data_J13 # _chem_comp.id J13 _chem_comp.name "(1S,2R,3R,4S,6S)-6-[(8-azidooctanoyl)amino]-2,3,4-trihydroxycyclohexane-1-carboxylate" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C15 H26 N4 O7" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2016-03-22 _chem_comp.pdbx_modified_date 2024-09-27 _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 374.390 _chem_comp.one_letter_code ? _chem_comp.three_letter_code J13 _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 5G0M _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI _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_backbone_atom_flag _chem_comp_atom.pdbx_n_terminal_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 J13 C1 C1 C 0 1 N N R N N N 41.083 10.153 21.802 -2.985 -0.170 0.996 C1 J13 1 J13 O1 O1 O 0 1 N N N N N N 39.380 12.245 22.977 -0.418 0.163 1.750 O1 J13 2 J13 C2 C2 C 0 1 N N S N N N 40.392 9.125 20.913 -3.418 1.288 1.160 C2 J13 3 J13 C3 C3 C 0 1 N N S N N N 41.147 9.094 19.549 -3.808 1.861 -0.205 C3 J13 4 J13 C4 C4 C 0 1 N N S N N N 42.620 8.681 19.699 -4.965 1.047 -0.787 C4 J13 5 J13 C5 C5 C 0 1 N N R N N N 43.338 9.695 20.608 -4.532 -0.411 -0.951 C5 J13 6 J13 C6 C6 C 0 1 N N S N N N 42.605 9.853 21.971 -4.142 -0.983 0.413 C6 J13 7 J13 N7 N7 N 0 1 N N N N N N 40.690 11.462 21.237 -1.835 -0.239 0.090 N7 J13 8 J13 C9 C9 C 0 1 N N N N N N 39.884 12.379 21.856 -0.588 -0.057 0.569 C9 J13 9 J13 C10 C10 C 0 1 N N N N N N 39.601 13.672 21.095 0.595 -0.128 -0.362 C10 J13 10 J13 C11 C11 C 0 1 N N N N N N 39.917 14.923 21.918 1.882 0.112 0.430 C11 J13 11 J13 C12 C12 C 0 1 N N N N N N 38.694 15.466 22.698 3.083 0.040 -0.516 C12 J13 12 J13 C13 C13 C 0 1 N N N N N N 38.069 16.738 22.109 4.370 0.279 0.276 C13 J13 13 J13 C14 C14 C 0 1 N N N N N N 39.093 17.866 21.879 5.571 0.207 -0.670 C14 J13 14 J13 C15 C15 C 0 1 N N N N N N 38.537 19.239 22.238 6.858 0.447 0.122 C15 J13 15 J13 C16 C16 C 0 1 N N N N N N 37.372 19.703 21.350 8.059 0.375 -0.823 C16 J13 16 J13 N17 N17 N 0 1 N N N N N N 37.879 20.737 20.439 9.292 0.604 -0.066 N17 J13 17 J13 N18 N18 N 1 1 N N N N N N 37.973 21.935 20.729 10.090 -0.187 -0.038 N18 J13 18 J13 N19 N19 N -1 1 N N N N N N 38.065 23.043 20.975 10.887 -0.978 -0.010 N19 J13 19 J13 C20 C20 C 0 1 N N N N N N 43.356 10.943 22.686 -3.715 -2.420 0.251 C20 J13 20 J13 O21 O21 O 0 1 N N N N N N 44.157 10.627 23.600 -2.600 -2.758 0.570 O21 J13 21 J13 O22 O22 O 0 1 N N N N N N 43.223 12.134 22.246 -4.574 -3.323 -0.246 O22 J13 22 J13 O23 O23 O 0 1 N N N N N N 44.712 9.270 20.833 -5.613 -1.171 -1.496 O23 J13 23 J13 O24 O24 O 0 1 N N N N N N 43.325 8.652 18.463 -5.329 1.582 -2.062 O24 J13 24 J13 O25 O25 O 0 1 N N N N N N 40.356 8.356 18.620 -4.213 3.223 -0.052 O25 J13 25 J13 H1 H1 H 0 1 N N N N N N 40.632 10.072 22.802 -2.707 -0.578 1.967 H1 J13 26 J13 H12 H12 H 0 1 N N N N N N 39.372 9.487 20.714 -2.593 1.868 1.575 H12 J13 27 J13 H3 H3 H 0 1 N N N N N N 41.164 10.137 19.199 -2.952 1.810 -0.878 H3 J13 28 J13 H4 H4 H 0 1 N N N N N N 42.659 7.692 20.180 -5.821 1.099 -0.114 H4 J13 29 J13 H5 H5 H 0 1 N N N N N N 43.336 10.673 20.104 -3.676 -0.462 -1.625 H5 J13 30 J13 H6 H6 H 0 1 N N N N N N 42.712 8.914 22.534 -4.997 -0.932 1.086 H6 J13 31 J13 HN7 HN7 H 0 1 N N N N N N 41.041 11.696 20.330 -1.971 -0.415 -0.854 HN7 J13 32 J13 H110 H110 H 0 0 N N N N N N 40.217 13.686 20.183 0.632 -1.113 -0.827 H110 J13 33 J13 H210 H210 H 0 0 N N N N N N 38.536 13.692 20.819 0.495 0.635 -1.134 H210 J13 34 J13 H111 H111 H 0 0 N N N N N N 40.710 14.676 22.639 1.844 1.096 0.895 H111 J13 35 J13 H211 H211 H 0 0 N N N N N N 40.274 15.709 21.236 1.981 -0.652 1.202 H211 J13 36 J13 H112 H112 H 0 0 N N N N N N 37.923 14.682 22.715 3.120 -0.946 -0.981 H112 J13 37 J13 H212 H212 H 0 0 N N N N N N 39.015 15.687 23.727 2.984 0.803 -1.288 H212 J13 38 J13 H113 H113 H 0 0 N N N N N N 37.297 17.102 22.803 4.332 1.264 0.741 H113 J13 39 J13 H213 H213 H 0 0 N N N N N N 37.605 16.485 21.144 4.469 -0.484 1.048 H213 J13 40 J13 H114 H114 H 0 0 N N N N N N 39.979 17.670 22.501 5.608 -0.778 -1.135 H114 J13 41 J13 H214 H214 H 0 0 N N N N N N 39.383 17.869 20.818 5.472 0.970 -1.442 H214 J13 42 J13 H115 H115 H 0 0 N N N N N N 39.351 19.974 22.150 6.820 1.432 0.587 H115 J13 43 J13 H215 H215 H 0 0 N N N N N N 38.184 19.206 23.279 6.957 -0.316 0.894 H215 J13 44 J13 H116 H116 H 0 0 N N N N N N 36.568 20.118 21.976 8.097 -0.610 -1.289 H116 J13 45 J13 H216 H216 H 0 0 N N N N N N 36.983 18.853 20.770 7.960 1.138 -1.596 H216 J13 46 J13 HO23 HO23 H 0 0 N N N N N N 45.151 9.899 21.394 -5.913 -0.863 -2.362 HO23 J13 47 J13 HO24 HO24 H 0 0 N N N N N N 44.225 8.391 18.618 -5.615 2.506 -2.033 HO24 J13 48 J13 HO25 HO25 H 0 0 N N N N N N 39.470 8.700 18.614 -4.474 3.651 -0.878 HO25 J13 49 J13 HO22 HO22 H 0 0 N N N N N N 43.813 12.713 22.714 -4.255 -4.232 -0.331 HO22 J13 50 J13 O2 O2 O 0 1 N Y N N N N 40.311 7.911 21.682 -4.539 1.355 2.043 O2 J13 51 J13 HO2 HO2 H 0 1 N N N N N N 39.827 8.075 22.483 -4.868 2.252 2.193 HO2 J13 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 J13 O24 C4 SING N N 1 J13 O25 C3 SING N N 2 J13 C3 C4 SING N N 3 J13 C3 C2 SING N N 4 J13 C4 C5 SING N N 5 J13 N17 N18 DOUB N N 6 J13 N17 C16 SING N N 7 J13 C5 O23 SING N N 8 J13 C5 C6 SING N N 9 J13 N18 N19 DOUB N N 10 J13 C2 C1 SING N N 11 J13 C10 C9 SING N N 12 J13 C10 C11 SING N N 13 J13 N7 C1 SING N N 14 J13 N7 C9 SING N N 15 J13 C16 C15 SING N N 16 J13 C1 C6 SING N N 17 J13 C9 O1 DOUB N N 18 J13 C14 C13 SING N N 19 J13 C14 C15 SING N N 20 J13 C11 C12 SING N N 21 J13 C6 C20 SING N N 22 J13 C13 C12 SING N N 23 J13 O22 C20 SING N N 24 J13 C20 O21 DOUB N N 25 J13 C1 H1 SING N N 26 J13 C2 H12 SING N N 27 J13 C3 H3 SING N N 28 J13 C4 H4 SING N N 29 J13 C5 H5 SING N N 30 J13 C6 H6 SING N N 31 J13 N7 HN7 SING N N 32 J13 C10 H110 SING N N 33 J13 C10 H210 SING N N 34 J13 C11 H111 SING N N 35 J13 C11 H211 SING N N 36 J13 C12 H112 SING N N 37 J13 C12 H212 SING N N 38 J13 C13 H113 SING N N 39 J13 C13 H213 SING N N 40 J13 C14 H114 SING N N 41 J13 C14 H214 SING N N 42 J13 C15 H115 SING N N 43 J13 C15 H215 SING N N 44 J13 C16 H116 SING N N 45 J13 C16 H216 SING N N 46 J13 O23 HO23 SING N N 47 J13 O24 HO24 SING N N 48 J13 O25 HO25 SING N N 49 J13 O22 HO22 SING N N 50 J13 C2 O2 SING N N 51 J13 O2 HO2 SING N N 52 # 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 J13 SMILES ACDLabs 12.01 "C1(C(C(C(C(C1)O)O)O)C(=O)[O-])NC(=O)CCCCCCCN=[N+]=[N-]" J13 InChI InChI 1.03 "InChI=1S/C15H26N4O7/c16-19-17-7-5-3-1-2-4-6-8(20)18-10-9(15(25)26)11(21)13(23)14(24)12(10)22/h9-14,21-24H,1-7H2,(H,18,20)(H,25,26)/t9-,10+,11+,12-,13-,14-/m0/s1" J13 InChIKey InChI 1.03 BTDXZNFDEBZDRR-KTEZLCCFSA-N J13 SMILES_CANONICAL CACTVS 3.385 "O[C@@H]1[C@@H](O)[C@H](O)[C@H]([C@@H](NC(=O)CCCCCCCN=[N+]=[N-])[C@@H]1O)C(O)=O" J13 SMILES CACTVS 3.385 "O[CH]1[CH](O)[CH](O)[CH]([CH](NC(=O)CCCCCCCN=[N+]=[N-])[CH]1O)C(O)=O" J13 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C(CCCC(=O)N[C@@H]1[C@@H]([C@H]([C@@H]([C@H]([C@H]1O)O)O)O)C(=O)O)CCCN=[N+]=[N-]" J13 SMILES "OpenEye OEToolkits" 1.7.6 "C(CCCC(=O)NC1C(C(C(C(C1O)O)O)O)C(=O)O)CCCN=[N+]=[N-]" # 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 J13 "SYSTEMATIC NAME" ACDLabs 12.01 "(1S,2R,3R,4S,6S)-6-[(8-azidooctanoyl)amino]-2,3,4-trihydroxycyclohexane-1-carboxylate" J13 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(1S,2R,3S,4S,5S,6R)-2-(8-azidooctanoylamino)-3,4,5,6-tetrakis(oxidanyl)cyclohexane-1-carboxylic 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 J13 "Create component" 2016-03-22 EBI J13 "Initial release" 2017-04-12 RCSB J13 "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id J13 _pdbx_chem_comp_pcm.modified_residue_id GLU _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 C2 _pdbx_chem_comp_pcm.modified_residue_id_linking_atom OE2 _pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ? _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #