data_A1EL1 # _chem_comp.id A1EL1 _chem_comp.name "(2~{S},5~{S})-6-[(2~{R},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]-2,5-bis(azanyl)hexanoic acid" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C25 H35 N12 O11 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2025-02-13 _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 710.593 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1EL1 _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 9LQH _chem_comp.pdbx_subcomponent_list "SFG 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 A1EL1 N26 N4 N 0 1 N N N N N N 8.758 -19.725 -37.854 -6.285 -5.966 0.223 N SFG 1 A1EL1 C22 C12 C 0 1 N N S N N N 7.721 -20.775 -37.872 -7.221 -4.857 -0.003 CA SFG 2 A1EL1 C23 C13 C 0 1 N N N N N N 6.391 -20.125 -38.136 -8.351 -5.326 -0.884 C SFG 3 A1EL1 O24 O4 O 0 1 N N N N N N 5.339 -20.891 -38.408 -8.214 -6.311 -1.569 O SFG 4 A1EL1 O25 O5 O 0 1 N N N N N N 6.270 -18.903 -38.129 -9.509 -4.648 -0.906 OXT SFG 5 A1EL1 C21 C11 C 0 1 N N N N N N 7.712 -21.622 -36.584 -6.487 -3.702 -0.687 CB SFG 6 A1EL1 C20 C10 C 0 1 N N N N N N 7.192 -20.879 -35.347 -5.421 -3.145 0.259 CG SFG 7 A1EL1 C19 C9 C 0 1 N N S N N N 7.472 -21.641 -34.040 -4.687 -1.989 -0.425 CD SFG 8 A1EL1 N49 N10 N 0 1 N N N N N N 8.899 -21.502 -33.665 -3.948 -2.497 -1.588 NE SFG 9 A1EL1 C18 C8 C 0 1 N N N N N N 7.092 -23.115 -34.176 -3.708 -1.351 0.563 "C5'" SFG 10 A1EL1 C16 C7 C 0 1 N N R N N N 7.035 -23.897 -32.858 -3.066 -0.120 -0.079 "C4'" SFG 11 A1EL1 O17 O3 O 0 1 N N N N N N 8.082 -23.538 -31.951 -4.039 0.937 -0.224 "O4'" SFG 12 A1EL1 C14 C6 C 0 1 N N S N N N 5.791 -23.658 -32.035 -1.982 0.468 0.852 "C3'" SFG 13 A1EL1 O15 O2 O 0 1 N N N N N N 4.656 -24.292 -32.606 -0.683 0.028 0.448 "O3'" SFG 14 A1EL1 C12 C5 C 0 1 N N R N N N 6.191 -24.205 -30.684 -2.117 1.996 0.669 "C2'" SFG 15 A1EL1 O13 O1 O 0 1 N N N N N N 6.118 -25.636 -30.677 -0.907 2.547 0.146 "O2'" SFG 16 A1EL1 C11 C4 C 0 1 N N R N N N 7.657 -23.808 -30.619 -3.267 2.151 -0.351 "C1'" SFG 17 A1EL1 N10 N3 N 0 1 Y N N N N N 7.772 -22.578 -29.801 -4.091 3.316 -0.019 N9 SFG 18 A1EL1 C9 C25 C 0 1 Y N N N N N 7.484 -21.325 -30.198 -5.203 3.319 0.770 C8 SFG 19 A1EL1 N8 N12 N 0 1 Y N N N N N 7.683 -20.439 -29.186 -5.686 4.525 0.852 N7 SFG 20 A1EL1 C7 C24 C 0 1 Y N N N N N 8.111 -21.147 -28.125 -4.916 5.370 0.125 C5 SFG 21 A1EL1 C2 C1 C 0 1 Y N N N N N 8.506 -20.844 -26.751 -4.948 6.748 -0.149 C6 SFG 22 A1EL1 N1 N2 N 0 1 N N N N N N 8.477 -19.571 -26.292 -5.941 7.552 0.382 N6 SFG 23 A1EL1 N3 N1 N 0 1 Y N N N N N 8.893 -21.862 -25.958 -4.002 7.260 -0.930 N1 SFG 24 A1EL1 C4 C2 C 0 1 Y N N N N N 8.914 -23.133 -26.408 -3.051 6.500 -1.441 C2 SFG 25 A1EL1 N5 N11 N 0 1 Y N N N N N 8.574 -23.488 -27.655 -2.981 5.206 -1.211 N3 SFG 26 A1EL1 C6 C3 C 0 1 Y N N N N N 8.166 -22.549 -28.531 -3.880 4.605 -0.438 C4 SFG 27 A1EL1 P27 P1 P 0 1 N N N N N N 3.425 -23.353 -33.037 0.293 -0.820 1.407 P AMP 28 A1EL1 O29 O7 O 0 1 N N N N N N 3.821 -22.457 -34.286 -0.413 -2.032 1.881 O1P AMP 29 A1EL1 O28 O6 O 0 1 N N N N N N 2.927 -22.592 -31.873 0.720 0.081 2.671 O2P AMP 30 A1EL1 O30 O8 O 0 1 N N N N N N 2.271 -24.380 -33.479 1.609 -1.252 0.586 "O5'" AMP 31 A1EL1 C31 C14 C 0 1 N N N N N N 2.165 -24.782 -34.845 2.620 -2.104 1.129 "C5'" AMP 32 A1EL1 C32 C15 C 0 1 N N R N N N 1.340 -26.062 -34.898 3.724 -2.311 0.090 "C4'" AMP 33 A1EL1 O38 O11 O 0 1 N N N N N N 2.176 -27.167 -34.535 4.408 -1.070 -0.150 "O4'" AMP 34 A1EL1 C33 C16 C 0 1 N N S N N N 0.196 -26.083 -33.893 4.766 -3.312 0.625 "C3'" AMP 35 A1EL1 O34 O9 O 0 1 N N N N N N -1.023 -25.576 -34.439 4.849 -4.453 -0.232 "O3'" AMP 36 A1EL1 C35 C17 C 0 1 N N R N N N 0.071 -27.547 -33.544 6.096 -2.522 0.606 "C2'" AMP 37 A1EL1 O36 O10 O 0 1 N N N N N N -0.668 -28.232 -34.559 7.172 -3.345 0.150 "O2'" AMP 38 A1EL1 C37 C18 C 0 1 N N R N N N 1.504 -28.013 -33.604 5.790 -1.395 -0.412 "C1'" AMP 39 A1EL1 N39 N5 N 0 1 Y N N N N N 2.170 -27.861 -32.290 6.648 -0.232 -0.169 N9 AMP 40 A1EL1 C40 C19 C 0 1 Y N N N N N 3.201 -27.032 -32.045 6.363 0.826 0.641 C8 AMP 41 A1EL1 N41 N6 N 0 1 Y N N N N N 3.603 -27.145 -30.755 7.346 1.677 0.624 N7 AMP 42 A1EL1 C42 C20 C 0 1 Y N N N N N 2.822 -28.061 -30.164 8.323 1.221 -0.196 C5 AMP 43 A1EL1 C47 C23 C 0 1 Y N N N N N 2.721 -28.655 -28.817 9.583 1.701 -0.595 C6 AMP 44 A1EL1 N48 N9 N 0 1 N N N N N N 3.555 -28.267 -27.818 10.065 2.906 -0.117 N6 AMP 45 A1EL1 N46 N8 N 0 1 Y N N N N N 1.767 -29.596 -28.622 10.299 0.969 -1.442 N1 AMP 46 A1EL1 C45 C22 C 0 1 Y N N N N N 0.941 -29.984 -29.610 9.847 -0.183 -1.903 C2 AMP 47 A1EL1 N44 N7 N 0 1 Y N N N N N 0.976 -29.491 -30.856 8.674 -0.671 -1.558 N3 AMP 48 A1EL1 C43 C21 C 0 1 Y N N N N N 1.880 -28.539 -31.185 7.890 -0.012 -0.711 C4 AMP 49 A1EL1 H25 H25 H 0 1 N N N N N N 9.651 -20.140 -37.679 -6.728 -6.717 0.731 HN1 SFG 50 A1EL1 H26 H26 H 0 1 N N N N N N 8.775 -19.258 -38.738 -5.899 -6.298 -0.649 HN2 SFG 51 A1EL1 H13 H13 H 0 1 N N N N N N 7.936 -21.454 -38.710 -7.621 -4.519 0.953 HA SFG 52 A1EL1 H34 H34 H 0 1 N N N N N N 5.372 -18.672 -38.335 -10.205 -4.986 -1.487 HXT SFG 53 A1EL1 H11 H11 H 0 1 N N N N N N 7.072 -22.500 -36.753 -6.012 -4.062 -1.599 HB1 SFG 54 A1EL1 H12 H12 H 0 1 N N N N N N 8.741 -21.952 -36.381 -7.200 -2.915 -0.934 HB2 SFG 55 A1EL1 H9 H9 H 0 1 N N N N N N 7.683 -19.896 -35.294 -5.896 -2.784 1.171 HG1 SFG 56 A1EL1 H10 H10 H 0 1 N N N N N N 6.105 -20.741 -35.449 -4.708 -3.931 0.507 HG2 SFG 57 A1EL1 H8 H8 H 0 1 N N N N N N 6.852 -21.198 -33.247 -5.411 -1.242 -0.752 HD SFG 58 A1EL1 H30 H30 H 0 1 N N N N N N 9.071 -22.000 -32.815 -3.271 -3.192 -1.310 HNE1 SFG 59 A1EL1 H31 H31 H 0 1 N N N N N N 9.473 -21.877 -34.393 -4.579 -2.866 -2.284 HNE2 SFG 60 A1EL1 H6 H6 H 0 1 N N N N N N 6.100 -23.169 -34.647 -4.243 -1.054 1.465 "H5'1" SFG 61 A1EL1 H7 H7 H 0 1 N N N N N N 7.834 -23.599 -34.828 -2.932 -2.072 0.822 "H5'2" SFG 62 A1EL1 H5 H5 H 0 1 N N N N N N 7.100 -24.970 -33.091 -2.636 -0.378 -1.046 "H4'" SFG 63 A1EL1 H4 H4 H 0 1 N N N N N N 5.620 -22.575 -31.948 -2.175 0.189 1.888 "H3'" SFG 64 A1EL1 H3 H3 H 0 1 N N N N N N 5.611 -23.743 -29.871 -2.376 2.473 1.614 "H2'" SFG 65 A1EL1 H33 H33 H 0 1 N N N N N N 6.372 -25.962 -29.822 -0.937 3.504 0.011 "HO2'" SFG 66 A1EL1 H2 H2 H 0 1 N N N N N N 8.245 -24.623 -30.171 -2.869 2.243 -1.362 "H1'" SFG 67 A1EL1 H22 H22 H 0 1 N N N N N N 7.141 -21.059 -31.187 -5.622 2.449 1.253 H8 SFG 68 A1EL1 H23 H23 H 0 1 N N N N N N 8.774 -19.554 -25.337 -6.625 7.167 0.950 HN61 SFG 69 A1EL1 H24 H24 H 0 1 N N N N N N 9.090 -19.004 -26.842 -5.952 8.502 0.185 HN62 SFG 70 A1EL1 H1 H1 H 0 1 N N N N N N 9.223 -23.910 -25.724 -2.302 6.957 -2.070 H2 SFG 71 A1EL1 H35 H35 H 0 1 N N N N N N 2.928 -21.664 -32.077 1.189 0.893 2.434 HOP2 AMP 72 A1EL1 H14 H14 H 0 1 N N N N N N 3.167 -24.967 -35.258 3.043 -1.642 2.021 "H5'1" AMP 73 A1EL1 H15 H15 H 0 1 N N N N N N 1.668 -23.993 -35.428 2.182 -3.067 1.391 "H5'2" AMP 74 A1EL1 H16 H16 H 0 1 N N N N N N 0.938 -26.196 -35.913 3.293 -2.682 -0.840 "H4'" AMP 75 A1EL1 H17 H17 H 0 1 N N N N N N 0.487 -25.515 -32.997 4.516 -3.616 1.642 "H3'" AMP 76 A1EL1 H36 H36 H 0 1 N N N N N N -1.704 -25.609 -33.778 5.491 -5.116 0.057 "HO3'" AMP 77 A1EL1 H18 H18 H 0 1 N N N N N N -0.356 -27.686 -32.540 6.317 -2.108 1.590 "H2'" AMP 78 A1EL1 H37 H37 H 0 1 N N N N N N -0.742 -29.151 -34.332 7.342 -4.115 0.709 "HO2'" AMP 79 A1EL1 H19 H19 H 0 1 N N N N N N 1.541 -29.063 -33.929 5.913 -1.757 -1.434 "H1'" AMP 80 A1EL1 H20 H20 H 0 1 N N N N N N 3.646 -26.370 -32.773 5.454 0.940 1.214 H8 AMP 81 A1EL1 H28 H28 H 0 1 N N N N N N 3.337 -28.775 -26.985 9.533 3.431 0.501 HN61 AMP 82 A1EL1 H29 H29 H 0 1 N N N N N N 4.501 -28.452 -28.083 10.936 3.227 -0.400 HN62 AMP 83 A1EL1 H21 H21 H 0 1 N N N N N N 0.203 -30.740 -29.385 10.462 -0.745 -2.590 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 A1EL1 O24 C23 DOUB N N 1 A1EL1 C23 O25 SING N N 2 A1EL1 C23 C22 SING N N 3 A1EL1 C22 N26 SING N N 4 A1EL1 C22 C21 SING N N 5 A1EL1 C21 C20 SING N N 6 A1EL1 C20 C19 SING N N 7 A1EL1 C32 C31 SING N N 8 A1EL1 C32 O38 SING N N 9 A1EL1 C32 C33 SING N N 10 A1EL1 C31 O30 SING N N 11 A1EL1 O36 C35 SING N N 12 A1EL1 O38 C37 SING N N 13 A1EL1 O34 C33 SING N N 14 A1EL1 O29 P27 DOUB N N 15 A1EL1 C18 C19 SING N N 16 A1EL1 C18 C16 SING N N 17 A1EL1 C19 N49 SING N N 18 A1EL1 C33 C35 SING N N 19 A1EL1 C37 C35 SING N N 20 A1EL1 C37 N39 SING N N 21 A1EL1 O30 P27 SING N N 22 A1EL1 P27 O15 SING N N 23 A1EL1 P27 O28 SING N N 24 A1EL1 C16 C14 SING N N 25 A1EL1 C16 O17 SING N N 26 A1EL1 O15 C14 SING N N 27 A1EL1 N39 C40 SING Y N 28 A1EL1 N39 C43 SING Y N 29 A1EL1 C40 N41 DOUB Y N 30 A1EL1 C14 C12 SING N N 31 A1EL1 O17 C11 SING N N 32 A1EL1 C43 N44 DOUB Y N 33 A1EL1 C43 C42 SING Y N 34 A1EL1 N44 C45 SING Y N 35 A1EL1 N41 C42 SING Y N 36 A1EL1 C12 O13 SING N N 37 A1EL1 C12 C11 SING N N 38 A1EL1 C11 N10 SING N N 39 A1EL1 C9 N10 SING Y N 40 A1EL1 C9 N8 DOUB Y N 41 A1EL1 C42 C47 DOUB Y N 42 A1EL1 N10 C6 SING Y N 43 A1EL1 C45 N46 DOUB Y N 44 A1EL1 N8 C7 SING Y N 45 A1EL1 C47 N46 SING Y N 46 A1EL1 C47 N48 SING N N 47 A1EL1 C6 C7 DOUB Y N 48 A1EL1 C6 N5 SING Y N 49 A1EL1 C7 C2 SING Y N 50 A1EL1 N5 C4 DOUB Y N 51 A1EL1 C2 N1 SING N N 52 A1EL1 C2 N3 DOUB Y N 53 A1EL1 C4 N3 SING Y N 54 A1EL1 C4 H1 SING N N 55 A1EL1 C11 H2 SING N N 56 A1EL1 C12 H3 SING N N 57 A1EL1 C14 H4 SING N N 58 A1EL1 C16 H5 SING N N 59 A1EL1 C18 H6 SING N N 60 A1EL1 C18 H7 SING N N 61 A1EL1 C19 H8 SING N N 62 A1EL1 C20 H9 SING N N 63 A1EL1 C20 H10 SING N N 64 A1EL1 C21 H11 SING N N 65 A1EL1 C21 H12 SING N N 66 A1EL1 C22 H13 SING N N 67 A1EL1 C31 H14 SING N N 68 A1EL1 C31 H15 SING N N 69 A1EL1 C32 H16 SING N N 70 A1EL1 C33 H17 SING N N 71 A1EL1 C35 H18 SING N N 72 A1EL1 C37 H19 SING N N 73 A1EL1 C40 H20 SING N N 74 A1EL1 C45 H21 SING N N 75 A1EL1 C9 H22 SING N N 76 A1EL1 N1 H23 SING N N 77 A1EL1 N1 H24 SING N N 78 A1EL1 N26 H25 SING N N 79 A1EL1 N26 H26 SING N N 80 A1EL1 N48 H28 SING N N 81 A1EL1 N48 H29 SING N N 82 A1EL1 N49 H30 SING N N 83 A1EL1 N49 H31 SING N N 84 A1EL1 O13 H33 SING N N 85 A1EL1 O25 H34 SING N N 86 A1EL1 O28 H35 SING N N 87 A1EL1 O34 H36 SING N N 88 A1EL1 O36 H37 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 A1EL1 InChI InChI 1.06 "InChI=1S/C25H35N12O11P/c26-9(1-2-10(27)25(41)42)3-11-18(17(40)24(46-11)37-8-35-14-20(29)31-6-33-22(14)37)48-49(43,44)45-4-12-15(38)16(39)23(47-12)36-7-34-13-19(28)30-5-32-21(13)36/h5-12,15-18,23-24,38-40H,1-4,26-27H2,(H,41,42)(H,43,44)(H2,28,30,32)(H2,29,31,33)/t9-,10-,11+,12+,15+,16+,17+,18+,23+,24+/m0/s1" A1EL1 InChIKey InChI 1.06 XNBPELUUEBZQEC-PYTRVWNWSA-N A1EL1 SMILES_CANONICAL CACTVS 3.385 "N[C@@H](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" A1EL1 SMILES CACTVS 3.385 "N[CH](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" A1EL1 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O[C@@H]4[C@H](O[C@H]([C@@H]4O)n5cnc6c5ncnc6N)C[C@H](CC[C@@H](C(=O)O)N)N)O)O)N" A1EL1 SMILES "OpenEye OEToolkits" 2.0.7 "c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OC4C(OC(C4O)n5cnc6c5ncnc6N)CC(CCC(C(=O)O)N)N)O)O)N" # _pdbx_chem_comp_identifier.comp_id A1EL1 _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},5~{S})-6-[(2~{R},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]-2,5-bis(azanyl)hexanoic 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 A1EL1 "Create component" 2025-02-13 PDBC A1EL1 "Initial release" 2025-11-26 RCSB #