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 2023-11-03 _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 # 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 #