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      ? 
# 
