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      ? 
# 
