data_A1JLN # _chem_comp.id A1JLN _chem_comp.name "[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] 3-azanyl-4-oxidanyl-benzoate" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C17 H19 N6 O9 P" _chem_comp.mon_nstd_parent_comp_id AMP _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2025-07-29 _chem_comp.pdbx_modified_date 2026-03-13 _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 482.341 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1JLN _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 9S45 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE _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 A1JLN N2 N1 N 0 1 N N N N N N 70.725 2.636 4.585 9.105 1.255 -0.365 N2 A1JLN 1 A1JLN C1 C1 C 0 1 Y N N N N N 71.024 2.678 3.250 7.778 1.303 0.078 C1 A1JLN 2 A1JLN C7 C2 C 0 1 Y N N N N N 69.978 2.652 2.311 6.846 0.417 -0.432 C7 A1JLN 3 A1JLN C3 C3 C 0 1 Y N N N N N 70.278 2.678 0.970 5.522 0.468 0.013 C3 A1JLN 4 A1JLN C9 C4 C 0 1 N N N N N N 69.158 2.609 0.002 4.524 -0.474 -0.526 C9 A1JLN 5 A1JLN O1 O1 O 0 1 N N N N N N 69.540 2.496 -1.126 4.853 -1.296 -1.358 O1 A1JLN 6 A1JLN O1P O2 O 0 1 N N N N N N 67.951 2.430 0.584 3.248 -0.424 -0.096 O1P A1JLN 7 A1JLN P P1 P 0 1 N N N N N N 66.645 1.550 0.151 2.220 -1.486 -0.733 P A1JLN 8 A1JLN O2P O3 O 0 1 N N N N N N 65.699 2.388 -0.624 2.746 -2.856 -0.544 O2P A1JLN 9 A1JLN O3P O4 O 0 1 N N N N N N 66.134 0.749 1.276 2.048 -1.190 -2.306 O3P A1JLN 10 A1JLN "O5'" O5 O 0 1 N N N N N N 67.196 0.497 -1.071 0.791 -1.354 -0.003 "O5'" A1JLN 11 A1JLN "C5'" C5 C 0 1 N N N N N N 67.654 -0.844 -0.754 -0.305 -2.231 -0.271 "C5'" A1JLN 12 A1JLN "C4'" C6 C 0 1 N N R N N N 68.052 -1.592 -2.011 -1.504 -1.828 0.589 "C4'" A1JLN 13 A1JLN "O4'" O6 O 0 1 N N N N N N 68.851 -0.726 -2.849 -2.043 -0.566 0.140 "O4'" A1JLN 14 A1JLN "C1'" C7 C 0 1 N N R N N N 69.844 -1.490 -3.543 -3.395 -0.528 0.647 "C1'" A1JLN 15 A1JLN N9 N2 N 0 1 Y N N N N N 71.184 -0.975 -3.253 -4.200 0.428 -0.117 N9 A1JLN 16 A1JLN C8 C8 C 0 1 Y N N N N N 71.517 0.136 -2.514 -3.923 0.897 -1.367 C8 A1JLN 17 A1JLN N7 N3 N 0 1 Y N N N N N 72.808 0.413 -2.508 -4.848 1.732 -1.743 N7 A1JLN 18 A1JLN C5 C9 C 0 1 Y N N N N N 73.356 -0.568 -3.318 -5.774 1.851 -0.761 C5 A1JLN 19 A1JLN C6 C10 C 0 1 Y N N N N N 74.675 -0.813 -3.721 -6.962 2.586 -0.607 C6 A1JLN 20 A1JLN N6 N4 N 0 1 N N N N N N 75.708 -0.043 -3.384 -7.412 3.425 -1.612 N6 A1JLN 21 A1JLN N1 N5 N 0 1 Y N N N N N 74.889 -1.892 -4.513 -7.644 2.457 0.526 N1 A1JLN 22 A1JLN C2 C11 C 0 1 Y N N N N N 73.846 -2.649 -4.883 -7.223 1.659 1.491 C2 A1JLN 23 A1JLN N3 N6 N 0 1 Y N N N N N 72.559 -2.485 -4.597 -6.117 0.952 1.390 N3 A1JLN 24 A1JLN C4 C12 C 0 1 Y N N N N N 72.369 -1.419 -3.798 -5.372 1.012 0.291 C4 A1JLN 25 A1JLN "C2'" C13 C 0 1 N N R N N N 69.623 -2.954 -3.192 -3.932 -1.963 0.447 "C2'" A1JLN 26 A1JLN "O2'" O7 O 0 1 N N N N N N 68.821 -3.557 -4.202 -4.767 -2.342 1.543 "O2'" A1JLN 27 A1JLN "C3'" C14 C 0 1 N N S N N N 68.960 -2.810 -1.820 -2.659 -2.838 0.408 "C3'" A1JLN 28 A1JLN "O3'" O8 O 0 1 N N N N N N 68.394 -4.098 -1.709 -2.669 -3.784 1.479 "O3'" A1JLN 29 A1JLN C15 C15 C 0 1 Y N N N N N 71.613 2.735 0.545 5.146 1.414 0.970 C15 A1JLN 30 A1JLN C16 C16 C 0 1 Y N N N N N 72.648 2.780 1.451 6.079 2.294 1.474 C16 A1JLN 31 A1JLN C17 C17 C 0 1 Y N N N N N 72.368 2.734 2.821 7.395 2.241 1.038 C17 A1JLN 32 A1JLN O9 O9 O 0 1 N N N N N N 73.355 2.778 3.753 8.311 3.110 1.538 O9 A1JLN 33 A1JLN H1 H1 H 0 1 N N N N N N 71.571 2.662 5.118 9.371 0.600 -1.030 H1 A1JLN 34 A1JLN H4 H2 H 0 1 N N N N N N 70.157 3.423 4.824 9.757 1.879 -0.011 H4 A1JLN 35 A1JLN H3 H3 H 0 1 N N N N N N 68.950 2.612 2.640 7.141 -0.312 -1.172 H3 A1JLN 36 A1JLN HOP3 H4 H 0 0 N N N N N N 65.198 0.885 1.363 1.706 -0.307 -2.505 HOP3 A1JLN 37 A1JLN "H5'1" H5 H 0 0 N N N N N N 66.844 -1.392 -0.251 -0.574 -2.163 -1.325 "H5'1" A1JLN 38 A1JLN "H5'2" H6 H 0 0 N N N N N N 68.524 -0.778 -0.084 -0.016 -3.256 -0.035 "H5'2" A1JLN 39 A1JLN "H4'" H7 H 0 1 N N N N N N 67.144 -1.904 -2.547 -1.214 -1.767 1.638 "H4'" A1JLN 40 A1JLN "H1'" H8 H 0 1 N N N N N N 69.668 -1.385 -4.624 -3.398 -0.266 1.705 "H1'" A1JLN 41 A1JLN H8 H9 H 0 1 N N N N N N 70.786 0.730 -1.985 -3.064 0.618 -1.958 H8 A1JLN 42 A1JLN HN61 H10 H 0 0 N N N N N N 76.543 -0.406 -3.797 -6.905 3.510 -2.435 HN61 A1JLN 43 A1JLN HN62 H11 H 0 0 N N N N N N 75.551 0.888 -3.713 -8.233 3.927 -1.493 HN62 A1JLN 44 A1JLN H2 H12 H 0 1 N N N N N N 74.084 -3.506 -5.495 -7.805 1.587 2.398 H2 A1JLN 45 A1JLN "H2'" H13 H 0 1 N N N N N N 70.591 -3.466 -3.088 -4.477 -2.039 -0.493 "H2'" A1JLN 46 A1JLN "HO2'" H14 H 0 0 N N N N N N 68.679 -4.472 -3.990 -5.131 -3.235 1.470 "HO2'" A1JLN 47 A1JLN "H3'" H15 H 0 1 N N N N N N 69.714 -2.614 -1.044 -2.575 -3.347 -0.552 "H3'" A1JLN 48 A1JLN "HO3'" H16 H 0 0 N N N N N N 67.932 -4.171 -0.882 -3.375 -4.442 1.416 "HO3'" A1JLN 49 A1JLN H17 H17 H 0 1 N N N N N N 71.833 2.744 -0.512 4.123 1.456 1.316 H17 A1JLN 50 A1JLN H18 H18 H 0 1 N N N N N N 73.669 2.850 1.107 5.786 3.025 2.214 H18 A1JLN 51 A1JLN H19 H19 H 0 1 N N N N N N 72.973 2.736 4.622 8.767 2.790 2.329 H19 A1JLN 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 A1JLN C2 N3 DOUB Y N 1 A1JLN C2 N1 SING Y N 2 A1JLN N3 C4 SING Y N 3 A1JLN N1 C6 DOUB Y N 4 A1JLN "O2'" "C2'" SING N N 5 A1JLN C4 C5 DOUB Y N 6 A1JLN C4 N9 SING Y N 7 A1JLN C6 N6 SING N N 8 A1JLN C6 C5 SING Y N 9 A1JLN "C1'" N9 SING N N 10 A1JLN "C1'" "C2'" SING N N 11 A1JLN "C1'" "O4'" SING N N 12 A1JLN C5 N7 SING Y N 13 A1JLN N9 C8 SING Y N 14 A1JLN "C2'" "C3'" SING N N 15 A1JLN "O4'" "C4'" SING N N 16 A1JLN C8 N7 DOUB Y N 17 A1JLN "C4'" "C3'" SING N N 18 A1JLN "C4'" "C5'" SING N N 19 A1JLN "C3'" "O3'" SING N N 20 A1JLN O1 C9 DOUB N N 21 A1JLN "O5'" "C5'" SING N N 22 A1JLN "O5'" P SING N N 23 A1JLN O2P P DOUB N N 24 A1JLN C9 O1P SING N N 25 A1JLN C9 C3 SING N N 26 A1JLN P O1P SING N N 27 A1JLN P O3P SING N N 28 A1JLN C15 C3 DOUB Y N 29 A1JLN C15 C16 SING Y N 30 A1JLN C3 C7 SING Y N 31 A1JLN C16 C17 DOUB Y N 32 A1JLN C7 C1 DOUB Y N 33 A1JLN C17 C1 SING Y N 34 A1JLN C17 O9 SING N N 35 A1JLN C1 N2 SING N N 36 A1JLN N2 H1 SING N N 37 A1JLN N2 H4 SING N N 38 A1JLN C7 H3 SING N N 39 A1JLN O3P HOP3 SING N N 40 A1JLN "C5'" "H5'1" SING N N 41 A1JLN "C5'" "H5'2" SING N N 42 A1JLN "C4'" "H4'" SING N N 43 A1JLN "C1'" "H1'" SING N N 44 A1JLN C8 H8 SING N N 45 A1JLN N6 HN61 SING N N 46 A1JLN N6 HN62 SING N N 47 A1JLN C2 H2 SING N N 48 A1JLN "C2'" "H2'" SING N N 49 A1JLN "O2'" "HO2'" SING N N 50 A1JLN "C3'" "H3'" SING N N 51 A1JLN "O3'" "HO3'" SING N N 52 A1JLN C15 H17 SING N N 53 A1JLN C16 H18 SING N N 54 A1JLN O9 H19 SING N N 55 # 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 A1JLN InChI InChI 1.06 "InChI=1S/C17H19N6O9P/c18-8-3-7(1-2-9(8)24)17(27)32-33(28,29)30-4-10-12(25)13(26)16(31-10)23-6-22-11-14(19)20-5-21-15(11)23/h1-3,5-6,10,12-13,16,24-26H,4,18H2,(H,28,29)(H2,19,20,21)/t10-,12-,13-,16-/m1/s1" A1JLN InChIKey InChI 1.06 RAKNJTPSSKGACV-XNIJJKJLSA-N A1JLN SMILES_CANONICAL CACTVS 3.385 "Nc1cc(ccc1O)C(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4c(N)ncnc34" A1JLN SMILES CACTVS 3.385 "Nc1cc(ccc1O)C(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)n3cnc4c(N)ncnc34" A1JLN SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1cc(c(cc1C(=O)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O)N)O" A1JLN SMILES "OpenEye OEToolkits" 2.0.7 "c1cc(c(cc1C(=O)OP(=O)(O)OCC2C(C(C(O2)n3cnc4c3ncnc4N)O)O)N)O" # _pdbx_chem_comp_identifier.comp_id A1JLN _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~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] 3-azanyl-4-oxidanyl-benzoate" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site A1JLN "Create component" 2025-07-29 PDBE A1JLN "Modify parent residue" 2025-11-04 PDBE A1JLN "Initial release" 2026-03-18 RCSB #