36-9-34-14-20(28)30-7-32-22(14)36)47-48(42,43)44-4-11-15(37)16(38)23(45-11)35-8-33-13-19(27)29-6-31-21(13)35/h6-12,15-18,23-24,37-39H,2-5,26H2,1H3,(H5-,27,28,29,30,31,32,40,41,42,43)/p+1/t10-,11+,12+,15+,16+,17+,18+,23+,24+,49+/m0/s1" A1EL3 InChIKey InChI 1.06 AKDVTEPPXUCZRD-YBZFFHRHSA-O A1EL3 SMILES_CANONICAL CACTVS 3.385 "C[S@+](CC[C@H](N)C(O)=O)C[C@H]1O[C@H]([C@H](O)[C@@H]1O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4c(N)ncnc34)n5cnc6c(N)ncnc56" A1EL3 SMILES CACTVS 3.385 "C[S+](CC[CH](N)C(O)=O)C[CH]1O[CH]([CH](O)[CH]1O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)n3cnc4c(N)ncnc34)n5cnc6c(N)ncnc56" A1EL3 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[S@+](CC[C@@H](C(=O)O)N)C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)OP(=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O" A1EL3 SMILES "OpenEye OEToolkits" 2.0.7 "C[S+](CCC(C(=O)O)N)CC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O" # _pdbx_chem_comp_identifier.comp_id A1EL3 _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 "[(2~{S},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-4-oxidanyl-oxolan-2-yl]methyl-[(3~{S})-3-azanyl-4-oxidanyl-4-oxidanylidene-butyl]-methyl-sulfanium" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site A1EL3 "Create component" 2025-02-14 PDBC A1EL3 "Initial release" 2025-11-26 RCSB #