data_VDE
# 
_chem_comp.id                                    VDE 
_chem_comp.name                                  "(2S)-2-azanyl-6-[4-[(2S)-2,3-bis(azanyl)-3-oxidanylidene-propyl]-1,2,3-triazol-1-yl]hexanoic acid" 
_chem_comp.type                                  "peptide linking" 
_chem_comp.pdbx_type                             ATOMP 
_chem_comp.formula                               "C11 H20 N6 O3" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2021-05-06 
_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                        284.315 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     VDE 
_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        7OFJ 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
_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 
VDE CA   C15  C 0 1 N N S Y N N -43.862 23.759 -22.098 5.583  -0.336 -0.385 C15  VDE 1  
VDE C17  C17  C 0 1 N N N N N N -44.757 24.827 -21.434 4.231  0.248  0.029  C17  VDE 2  
VDE C20  C20  C 0 1 N N N N N N -46.961 25.352 -22.767 0.640  -1.066 -0.420 C20  VDE 3  
VDE C24  C24  C 0 1 Y N N N N N -46.936 29.180 -22.787 -2.685 0.240  -0.069 C24  VDE 4  
VDE C    C14  C 0 1 N N N Y N Y -42.493 24.036 -21.440 6.676  0.653  -0.071 C14  VDE 5  
VDE C18  C18  C 0 1 N N N N N N -46.066 24.258 -20.710 3.112  -0.701 -0.403 C18  VDE 6  
VDE C19  C19  C 0 1 N N N N N N -47.330 25.105 -21.198 1.760  -0.117 0.012  C19  VDE 7  
VDE C25  C25  C 0 1 Y N N N N N -46.516 27.798 -22.308 -1.704 -0.276 -0.846 C25  VDE 8  
VDE C70  C70  C 0 1 N N S N N N -45.921 30.530 -20.675 -5.116 -0.062 0.320  C70  VDE 9  
VDE C71  C71  C 0 1 N N N N N N -46.468 30.602 -22.170 -4.060 0.664  -0.517 C71  VDE 10 
VDE C72  C72  C 0 1 N N N N N N -45.011 29.293 -20.784 -6.485 0.453  -0.043 C72  VDE 11 
VDE N    N1   N 0 1 N N N Y Y N -44.266 22.429 -21.782 5.825  -1.583 0.353  N1   VDE 12 
VDE N21  N21  N 0 1 Y N N N N N -47.100 26.853 -23.069 -0.655 -0.507 -0.023 N21  VDE 13 
VDE N22  N22  N 0 1 Y N N N N N -47.917 27.552 -23.980 -0.989 -0.150 1.167  N22  VDE 14 
VDE N23  N23  N 0 1 Y N N N N N -47.821 28.919 -23.832 -2.196 0.294  1.175  N23  VDE 15 
VDE N2   N2   N 0 1 N N N N N N -44.982 31.622 -20.556 -5.047 -1.504 0.050  N2   VDE 16 
VDE N3   N3   N 0 1 N N N N N N -44.945 28.204 -19.797 -6.926 1.617  0.473  N3   VDE 17 
VDE O    O1   O 0 1 N N N Y N Y -42.292 23.876 -20.276 7.344  0.518  0.926  O1   VDE 18 
VDE O2   O2   O 0 1 N N N N N N -44.447 29.060 -21.843 -7.190 -0.181 -0.799 O2   VDE 19 
VDE HA   H151 H 0 0 N N N Y N N -43.806 23.928 -23.183 5.577  -0.543 -1.456 H151 VDE 20 
VDE H172 H172 H 0 0 N N N N N N -44.154 25.357 -20.682 4.205  0.372  1.112  H172 VDE 21 
VDE H171 H171 H 0 0 N N N N N N -45.078 25.535 -22.212 4.091  1.217  -0.451 H171 VDE 22 
VDE H202 H202 H 0 0 N N N N N N -47.650 24.780 -23.405 0.666  -1.190 -1.503 H202 VDE 23 
VDE H201 H201 H 0 0 N N N N N N -45.928 25.028 -22.961 0.780  -2.035 0.060  H201 VDE 24 
VDE H182 H182 H 0 0 N N N N N N -46.205 23.199 -20.975 3.138  -0.825 -1.485 H182 VDE 25 
VDE H181 H181 H 0 0 N N N N N N -45.956 24.352 -19.620 3.251  -1.670 0.077  H181 VDE 26 
VDE H192 H192 H 0 0 N N N N N N -47.415 26.055 -20.650 1.620  0.852  -0.468 H192 VDE 27 
VDE H191 H191 H 0 0 N N N N N N -48.264 24.534 -21.089 1.734  0.007  1.094  H191 VDE 28 
VDE H251 H251 H 0 0 N N N N N N -45.849 27.604 -21.481 -1.750 -0.467 -1.908 H251 VDE 29 
VDE H701 H701 H 0 0 N N N N N N -46.708 30.465 -19.909 -4.928 0.119  1.378  H701 VDE 30 
VDE H711 H711 H 0 0 N N N N N N -45.669 31.006 -22.808 -4.169 1.741  -0.385 H711 VDE 31 
VDE H712 H712 H 0 0 N N N N N N -47.331 31.284 -22.187 -4.194 0.412  -1.569 H712 VDE 32 
VDE H    H161 H 0 0 N N N Y Y N -45.153 22.240 -22.204 5.835  -1.418 1.348  H161 VDE 33 
VDE H2   H162 H 0 0 N N N Y Y N -43.587 21.783 -22.130 5.142  -2.285 0.110  H162 VDE 34 
VDE H21  H21  H 0 1 N N N N N N -44.599 31.633 -19.633 -5.690 -2.013 0.638  H21  VDE 35 
VDE H22  H22  H 0 1 N Y N N N N -44.245 31.502 -21.221 -5.218 -1.698 -0.925 H22  VDE 36 
VDE H32  H32  H 0 1 N N N N N N -44.464 27.356 -20.020 -6.362 2.124  1.078  H32  VDE 37 
VDE H31  H31  H 0 1 N N N N N N -45.381 28.312 -18.903 -7.807 1.948  0.240  H31  VDE 38 
VDE OXT  OXT  O 0 1 N Y N Y N Y -41.364 24.538 -22.184 6.905  1.685  -0.898 OXT  VDE 39 
VDE HXT  HXT  H 0 1 N Y N Y N Y -40.627 24.660 -21.598 7.617  2.293  -0.655 HXT  VDE 40 
# 
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 
VDE N22 N23  DOUB Y N 1  
VDE N22 N21  SING Y N 2  
VDE N23 C24  SING Y N 3  
VDE N21 C20  SING N N 4  
VDE N21 C25  SING Y N 5  
VDE C24 C25  DOUB Y N 6  
VDE C24 C71  SING N N 7  
VDE C20 C19  SING N N 8  
VDE C71 C70  SING N N 9  
VDE CA  N    SING N N 10 
VDE CA  C    SING N N 11 
VDE CA  C17  SING N N 12 
VDE O2  C72  DOUB N N 13 
VDE C   O    DOUB N N 14 
VDE C17 C18  SING N N 15 
VDE C19 C18  SING N N 16 
VDE C72 C70  SING N N 17 
VDE C72 N3   SING N N 18 
VDE C70 N2   SING N N 19 
VDE CA  HA   SING N N 20 
VDE C17 H172 SING N N 21 
VDE C17 H171 SING N N 22 
VDE C20 H202 SING N N 23 
VDE C20 H201 SING N N 24 
VDE C18 H182 SING N N 25 
VDE C18 H181 SING N N 26 
VDE C19 H192 SING N N 27 
VDE C19 H191 SING N N 28 
VDE C25 H251 SING N N 29 
VDE C70 H701 SING N N 30 
VDE C71 H711 SING N N 31 
VDE C71 H712 SING N N 32 
VDE N   H    SING N N 33 
VDE N   H2   SING N N 34 
VDE N2  H21  SING N N 35 
VDE N2  H22  SING N N 36 
VDE N3  H32  SING N N 37 
VDE N3  H31  SING N N 38 
VDE C   OXT  SING N N 39 
VDE OXT HXT  SING N N 40 
# 
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 
VDE InChI            InChI                1.06  "InChI=1S/C11H20N6O3/c12-8(11(19)20)3-1-2-4-17-6-7(15-16-17)5-9(13)10(14)18/h6,8-9H,1-5,12-13H2,(H2,14,18)(H,19,20)/t8-,9-/m0/s1" 
VDE InChIKey         InChI                1.06  OXPRPPLOGXKLGL-IUCAKERBSA-N                                                                                                       
VDE SMILES_CANONICAL CACTVS               3.385 "N[C@@H](CCCCn1cc(C[C@H](N)C(N)=O)nn1)C(O)=O"                                                                                     
VDE SMILES           CACTVS               3.385 "N[CH](CCCCn1cc(C[CH](N)C(N)=O)nn1)C(O)=O"                                                                                        
VDE SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "c1c(nnn1CCCC[C@@H](C(=O)O)N)C[C@@H](C(=O)N)N"                                                                                    
VDE SMILES           "OpenEye OEToolkits" 2.0.7 "c1c(nnn1CCCCC(C(=O)O)N)CC(C(=O)N)N"                                                                                              
# 
_pdbx_chem_comp_identifier.comp_id           VDE 
_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~{S})-2-azanyl-6-[4-[(2~{S})-2,3-bis(azanyl)-3-oxidanylidene-propyl]-1,2,3-triazol-1-yl]hexanoic 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 
VDE "Create component"         2021-05-06 PDBE 
VDE "Modify leaving atom flag" 2023-04-19 PDBE 
VDE "Initial release"          2023-04-26 RCSB 
VDE "Modify backbone"          2023-11-03 PDBE 
VDE "Modify PCM"               2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            VDE 
_pdbx_chem_comp_pcm.modified_residue_id                ? 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Non-standard residue" 
_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               ? 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   ? 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
