data_A1AVJ # _chem_comp.id A1AVJ _chem_comp.name "(1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 7-acetamido-2-amino-2,3,7-trideoxy-L-glycero-alpha-D-allo-octopyranoside" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C16 H32 N4 O8" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2024-06-17 _chem_comp.pdbx_modified_date 2025-08-01 _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 408.447 _chem_comp.one_letter_code ? _chem_comp.three_letter_code A1AVJ _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 9C9B _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB _chem_comp.pdbx_pcm Y # 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 A1AVJ C01 C1 C 0 1 N N N N N N -6.253 -4.883 -54.648 -2.878 0.468 3.581 C01 A1AVJ 1 A1AVJ C02 C2 C 0 1 N N N N N N -5.801 -5.773 -55.783 -3.440 0.308 2.192 C02 A1AVJ 2 A1AVJ C05 C3 C 0 1 N N S N N N -4.461 -7.791 -56.490 -3.398 0.792 -0.196 C05 A1AVJ 3 A1AVJ C06 C4 C 0 1 N N N N N N -2.955 -7.878 -56.311 -4.392 1.945 -0.352 C06 A1AVJ 4 A1AVJ C18 C5 C 0 1 N N R N N N -5.068 -9.249 -56.277 -2.303 0.916 -1.257 C18 A1AVJ 5 A1AVJ C20 C6 C 0 1 N N S N N N -6.333 -9.412 -56.762 -1.340 -0.267 -1.135 C20 A1AVJ 6 A1AVJ C22 C7 C 0 1 N N S N N N -7.345 -9.665 -59.007 0.143 -1.361 0.399 C22 A1AVJ 7 A1AVJ C24 C8 C 0 1 N N R N N N -8.522 -7.551 -58.962 2.099 -0.135 -0.248 C24 A1AVJ 8 A1AVJ C25 C9 C 0 1 N N S N N N -9.918 -7.051 -58.518 2.771 0.321 -1.544 C25 A1AVJ 9 A1AVJ C27 C10 C 0 1 N N N N N N -10.197 -5.541 -58.760 3.705 1.496 -1.248 C27 A1AVJ 10 A1AVJ C28 C11 C 0 1 N N R N N N -9.728 -5.042 -60.134 4.775 1.057 -0.246 C28 A1AVJ 11 A1AVJ C30 C12 C 0 1 N N S N N N -8.277 -5.464 -60.375 4.102 0.601 1.051 C30 A1AVJ 12 A1AVJ C32 C13 C 0 1 N N R N N N -8.140 -7.007 -60.348 3.168 -0.574 0.755 C32 A1AVJ 13 A1AVJ C34 C14 C 0 1 N N R N N N -7.581 -11.115 -58.743 -0.552 -2.708 0.186 C34 A1AVJ 14 A1AVJ C36 C15 C 0 1 N N N N N N -7.806 -11.370 -57.385 -1.139 -2.753 -1.228 C36 A1AVJ 15 A1AVJ C37 C16 C 0 1 N N S N N N -6.761 -10.825 -56.489 -2.095 -1.570 -1.410 C37 A1AVJ 16 A1AVJ N04 N1 N 0 1 N N N N N N -4.950 -6.894 -55.487 -2.794 0.846 1.138 N04 A1AVJ 17 A1AVJ N26 N2 N 0 1 N N N N N N -10.082 -7.314 -57.086 1.744 0.742 -2.506 N26 A1AVJ 18 A1AVJ N29 N3 N 0 1 N N N N N N -9.831 -3.580 -60.180 5.672 2.185 0.038 N29 A1AVJ 19 A1AVJ N35 N4 N 0 1 N N N N N N -8.835 -11.546 -59.531 0.423 -3.795 0.348 N35 A1AVJ 20 A1AVJ O03 O1 O 0 1 N N N N N N -6.150 -5.539 -56.910 -4.472 -0.306 2.022 O03 A1AVJ 21 A1AVJ O07 O2 O 0 1 N N N N N N -2.692 -8.466 -55.047 -3.690 3.189 -0.305 O07 A1AVJ 22 A1AVJ O19 O3 O 0 1 N N N N N N -5.039 -9.557 -54.830 -1.585 2.136 -1.061 O19 A1AVJ 23 A1AVJ O21 O4 O 0 1 N N N N N N -6.336 -9.043 -58.117 -0.794 -0.304 0.184 O21 A1AVJ 24 A1AVJ O23 O5 O 0 1 N N N N N N -8.599 -8.982 -58.956 1.227 -1.233 -0.524 O23 A1AVJ 25 A1AVJ O31 O6 O 0 1 N N N N N N -7.817 -5.005 -61.612 5.101 0.192 1.987 O31 A1AVJ 26 A1AVJ O33 O7 O 0 1 N N N N N N -6.803 -7.289 -60.698 2.540 -1.000 1.966 O33 A1AVJ 27 A1AVJ O38 O8 O 0 1 N N N N N N -7.313 -10.886 -55.105 -2.593 -1.561 -2.749 O38 A1AVJ 28 A1AVJ H1 H1 H 0 1 N N N N N N -6.891 -4.079 -55.044 -2.728 1.526 3.793 H1 A1AVJ 29 A1AVJ H2 H2 H 0 1 N N N N N N -6.823 -5.479 -53.920 -3.575 0.047 4.306 H2 A1AVJ 30 A1AVJ H3 H3 H 0 1 N N N N N N -5.374 -4.444 -54.154 -1.924 -0.055 3.650 H3 A1AVJ 31 A1AVJ H4 H4 H 0 1 N N N N N N -4.706 -7.439 -57.503 -3.920 -0.156 -0.321 H4 A1AVJ 32 A1AVJ H5 H5 H 0 1 N N N N N N -2.521 -8.499 -57.108 -4.906 1.854 -1.309 H5 A1AVJ 33 A1AVJ H6 H6 H 0 1 N N N N N N -2.516 -6.870 -56.351 -5.121 1.908 0.457 H6 A1AVJ 34 A1AVJ H7 H7 H 0 1 N N N N N N -4.388 -9.949 -56.785 -2.755 0.915 -2.248 H7 A1AVJ 35 A1AVJ H8 H8 H 0 1 N N N N N N -7.019 -8.749 -56.215 -0.533 -0.155 -1.860 H8 A1AVJ 36 A1AVJ H9 H9 H 0 1 N N N N N N -6.962 -9.585 -60.035 0.526 -1.307 1.418 H9 A1AVJ 37 A1AVJ H10 H10 H 0 1 N N N N N N -7.777 -7.208 -58.229 1.523 0.689 0.173 H10 A1AVJ 38 A1AVJ H11 H11 H 0 1 N N N N N N -10.674 -7.625 -59.074 3.347 -0.504 -1.964 H11 A1AVJ 39 A1AVJ H12 H12 H 0 1 N N N N N N -9.676 -4.962 -57.983 4.184 1.821 -2.172 H12 A1AVJ 40 A1AVJ H13 H13 H 0 1 N N N N N N -11.281 -5.370 -58.679 3.130 2.320 -0.828 H13 A1AVJ 41 A1AVJ H14 H14 H 0 1 N N N N N N -10.365 -5.487 -60.913 5.350 0.233 -0.666 H14 A1AVJ 42 A1AVJ H15 H15 H 0 1 N N N N N N -7.658 -5.052 -59.564 3.527 1.426 1.471 H15 A1AVJ 43 A1AVJ H16 H16 H 0 1 N N N N N N -8.828 -7.431 -61.094 3.744 -1.399 0.334 H16 A1AVJ 44 A1AVJ H17 H17 H 0 1 N N N N N N -6.721 -11.695 -59.108 -1.353 -2.824 0.917 H17 A1AVJ 45 A1AVJ H18 H18 H 0 1 N N N N N N -8.771 -10.922 -57.104 -0.333 -2.687 -1.959 H18 A1AVJ 46 A1AVJ H19 H19 H 0 1 N N N N N N -7.852 -12.460 -57.241 -1.684 -3.687 -1.367 H19 A1AVJ 47 A1AVJ H20 H20 H 0 1 N N N N N N -5.875 -11.475 -56.543 -2.927 -1.663 -0.712 H20 A1AVJ 48 A1AVJ H21 H21 H 0 1 N N N N N N -4.687 -7.055 -54.536 -1.930 1.269 1.263 H21 A1AVJ 49 A1AVJ H22 H22 H 0 1 N N N N N N -10.982 -6.994 -56.789 2.163 1.037 -3.376 H22 A1AVJ 50 A1AVJ H23 H23 H 0 1 N N N N N N -10.005 -8.297 -56.917 1.071 0.007 -2.661 H23 A1AVJ 51 A1AVJ H25 H25 H 0 1 N N N N N N -10.780 -3.307 -60.022 6.128 2.505 -0.803 H25 A1AVJ 52 A1AVJ H26 H26 H 0 1 N N N N N N -9.248 -3.182 -59.472 5.174 2.939 0.488 H26 A1AVJ 53 A1AVJ H28 H28 H 0 1 N N N N N N -9.014 -12.517 -59.369 -0.013 -4.695 0.212 H28 A1AVJ 54 A1AVJ H29 H29 H 0 1 N N N N N N -9.621 -11.007 -59.227 1.206 -3.674 -0.277 H29 A1AVJ 55 A1AVJ H31 H31 H 0 1 N N N N N N -1.753 -8.529 -54.916 -4.259 3.965 -0.398 H31 A1AVJ 56 A1AVJ H32 H32 H 0 1 N N N N N N -4.156 -9.442 -54.499 -1.155 2.205 -0.198 H32 A1AVJ 57 A1AVJ H33 H33 H 0 1 N N N N N N -7.893 -4.059 -61.647 4.746 -0.111 2.834 H33 A1AVJ 58 A1AVJ H34 H34 H 0 1 N N N N N N -6.666 -8.229 -60.696 3.160 -1.293 2.648 H34 A1AVJ 59 A1AVJ H35 H35 H 0 1 N N N N N N -6.672 -10.544 -54.493 -3.083 -2.358 -2.993 H35 A1AVJ 60 # 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 A1AVJ O31 C30 SING N N 1 A1AVJ O33 C32 SING N N 2 A1AVJ C30 C32 SING N N 3 A1AVJ C30 C28 SING N N 4 A1AVJ C32 C24 SING N N 5 A1AVJ N29 C28 SING N N 6 A1AVJ C28 C27 SING N N 7 A1AVJ N35 C34 SING N N 8 A1AVJ C22 O23 SING N N 9 A1AVJ C22 C34 SING N N 10 A1AVJ C22 O21 SING N N 11 A1AVJ C24 O23 SING N N 12 A1AVJ C24 C25 SING N N 13 A1AVJ C27 C25 SING N N 14 A1AVJ C34 C36 SING N N 15 A1AVJ C25 N26 SING N N 16 A1AVJ O21 C20 SING N N 17 A1AVJ C36 C37 SING N N 18 A1AVJ O03 C02 DOUB N N 19 A1AVJ C20 C37 SING N N 20 A1AVJ C20 C18 SING N N 21 A1AVJ C05 C06 SING N N 22 A1AVJ C05 C18 SING N N 23 A1AVJ C05 N04 SING N N 24 A1AVJ C37 O38 SING N N 25 A1AVJ C06 O07 SING N N 26 A1AVJ C18 O19 SING N N 27 A1AVJ C02 N04 SING N N 28 A1AVJ C02 C01 SING N N 29 A1AVJ C01 H1 SING N N 30 A1AVJ C01 H2 SING N N 31 A1AVJ C01 H3 SING N N 32 A1AVJ C05 H4 SING N N 33 A1AVJ C06 H5 SING N N 34 A1AVJ C06 H6 SING N N 35 A1AVJ C18 H7 SING N N 36 A1AVJ C20 H8 SING N N 37 A1AVJ C22 H9 SING N N 38 A1AVJ C24 H10 SING N N 39 A1AVJ C25 H11 SING N N 40 A1AVJ C27 H12 SING N N 41 A1AVJ C27 H13 SING N N 42 A1AVJ C28 H14 SING N N 43 A1AVJ C30 H15 SING N N 44 A1AVJ C32 H16 SING N N 45 A1AVJ C34 H17 SING N N 46 A1AVJ C36 H18 SING N N 47 A1AVJ C36 H19 SING N N 48 A1AVJ C37 H20 SING N N 49 A1AVJ N04 H21 SING N N 50 A1AVJ N26 H22 SING N N 51 A1AVJ N26 H23 SING N N 52 A1AVJ N29 H25 SING N N 53 A1AVJ N29 H26 SING N N 54 A1AVJ N35 H28 SING N N 55 A1AVJ N35 H29 SING N N 56 A1AVJ O07 H31 SING N N 57 A1AVJ O19 H32 SING N N 58 A1AVJ O31 H33 SING N N 59 A1AVJ O33 H34 SING N N 60 A1AVJ O38 H35 SING N N 61 # 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 A1AVJ SMILES ACDLabs 12.01 "CC(=O)NC(CO)C(O)C1OC(OC2C(O)C(O)C(N)CC2N)C(N)CC1O" A1AVJ InChI InChI 1.06 "InChI=1S/C16H32N4O8/c1-5(22)20-9(4-21)12(25)15-10(23)3-8(19)16(28-15)27-14-7(18)2-6(17)11(24)13(14)26/h6-16,21,23-26H,2-4,17-19H2,1H3,(H,20,22)/t6-,7+,8-,9+,10+,11+,12-,13-,14-,15+,16+/m1/s1" A1AVJ InChIKey InChI 1.06 MJGXTLDNWXSQPF-JBBPOTEGSA-N A1AVJ SMILES_CANONICAL CACTVS 3.385 "CC(=O)N[C@@H](CO)[C@@H](O)[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H](O)[C@H]2O)[C@H](N)C[C@@H]1O" A1AVJ SMILES CACTVS 3.385 "CC(=O)N[CH](CO)[CH](O)[CH]1O[CH](O[CH]2[CH](N)C[CH](N)[CH](O)[CH]2O)[CH](N)C[CH]1O" A1AVJ SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(=O)N[C@@H](CO)[C@H]([C@@H]1[C@H](C[C@H]([C@H](O1)O[C@@H]2[C@H](C[C@H]([C@@H]([C@H]2O)O)N)N)N)O)O" A1AVJ SMILES "OpenEye OEToolkits" 2.0.7 "CC(=O)NC(CO)C(C1C(CC(C(O1)OC2C(CC(C(C2O)O)N)N)N)O)O" # loop_ _pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier A1AVJ "SYSTEMATIC NAME" ACDLabs 12.01 "(1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl 7-acetamido-2-amino-2,3,7-trideoxy-L-glycero-alpha-D-allo-octopyranoside" A1AVJ "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "~{N}-[(1~{R},2~{S})-1-[(2~{S},3~{S},5~{R},6~{S})-5-azanyl-6-[(1~{R},2~{R},3~{S},4~{R},6~{S})-4,6-bis(azanyl)-2,3-bis(oxidanyl)cyclohexyl]oxy-3-oxidanyl-oxan-2-yl]-1,3-bis(oxidanyl)propan-2-yl]ethanamide" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site A1AVJ "Create component" 2024-06-17 RCSB A1AVJ "Modify PCM" 2024-09-27 PDBE A1AVJ "Initial release" 2025-08-06 RCSB # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id A1AVJ _pdbx_chem_comp_pcm.modified_residue_id LYS _pdbx_chem_comp_pcm.type None _pdbx_chem_comp_pcm.category "Covalent chemical modification" _pdbx_chem_comp_pcm.position "Amino-acid side chain" _pdbx_chem_comp_pcm.polypeptide_position "Any position" _pdbx_chem_comp_pcm.comp_id_linking_atom C06 _pdbx_chem_comp_pcm.modified_residue_id_linking_atom NZ _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #