data_56C # _chem_comp.id 56C _chem_comp.name "N~5~-{N-[2-(2-{2-[2-(triaza-1,2-dien-2-ium-1-yl)ethoxy]ethoxy}ethoxy)ethyl]carbamimidoyl}-L-ornithine" _chem_comp.type "L-peptide linking" _chem_comp.pdbx_type ATOMP _chem_comp.formula "C14 H30 N7 O5" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 1 _chem_comp.pdbx_initial_date 2015-08-03 _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 376.432 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 56C _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 5CZQ _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 56C N N N 0 1 N N N Y Y N -21.377 20.319 -23.471 7.223 2.213 1.278 N 56C 1 56C CA CA C 0 1 N N S Y N N -20.729 20.309 -22.166 7.817 1.059 0.590 CA 56C 2 56C C C C 0 1 N N N Y N Y -20.705 21.741 -21.620 9.087 1.485 -0.100 C 56C 3 56C O O O 0 1 N N N Y N Y -19.762 22.141 -20.892 9.280 2.653 -0.343 O 56C 4 56C CB CB C 0 1 N N N N N N -19.313 19.741 -22.224 6.830 0.518 -0.446 CB 56C 5 56C CG CG C 0 1 N N N N N N -19.231 18.366 -22.884 5.592 -0.029 0.267 CG 56C 6 56C CD CD C 0 1 N N N N N N -18.866 17.328 -21.842 4.604 -0.570 -0.770 CD 56C 7 56C NE NE N 0 1 N N N N N N -18.751 15.947 -22.275 3.418 -1.094 -0.087 NE 56C 8 56C CZ CZ C 0 1 N N N N N N -17.748 15.199 -21.849 2.388 -1.635 -0.819 CZ 56C 9 56C NH1 NH1 N 0 1 N N N N N N -16.850 15.736 -21.039 2.466 -1.682 -2.119 NH1 56C 10 56C C01 C01 C 0 1 N N N N N N -18.306 11.795 -23.401 -0.929 -3.172 -0.010 C01 56C 11 56C N01 N01 N 0 1 N N N N N N -17.623 13.929 -22.190 1.275 -2.127 -0.179 N01 56C 12 56C O01 O01 O 0 1 N N N N N N -19.496 11.057 -23.458 -1.494 -2.043 0.659 O01 56C 13 56C C02 C02 C 0 1 N N N N N N -18.568 13.263 -23.067 0.177 -2.704 -0.958 C02 56C 14 56C N02 N02 N 0 1 N N N N N N -13.536 5.065 -23.083 -8.798 0.785 -0.401 N02 56C 15 56C O02 O02 O 0 1 N N N N N N -19.586 7.883 -23.363 -3.678 -0.266 1.234 O02 56C 16 56C C03 C03 C 0 1 N N N N N N -19.468 10.044 -24.425 -2.542 -2.372 1.572 C03 56C 17 56C N03 N03 N 1 1 N N N N N N -12.755 4.133 -23.098 -9.840 1.170 -0.571 N03 56C 18 56C C04 C04 C 0 1 N N N N N N -20.350 8.876 -23.989 -3.068 -1.094 2.227 C04 56C 19 56C N04 N04 N 0 1 N N N N N N -11.935 3.166 -23.114 -10.882 1.556 -0.742 N04 56C 20 56C O04 O04 O 0 1 N N N N N N -16.582 6.487 -23.175 -5.957 1.052 0.081 O04 56C 21 56C C05 C05 C 0 1 N N N N N N -18.582 7.334 -24.172 -4.205 0.960 1.744 C05 56C 22 56C C06 C06 C 0 1 N N N N N N -17.916 6.165 -23.454 -4.830 1.761 0.600 C06 56C 23 56C C07 C07 C 0 1 N N N N N N -15.641 5.883 -24.022 -6.617 1.717 -0.998 C07 56C 24 56C C08 C08 C 0 1 N N N N N N -14.938 4.741 -23.292 -7.801 0.871 -1.471 C08 56C 25 56C H H1 H 0 1 N N N Y Y N -22.298 20.698 -23.383 7.829 2.549 2.011 H1 56C 26 56C H2 H2 H 0 1 N Y N Y Y N -20.844 20.881 -24.103 7.004 2.950 0.624 H2 56C 27 56C HA H4 H 0 1 N N N Y N N -21.320 19.689 -21.475 8.043 0.280 1.318 H4 56C 28 56C OXT OXT O 0 1 N Y N Y N Y -21.475 22.387 -21.854 10.004 0.567 -0.445 OXT 56C 29 56C H6 H6 H 0 1 N N N N N N -18.930 19.657 -21.196 6.536 1.322 -1.121 H6 56C 30 56C H7 H7 H 0 1 N N N N N N -18.682 20.438 -22.794 7.304 -0.280 -1.016 H7 56C 31 56C H8 H8 H 0 1 N N N N N N -20.205 18.113 -23.328 5.886 -0.832 0.942 H8 56C 32 56C H9 H9 H 0 1 N N N N N N -18.463 18.382 -23.671 5.118 0.770 0.837 H9 56C 33 56C H10 H10 H 0 1 N N N N N N -17.896 17.620 -21.414 4.310 0.234 -1.445 H10 56C 34 56C H11 H11 H 0 1 N N N N N N -19.638 17.363 -21.059 5.078 -1.368 -1.340 H11 56C 35 56C H12 H12 H 0 1 N N N N N N -19.432 15.561 -22.897 3.360 -1.058 0.880 H12 56C 36 56C H13 H13 H 0 1 N N N N N N -16.147 15.077 -20.769 1.739 -2.065 -2.635 H13 56C 37 56C H14 H14 H 0 1 N N N N N N -17.655 11.363 -22.626 -0.511 -3.859 0.725 H14 56C 38 56C H15 H15 H 0 1 N N N N N N -17.802 11.736 -24.377 -1.706 -3.681 -0.582 H15 56C 39 56C H16 H16 H 0 1 N N N N N N -18.585 13.819 -24.016 0.546 -3.553 -1.533 H16 56C 40 56C H17 H17 H 0 1 N N N N N N -18.434 9.691 -24.552 -3.352 -2.865 1.033 H17 56C 41 56C H18 H18 H 0 1 N N N N N N -19.839 10.443 -25.380 -2.157 -3.042 2.341 H18 56C 42 56C H19 H19 H 0 1 N N N N N N -21.112 9.242 -23.285 -2.241 -0.556 2.690 H19 56C 43 56C H20 H20 H 0 1 N N N N N N -20.844 8.447 -24.873 -3.806 -1.352 2.987 H20 56C 44 56C H21 H21 H 0 1 N N N N N N -10.987 3.480 -23.164 -11.097 2.479 -0.536 H21 56C 45 56C H22 H22 H 0 1 N N N N N N -17.828 8.105 -24.391 -4.966 0.745 2.494 H22 56C 46 56C H23 H23 H 0 1 N N N N N N -19.026 6.978 -25.113 -3.402 1.541 2.197 H23 56C 47 56C H24 H24 H 0 1 N N N N N N -18.448 5.961 -22.513 -4.093 1.900 -0.191 H24 56C 48 56C H25 H25 H 0 1 N N N N N N -17.951 5.272 -24.096 -5.153 2.734 0.971 H25 56C 49 56C H26 H26 H 0 1 N N N N N N -14.896 6.631 -24.331 -6.977 2.689 -0.660 H26 56C 50 56C H27 H27 H 0 1 N N N N N N -16.153 5.486 -24.911 -5.917 1.855 -1.822 H27 56C 51 56C H28 H28 H 0 1 N N N N N N -15.423 4.580 -22.318 -7.454 -0.130 -1.725 H28 56C 52 56C H29 H29 H 0 1 N N N N N N -15.013 3.824 -23.895 -8.250 1.334 -2.349 H29 56C 53 56C H30 H30 H 0 1 N N N N N N -16.849 13.408 -21.831 1.217 -2.092 0.789 H30 56C 54 56C H3 H3 H 0 1 N N N N N N -19.558 13.321 -22.590 -0.222 -1.951 -1.637 H3 56C 55 56C HXT HXT H 0 1 N Y N Y N Y -21.317 23.230 -21.445 10.802 0.889 -0.886 HXT 56C 56 # 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 56C C03 C04 SING N N 1 56C C03 O01 SING N N 2 56C C05 C06 SING N N 3 56C C05 O02 SING N N 4 56C C07 C08 SING N N 5 56C C07 O04 SING N N 6 56C C04 O02 SING N N 7 56C N CA SING N N 8 56C O01 C01 SING N N 9 56C C06 O04 SING N N 10 56C C01 C02 SING N N 11 56C C08 N02 SING N N 12 56C N04 N03 DOUB N N 13 56C N03 N02 DOUB N N 14 56C C02 N01 SING N N 15 56C CG CB SING N N 16 56C CG CD SING N N 17 56C NE CZ SING N N 18 56C NE CD SING N N 19 56C CB CA SING N N 20 56C N01 CZ SING N N 21 56C CA C SING N N 22 56C CZ NH1 DOUB N N 23 56C C O DOUB N N 24 56C N H SING N N 25 56C N H2 SING N N 26 56C CA HA SING N N 27 56C C OXT SING N N 28 56C CB H6 SING N N 29 56C CB H7 SING N N 30 56C CG H8 SING N N 31 56C CG H9 SING N N 32 56C CD H10 SING N N 33 56C CD H11 SING N N 34 56C NE H12 SING N N 35 56C NH1 H13 SING N N 36 56C C01 H14 SING N N 37 56C C01 H15 SING N N 38 56C C02 H16 SING N N 39 56C C03 H17 SING N N 40 56C C03 H18 SING N N 41 56C C04 H19 SING N N 42 56C C04 H20 SING N N 43 56C N04 H21 SING N N 44 56C C05 H22 SING N N 45 56C C05 H23 SING N N 46 56C C06 H24 SING N N 47 56C C06 H25 SING N N 48 56C C07 H26 SING N N 49 56C C07 H27 SING N N 50 56C C08 H28 SING N N 51 56C C08 H29 SING N N 52 56C N01 H30 SING N N 53 56C C02 H3 SING N N 54 56C OXT HXT SING N N 55 # 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 56C SMILES ACDLabs 12.01 "NC(C(=O)O)CCCN\C(=N)NCCOCCOCCOCC/N=[N+]=N" 56C InChI InChI 1.03 "InChI=1S/C14H29N7O5/c15-12(13(22)23)2-1-3-18-14(16)19-4-6-24-8-10-26-11-9-25-7-5-20-21-17/h12,17H,1-11,15H2,(H3-,16,18,19,22,23)/p+1/t12-/m0/s1" 56C InChIKey InChI 1.03 WGFPPYKACPCFRG-LBPRGKRZSA-O 56C SMILES_CANONICAL CACTVS 3.385 "N[C@@H](CCCNC(=N)NCCOCCOCCOCCN=[N+]=N)C(O)=O" 56C SMILES CACTVS 3.385 "N[CH](CCCNC(=N)NCCOCCOCCOCCN=[N+]=N)C(O)=O" 56C SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "[H]/N=C(\NCCC[C@@H](C(=O)O)N)/NCCOCCOCCOCCN=[N+]=N" 56C SMILES "OpenEye OEToolkits" 1.9.2 "C(CC(C(=O)O)N)CNC(=N)NCCOCCOCCOCCN=[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 56C "SYSTEMATIC NAME" ACDLabs 12.01 "N~5~-{N-[2-(2-{2-[2-(triaza-1,2-dien-2-ium-1-yl)ethoxy]ethoxy}ethoxy)ethyl]carbamimidoyl}-L-ornithine" 56C "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "azanylidene-[2-[2-[2-[2-[[N-[(4S)-4-azanyl-5-oxidanyl-5-oxidanylidene-pentyl]carbamimidoyl]amino]ethoxy]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 56C "Create component" 2015-08-03 RCSB 56C "Initial release" 2018-03-14 RCSB 56C "Other modification" 2020-06-27 RCSB 56C "Modify backbone" 2023-11-03 PDBE 56C "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id 56C _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 ? #