data_562 # _chem_comp.id 562 _chem_comp.name "N~5~-[N-(2-{2-[2-(triaza-1,2-dien-2-ium-1-yl)ethoxy]ethoxy}ethyl)carbamimidoyl]-L-ornithine" _chem_comp.type "L-peptide linking" _chem_comp.pdbx_type ATOMP _chem_comp.formula "C12 H26 N7 O4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 1 _chem_comp.pdbx_initial_date 2015-07-31 _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 332.379 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 562 _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 5CUT _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_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 562 N N N 0 1 N N N Y Y N -21.300 20.314 -23.478 5.991 2.257 1.091 N 562 1 562 CA CA C 0 1 N N S Y N N -20.718 20.331 -22.137 6.570 0.982 0.649 CA 562 2 562 C C C 0 1 N N N Y N Y -20.606 21.759 -21.648 7.899 1.236 -0.013 C 562 3 562 O O O 0 1 N N N Y N Y -19.609 22.139 -20.992 8.164 2.338 -0.433 O 562 4 562 CB CB C 0 1 N N N N N N -19.371 19.632 -22.086 5.623 0.311 -0.349 CB 562 5 562 CG CG C 0 1 N N N N N N -19.598 18.165 -22.426 4.318 -0.060 0.357 CG 562 6 562 CD CD C 0 1 N N N N N N -18.302 17.425 -22.259 3.371 -0.731 -0.640 CD 562 7 562 NE NE N 0 1 N N N N N N -18.439 16.005 -22.499 2.121 -1.087 0.036 NE 562 8 562 CZ CZ C 0 1 N N N N N N -17.455 15.146 -21.903 1.113 -1.705 -0.665 CZ 562 9 562 NH1 NH1 N 0 1 N N N N N N -16.489 15.681 -21.169 1.269 -1.975 -1.930 NH1 562 10 562 C01 C01 C 0 1 N N N N N N -18.739 11.741 -22.462 -2.320 -2.957 0.156 C01 562 11 562 NH2 NH2 N 0 1 N N N N N N -17.498 13.835 -22.097 -0.060 -2.039 -0.030 NH2 562 12 562 N08 N08 N 0 1 N N N N N N -21.781 4.531 -26.990 -9.149 2.404 -1.072 N08 562 13 562 O01 O01 O 0 1 N N N N N N -19.807 11.166 -23.141 -2.868 -1.709 0.587 O01 562 14 562 C02 C02 C 0 1 N N N N N N -18.536 13.195 -22.876 -1.135 -2.698 -0.777 C02 562 15 562 N02 N02 N 0 1 N N N N N N -21.867 5.297 -24.591 -7.159 1.390 -0.818 N02 562 16 562 O02 O02 O 0 1 N N N N N N -19.946 8.126 -23.602 -4.995 0.221 0.705 O02 562 17 562 C03 C03 C 0 1 N N N N N N -19.346 10.366 -24.192 -3.986 -1.839 1.468 C03 562 18 562 N03 N03 N 1 1 N N N N N N -21.823 4.916 -25.793 -8.154 1.897 -0.945 N03 562 19 562 C04 C04 C 0 1 N N N N N N -20.328 9.224 -24.367 -4.489 -0.449 1.862 C04 562 20 562 C05 C05 C 0 1 N N N N N N -21.009 7.229 -23.469 -5.492 1.535 0.966 C05 562 21 562 C06 C06 C 0 1 N N N N N N -20.651 5.879 -24.058 -6.005 2.153 -0.337 C06 562 22 562 H H1 H 0 1 N N N Y Y N -22.183 20.783 -23.465 6.566 2.689 1.799 H1 562 23 562 H2 H2 H 0 1 N Y N Y Y N -20.685 20.779 -24.114 5.849 2.880 0.310 H2 562 24 562 HA H4 H 0 1 N N N Y N N -21.398 19.796 -21.457 6.712 0.329 1.510 H4 562 25 562 OXT OXT O 0 1 N Y N Y N Y -21.397 22.460 -21.868 8.790 0.239 -0.136 OXT 562 26 562 H6 H6 H 0 1 N N N N N N -18.941 19.721 -21.078 5.411 0.999 -1.167 H6 562 27 562 H7 H7 H 0 1 N N N N N N -18.686 20.085 -22.818 6.092 -0.591 -0.744 H7 562 28 562 H8 H8 H 0 1 N N N N N N -19.944 18.076 -23.466 4.530 -0.748 1.176 H8 562 29 562 H9 H9 H 0 1 N N N N N N -20.356 17.742 -21.750 3.849 0.841 0.753 H9 562 30 562 H10 H10 H 0 1 N N N N N N -17.940 17.576 -21.231 3.159 -0.043 -1.459 H10 562 31 562 H11 H11 H 0 1 N N N N N N -17.569 17.834 -22.970 3.840 -1.633 -1.036 H11 562 32 562 H12 H12 H 0 1 N N N N N N -19.185 15.638 -23.055 2.005 -0.886 0.978 H12 562 33 562 H13 H13 H 0 1 N N N N N N -15.857 14.989 -20.820 0.557 -2.411 -2.424 H13 562 34 562 H14 H14 H 0 1 N N N N N N -18.939 11.701 -21.381 -1.982 -3.524 1.024 H14 562 35 562 H15 H15 H 0 1 N N N N N N -17.824 11.173 -22.687 -3.083 -3.525 -0.375 H15 562 36 562 H16 H16 H 0 1 N N N N N N -16.784 13.266 -21.689 -0.177 -1.838 0.911 H16 562 37 562 H17 H17 H 0 1 N N N N N N -22.077 3.581 -27.088 -9.780 2.426 -0.335 H17 562 38 562 H18 H18 H 0 1 N N N N N N -18.254 13.227 -23.939 -0.773 -3.645 -1.175 H18 562 39 562 H19 H19 H 0 1 N N N N N N -19.479 13.742 -22.730 -1.453 -2.056 -1.598 H19 562 40 562 H20 H20 H 0 1 N N N N N N -18.349 9.969 -23.951 -4.784 -2.385 0.964 H20 562 41 562 H21 H21 H 0 1 N N N N N N -19.291 10.958 -25.117 -3.683 -2.383 2.362 H21 562 42 562 H22 H22 H 0 1 N N N N N N -21.328 9.555 -24.049 -3.667 0.128 2.286 H22 562 43 562 H23 H23 H 0 1 N N N N N N -20.358 8.933 -25.427 -5.284 -0.546 2.602 H23 562 44 562 H24 H24 H 0 1 N N N N N N -21.888 7.630 -23.995 -6.307 1.479 1.687 H24 562 45 562 H25 H25 H 0 1 N N N N N N -21.245 7.106 -22.402 -4.691 2.153 1.370 H25 562 46 562 H26 H26 H 0 1 N N N N N N -20.235 5.227 -23.276 -5.214 2.128 -1.087 H26 562 47 562 H27 H27 H 0 1 N N N N N N -19.911 6.005 -24.863 -6.302 3.186 -0.156 H27 562 48 562 HXT HXT H 0 1 N Y N Y N Y -21.182 23.308 -21.497 9.629 0.451 -0.568 HXT 562 49 # 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 562 N08 N03 DOUB N N 1 562 N03 N02 DOUB N N 2 562 N02 C06 SING N N 3 562 C04 C03 SING N N 4 562 C04 O02 SING N N 5 562 C03 O01 SING N N 6 562 C06 C05 SING N N 7 562 O02 C05 SING N N 8 562 N CA SING N N 9 562 O01 C01 SING N N 10 562 C02 C01 SING N N 11 562 C02 NH2 SING N N 12 562 NE CD SING N N 13 562 NE CZ SING N N 14 562 CG CD SING N N 15 562 CG CB SING N N 16 562 CA CB SING N N 17 562 CA C SING N N 18 562 NH2 CZ SING N N 19 562 CZ NH1 DOUB N N 20 562 C O DOUB N N 21 562 N H SING N N 22 562 N H2 SING N N 23 562 CA HA SING N N 24 562 C OXT SING N N 25 562 CB H6 SING N N 26 562 CB H7 SING N N 27 562 CG H8 SING N N 28 562 CG H9 SING N N 29 562 CD H10 SING N N 30 562 CD H11 SING N N 31 562 NE H12 SING N N 32 562 NH1 H13 SING N N 33 562 C01 H14 SING N N 34 562 C01 H15 SING N N 35 562 NH2 H16 SING N N 36 562 N08 H17 SING N N 37 562 C02 H18 SING N N 38 562 C02 H19 SING N N 39 562 C03 H20 SING N N 40 562 C03 H21 SING N N 41 562 C04 H22 SING N N 42 562 C04 H23 SING N N 43 562 C05 H24 SING N N 44 562 C05 H25 SING N N 45 562 C06 H26 SING N N 46 562 C06 H27 SING N N 47 562 OXT HXT SING N N 48 # 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 562 SMILES ACDLabs 12.01 "NC(CCCN\C(=N)NCCOCCOCC\N=[N+]=N)C(=O)O" 562 InChI InChI 1.03 "InChI=1S/C12H25N7O4/c13-10(11(20)21)2-1-3-16-12(14)17-4-6-22-8-9-23-7-5-18-19-15/h10,15H,1-9,13H2,(H3-,14,16,17,20,21)/p+1/t10-/m0/s1" 562 InChIKey InChI 1.03 LSTVCWRTCOJGHW-JTQLQIEISA-O 562 SMILES_CANONICAL CACTVS 3.385 "N[C@@H](CCCNC(=N)NCCOCCOCCN=[N+]=N)C(O)=O" 562 SMILES CACTVS 3.385 "N[CH](CCCNC(=N)NCCOCCOCCN=[N+]=N)C(O)=O" 562 SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "[H]/N=C(/NCCC[C@@H](C(=O)O)N)\NCCOCCOCCN=[N+]=N" 562 SMILES "OpenEye OEToolkits" 1.9.2 "C(CC(C(=O)O)N)CNC(=N)NCCOCCOCCN=[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 562 "SYSTEMATIC NAME" ACDLabs 12.01 "N~5~-[N-(2-{2-[2-(triaza-1,2-dien-2-ium-1-yl)ethoxy]ethoxy}ethyl)carbamimidoyl]-L-ornithine" 562 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "azanylidene-[2-[2-[2-[[N-[(4S)-4-azanyl-5-oxidanyl-5-oxidanylidene-pentyl]carbamimidoyl]amino]ethoxy]ethoxy]ethylimino]azanium" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 562 "Create component" 2015-07-31 RCSB 562 "Initial release" 2018-03-14 RCSB 562 "Modify backbone" 2023-11-03 PDBE 562 "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id 562 _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 ? #