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class=\"affinity-chip__prefix\">pK<sub>d</sub></span>= 8.15","pkd":8.1549,"pkd_display":null,"measure_type":"Kd","bg_color":"#abc675","text_color":"#1A2433"},"raw":{"PDB code":"4U26","lowest_resolution_PDB_id":"4U26","Structure_method":"X-RAY DIFFRACTION","Resolution_A":"2.80 Å","Ligand_Name":"DOL","Ligand_auth_chain":"BA","Ligand_Res_Num":3001,"RNA_auth_chains (interacting)":"BA","identifier_entry_id":1,"identifier_all_entries_json":"{\"1\":{\"ligand_name\":\"DOL\",\"ligand_chain\":\"BA\",\"ligand_res_num\":\"3001\",\"rna_chains\":[\"BA\"]},\"2\":{\"ligand_name\":\"DOL\",\"ligand_chain\":\"DA\",\"ligand_res_num\":\"3001\",\"rna_chains\":[\"DA\"]}}","identifier_entry_json":"{\"1\":{\"ligand_name\":\"DOL\",\"ligand_chain\":\"BA\",\"ligand_res_num\":\"3001\",\"rna_chains\":[\"BA\"]}}","mean_occupancy":1.0,"mean_pocket_B_factor":5.7502,"Affinity Data":"7 ± 5 nM","Affinity (in Molar)":"Kd = 7 × 10⁻⁹ M ± 5 × 10⁻⁹ M","pKd":"8.1549 ± 0.3102","Kd determination 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\"O7\"]","num_rings":0,"aromatic_ring_atoms":"[]","logP":1.7856,"Charge":"neutral","RNA_sequence":"GUCAAGAUGGUAAGGGCCCACGGUGGAUGCCUCGGCACCCGAGCCGAUGAAGGACGUGGCUACCUGCGAUAAGCCAGGGGGAGCCGGUAGCGGGCGUGGAUCCCUGGAUGUCCGAAUGGGGGAACCCGGCCGGCGGGAACGCCGGUCACCGCGCUUUUGCGCGGGGGGAACCUGGGGAACUGAAACAUCUCAGUACCCAGAGGAGAGGAAAGAGAAAUCGACUCCCUGAGUAGCGGCGAGCGAAAGGGGACCAGCCUAAACCGUCCGGCUUGUCCGGGCGGGGUCGUGGGGCCCUCGGACACCGAAUCCCCAGCCUAGCCGAAGCUGUUGGGAAGCAGCGCCAGAGAGGGUGAAAGCCCCGUAGGCGAAAGGUGGGGGGAUAGGUGAGGGUACCCGAGUACCCCGUGGUUCGUGGAGCCAUGGGGGAAUCUGGGCGGACCACCGCCUAAGGCUAAGUACUCCGGGUGACCGAUAGCGCACCAGUACCGUGAGGGAAAGGUGAAAAGAACCCCGGGAGGGGAGUGAAAUAGAGCCUGAAACCGUGGGCUUACAAGCAGUCACGGCCCCGCAAGGGGUUGUGGCGUGCCUAUUGAAGCAUGAGCCGGCGACUCACGGUCGUGGGCGAGCUUAAGCCGUUGAGGCGGAGGCGUAGGGAAACCGAGUCCGAACAGGGCGCAAGCGGGCCGCACGCGGCCCGCAAAGUCCGCGGCCGUGGACCCGAAACCGGGCGAGCUAGCCCUGGCCAGGGUGAAGCUGGGGUGAGACCCAGUGGAGGCCCGAACCGGUGGGGGAUGCAAACCCCUCGGAUGAGCUGGGGCUAGGAGUGAAAAGCUAACCGAGCCCGGAGAUAGCUGGUUCUCCCCGAAAUGACUUUAGGGUCAGCCUCAGGCGCUGACUGGGGCCUGUAGAGCACUGAUAGGGCUAGGGGGCCCACCAGCCUACCAAACCCUGUCAAACUCCGAAGGGUCCCAGGUGGAGCCUGGGAGUGAGGGCGCGAGCGAUAACGUCCGCGUCCGAGCGCGGGAACAACCGAGACCGCCAGCUAAGGCCCCCAAGUCUGGGCUAAGUGGUAAAGGAUGUGGCGCCGCGAAGACAGCCAGGAGGUUGGCUUAGAAGCAGCCAUCCUUUAAAGAGUGCGUAAUAGCUCACUGGUCGAGUGGCGCCGCGCCGAAAAUGAUCGGGGCUUAAGCCCAGCGCCGAAGCUGCGGGUCUGGGGGAUGACCCCAGGCGGUAGGGGAGCGUUCCCGAUGCCGAUGAAGGCCGACCCGCGAGGGCGGCUGGAGGUAAGGGAAGUGCGAAUGCCGGCAUGAGUAACGAUAAAGAGGGUGAGAAUCCCUCUCGCCGUAAGCCCAAGGGUUCCUACGCAAUGGUCGUCAGCGUAGGGUUAGGCGGGACCUAAGGUGAAGCCGAAAGGCGUAGCCGAAGGGCAGCCGGUUAAUAUUCCGGCCCUUCCCGCAGGUGCGAUGGGGGGACGCUCUAGGCUAGGGGGACCGGAGCCAUGGACGAGCCCGGCCAGAAGCGCAGGGUGGGAGGUAGGCAAAUCCGCCUCCCAACAAGCUCUGCGUGGUGGGGAAGCCCGUACGGGUGACAACCCCCCGAAGCCAGGGAGCCAAGAAAAGCCUCUAAGCACAACCUGCGGGAACCCGUACCGCAAACCGACACAGGUGGGCGGGUGCAAGAGCACUCAGGCGCGCGGGAGAACCCUCGCCAAGGAACUCUGCAAGUUGGCCCCGUAACUUCGGGAGAAGGGGUGCUCCCUGGGGUGAUGAGCCCCGGGGAGCCGCAGUGAACAGGCUCUGGCGACUGUUUACCAAAAACACAGCUCUCUGCGAACUCGUAAGAGGAGGUAUAGGGAGCGACGCUUGCCCGGUGCCGGAAGGUCAAGGGGAGGGGUGCAAGCCCCGAACCGAAGCCCCGGUGAACGGCGGCCGUAACUAUAACGGUCCUAAGGUAGCGAAAUUCCUUGUCGGGUAAGUUCCGACCUGCACGAAAAGCGUAACGACCGGAGCGCUGUCUCGGCGAGGGACCCGGUGAAAUUGAACUGGCCGUGAAGAUGCGGCCUACCCGUGGCAGGACGAAAAGACCCCGUGGAGCUUUACUGCAGCCUGGUGUUGGCUCUUGGUCGCGCCUGCGUAGGAUAGGUGGGAGCCUGUGAACCCCCGCCUCCGGGUGGGGGGGAGGCGCCGGUGAAAUACCACCCUGGCGCGGCUGGGGGCCUAACCCUCGGAUGGGGGGACAGCGCUUGGCGGGCAGUUUGACUGGGGCGGUCGCCUCCUAAAAGGUAACGGAGGCGCCCAAAGGUCCCCUCAGGCGGGACGGAAAUCCGCCGGAGAGCGCAAGGGUAGAAGGGGGCCUGACUGCGAGGCCUGCAAGCCGAGCAGGGGCGAAAGCCGGGCCUAGUGAACCGGUGGUCCCGUGUGGAAGGGCCAUCGAUCAACGGAUAAAAGUUACCCCGGGGAUAACAGGCUGAUCUCCCCCGAGCGUCCACAGCGGCGGGGAGGUUUGGCACCUCGAUGUCGGCUCGUCGCAUCCUGGGGCUGAAGAAGGUCCCAAGGGUUGGGCUGUUCGCCCAUUAAAGCGGCACGCGAGCUGGGUUCAGAACGUCGUGAGACAGUUCGGUCUCUAUCCGCCACGGGCGCAGGAGGCUUGAGGGGGGCUCUUCCUAGUACGAGAGGACCGGAAGGGACGCACCUCUGGUUUCCCAGCUGUCCCUCCAGGGGCAUAAGCUGGGUAGCCAUGUGCGGAAGGGAUAACCGCUGAAAGCAUCUAAGCGGGAAGCCCGCCCCAAGAUGAGGCCUCCCACGGCGUCAAGCCGGUAAGGACCCGGGAAGACCACCCGGUGGAUGGGCCGGGGGUGUAAGCGCCGCGAGGCGUUGAGCCGACCGGUCCCAAUCGUCCGAGGUCUUGACCCCUCC|UUGUUGGAGAGUUUGAUCCUGGCUCAGGGUGAACGCUGGCGGCGUGCCUAAGACAUGCAAGUCGUGCGGGCCGCGGGGUUUUACUCCGUGGUCAGCGGCGGACGGGUGAGUAACGCGUGGGUGACCUACCCGGAAGAGGGGGACAACCCGGGGAAACUCGGGCUAAUCCCCCAUGUGGACCCGCCCCUUGGGGUGUGUCCAAAGGGCUUUGCCCGCUUCCGGAUGGGCCCGCGUCCCAUCAGCUAGUUGGUGGGGUAAUGGCCCACCAAGGCGACGACGGGUAGCCGGUCUGAGAGGAUGGCCGGCCACAGGGGCACUGAGACACGGGCCCCACUCCUACGGGAGGCAGCAGUUAGGAAUCUUCCGCAAUGGGCGCAAGCCUGACGGAGCGACGCCGCUUGGAGGAAGAAGCCCUUCGGGGUGUAAACUCCUGAACCCGGGACGAAACCCCCGACGAGGGGACUGACGGUACCGGGGUAAUAGCGCCGGCCAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGCGCGAGCGUUACCCGGAUUCACUGGGCGUAAAGGGCGUGUAGGCGGCCUGGGGCGUCCCAUGUGAAAGACCACGGCUCAACCGUGGGGGAGCGUGGGAUACGCUCAGGCUAGACGGUGGGAGAGGGUGGUGGAAUUCCCGGAGUAGCGGUGAAAUGCGCAGAUACCGGGAGGAACGCCGAUGGCGAAGGCAGCCACCUGGUCCACCCGUGACGCUGAGGCGCGAAAGCGUGGGGAGCAAACCGGAUUAGAUACCCGGGUAGUCCACGCCCUAAACGAUGCGCGCUAGGUCUCUGGGUCUCCUGGGGGCCGAAGCUAACGCGUUAAGCGCGCCGCCUGGGGAGUACGGCCGCAAGGCUGAAACUCAAAGGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAAGCAACGCGAAGAACCUUACCAGGCCUUGACAUGCUAGGGAACCCGGGUGAAAGCCUGGGGUGCCCCGCGAGGGGAGCCCUAGCACAGGUGCUGCAUGGCCGUCGUCAGCUCGUGCCGUGAGGUGUUGGGUUAAGUCCCGCAACGAGCGCAACCCCCGCCGUUAGUUGCCAGCGGUUCGGCCGGGCACUCUAACGGGACUGCCCGCGAAAGCGGGAGGAAGGAGGGGACGACGUCUGGUCAGCAUGGCCCUUACGGCCUGGGCGACACACGUGCUACAAUGCCCACUACAAAGCGAUGCCACCCGGCAACGGGGAGCUAAUCGCAAAAAGGUGGGCCCAGUUCGGAUUGGGGUCUGCAACCCGACCCCAUGAAGCCGGAAUCGCUAGUAAUCGCGGAUCAGCCAUGCCGCGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACGCCAUGGGAGCGGGCUCUACCCGAAGUCGCCGGGAGCCUACGGGCAGGCGCCGAGGGUAGGGCCCGUGACUGGGGCGAAGUCGUAACAAGGUAGCUGUACCGGAAGGUGCGGCUGGAUCACCUCCUUUCU","RNA_length":29151521,"RNA_class":"Ribosome 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0":null,"Ligand_Chain":null,"Affinity_type(Kd | Kd_apparent | Kd_macroscopic | Kd_cooperative)":"Kd","pkd":null,"stoichiometry (e.g. 2:1 (N=1.74±0.02)":null,"Mg2+":"10 mM MgCl2","Primary DOI":null,"kd_reference-DOI":" https://doi.org/10.1038/s41467-023-39653-5","Multiple_kd":null,"Remarks_student":null,"structre title":"Crystal structure of the Thermus thermophilus 70S ribosome in complex with protein Y, hygromycin A, and erythromycin at 2.50A resolution","pKd_value":7.991,"pKd_std":0.2531,"QED":0.2396,"pocket_contact_details":null,"pkd.1":null,"Remarks_full":null}},{"entry_id":"9B00_A1AIX_4085_competition-binding-assay","rna_id":"6d7af1bda4ddf9c6-2915","ligand_id":"UZHFALJZQVUPGZ-AYWVHJORSA-O|a1aix","pdb_id":"9B00","pdb_id_extended":"pdb_00009b00","rna_class":"Ribosome (full)","rna_name":"23S Ribosomal RNA | 16S Ribosomal RNA","rna_display":"Ribosome 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7.05","pkd":7.0458,"pkd_display":null,"measure_type":"Kd_apparent","bg_color":"#e4d784","text_color":"#1A2433"},"raw":{"PDB code":"9B00","lowest_resolution_PDB_id":"9B00","Structure_method":"X-RAY DIFFRACTION","Resolution_A":"2.80 Å","Ligand_Name":"A1AIX","Ligand_auth_chain":"1A","Ligand_Res_Num":4085,"RNA_auth_chains (interacting)":"1A","identifier_entry_id":1,"identifier_all_entries_json":"{\"1\":{\"ligand_name\":\"A1AIX\",\"ligand_chain\":\"1A\",\"ligand_res_num\":\"4085\",\"rna_chains\":[\"1A\",\"1w\",\"1x\"]},\"3\":{\"ligand_name\":\"A1AIX\",\"ligand_chain\":\"2A\",\"ligand_res_num\":\"3851\",\"rna_chains\":[\"2A\",\"2w\",\"2x\"]}}","identifier_entry_json":"{\"1\":{\"ligand_name\":\"A1AIX\",\"ligand_chain\":\"1A\",\"ligand_res_num\":\"4085\",\"rna_chains\":[\"1A\"]}}","mean_occupancy":1.0,"mean_pocket_B_factor":36.0947,"Affinity Data":"0.09 ± 0.01 µM","Affinity (in Molar)":"Kd = 9 × 10⁻⁸ M ± 1 × 10⁻⁸ M","pKd":"7.0458 ± 0.0483","Kd determination method":"Competition-binding 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\"NBQ-H28\", \"OAC-H29\", \"OBM-73\"]","HBA_atoms":"[\"NBK\", \"OAG\", \"OAQ\", \"OAR\", \"OBL\", \"OBN\", \"OBO\", \"NAI\"]","num_rings":3,"aromatic_ring_atoms":"[[\"CAF\", \"CAH\", \"CAJ\", \"CAK\", \"CAL\", \"CAM\", \"CAN\", \"CAO\", \"CAP\", \"NAI\"], [\"CAU\", \"CAV\", \"CAY\", \"CAZ\", \"CBA\", \"CBB\"], [\"CBE\", \"CBF\", \"CBG\", \"CBH\", \"CBI\", 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Since the available PDB/crystal structure contains only the ribosomal RNA and ligand, without the nascent peptide, a single Kd value cannot be assigned.","notes":null,"ligand_evaluation":null,"reference_doi":"https://doi.org/10.1016/s0022-2836(03)00668-5","deposition_year":null,"structure_method":"X-RAY DIFFRACTION","resolution":"3.00 Å","protein_contact":"no","protein_contact_residues":[],"ligand_type":"organic","alt_copies":null,"alt_copies_items":[],"related_pdbs":null,"related_pdb_items":[],"smiles":"c1cc(ccc1C(C(CO)NC(=O)C(Cl)Cl)O)[N+](=O)[O-]","ligand_code":"CLM","structure_path":"structures/1nji.cif","viewer_structure_path":"structures/1nji.cif","structure_format":"cif","structure_image_url":"https://cdn.rcsb.org/images/structures/1nji_assembly-1.jpeg","ligand_image_url":"https://cdn.rcsb.org/images/ccd/unlabeled/C/CLM.svg","combined_ligand_pdb_id":null,"chip":{"label":"5.23–5.82","text":"pK_d= 5.23–5.82","text_html":"<span class=\"affinity-chip__prefix\">pK<sub>d</sub></span>= 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