data_YF5
# 
_chem_comp.id                                    YF5 
_chem_comp.name                                  "Agmatinamic acid" 
_chem_comp.type                                  "peptide linking" 
_chem_comp.pdbx_type                             ATOMP 
_chem_comp.formula                               "C10 H22 N4 O5" 
_chem_comp.mon_nstd_parent_comp_id               YFZ 
_chem_comp.pdbx_synonyms                         "(2R,3S,5S,6R)-6-azanyl-9-carbamimidamido-2,3,5-tris(oxidanyl)nonanoic acid; AGA" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-12-04 
_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                        278.305 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YF5 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   Y 
_chem_comp.pdbx_ideal_coordinates_details        Corina 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        8R6C 
_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_n_terminal_atom_flag 
_chem_comp_atom.pdbx_backbone_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 
YF5 NZ6 N1  N 0 1 N N N N N N 246.834 195.510 232.022 6.908  1.260  0.733  NZ6 YF5 1  
YF5 CA  C1  C 0 1 N N R N Y N 251.974 194.934 239.217 -4.381 -0.374 -0.604 CA  YF5 2  
YF5 CG  C2  C 0 1 N N N N Y N 252.532 195.049 236.736 -1.887 -0.430 -0.473 CG  YF5 3  
YF5 CE  C3  C 0 1 N N R N Y N 253.047 195.336 234.207 0.608  -0.478 -0.337 CE  YF5 4  
YF5 C   C4  C 0 1 N N N N Y Y 251.739 193.929 240.342 -5.623 0.296  -0.076 C   YF5 5  
YF5 O   O1  O 0 1 N N N N Y Y 252.648 193.172 240.686 -6.376 -0.311 0.648  O   YF5 6  
YF5 O1  O2  O 0 1 N N N N N N 250.785 195.655 238.924 -4.376 -1.747 -0.208 O1  YF5 7  
YF5 CB  C5  C 0 1 N N S N Y N 252.484 194.173 237.984 -3.144 0.326  -0.038 CB  YF5 8  
YF5 O2  O3  O 0 1 N N N N N N 251.664 193.032 237.719 -3.219 0.344  1.389  O2  YF5 9  
YF5 CD  C6  C 0 1 N N S N Y N 253.143 194.455 235.461 -0.646 0.337  -0.012 CD  YF5 10 
YF5 O3  O4  O 0 1 N N N N N N 254.530 194.215 235.704 -0.585 1.594  -0.689 O3  YF5 11 
YF5 N   N2  N 0 1 N N N Y Y N 253.637 196.667 234.431 0.545  -1.770 0.359  N   YF5 12 
YF5 CZ  C7  C 0 1 N N N N N N 251.633 195.537 233.656 1.849  0.289  0.124  CZ  YF5 13 
YF5 CZ1 C8  C 0 1 N N N N N N 250.996 194.479 232.791 3.106  -0.466 -0.311 CZ1 YF5 14 
YF5 CZ2 C9  C 0 1 N N N N N N 249.606 195.018 232.467 4.347  0.301  0.149  CZ2 YF5 15 
YF5 NZ3 N3  N 0 1 N N N N N N 248.718 194.187 231.654 5.551  -0.422 -0.267 NZ3 YF5 16 
YF5 CZ4 C10 C 0 1 N N N N N N 247.416 194.438 231.483 6.794  0.079  0.037  CZ4 YF5 17 
YF5 NZ5 N4  N 0 1 N N N N N N 246.685 193.610 230.744 7.865  -0.564 -0.333 NZ5 YF5 18 
YF5 HA1 H3  H 0 1 N N N N Y N 252.761 195.633 239.538 -4.368 -0.310 -1.692 HA1 YF5 19 
YF5 HG1 H4  H 0 1 N N N N Y N 253.114 195.947 236.989 -1.887 -1.423 -0.025 HG1 YF5 20 
YF5 HG2 H5  H 0 1 N N N N Y N 251.497 195.337 236.499 -1.875 -0.521 -1.559 HG2 YF5 21 
YF5 HE  H6  H 0 1 N N N N Y N 253.632 194.839 233.419 0.663  -0.647 -1.412 HE  YF5 22 
YF5 HO1 H8  H 0 1 N N N N N N 250.493 196.115 239.702 -4.386 -1.880 0.750  HO1 YF5 23 
YF5 HB  H9  H 0 1 N N N N Y N 253.509 193.837 238.199 -3.101 1.348  -0.412 HB  YF5 24 
YF5 HO2 H10 H 0 1 N N N N N N 251.629 192.481 238.492 -3.260 -0.534 1.792  HO2 YF5 25 
YF5 HD  H11 H 0 1 N N N N Y N 252.636 193.502 235.250 -0.701 0.506  1.063  HD  YF5 26 
YF5 HO3 H12 H 0 1 N N N N N N 254.627 193.670 236.476 -0.534 1.521  -1.652 HO3 YF5 27 
YF5 H   H13 H 0 1 N N N Y Y N 254.564 196.565 234.792 1.330  -2.353 0.110  H   YF5 28 
YF5 H2  H14 H 0 1 N Y N Y Y N 253.670 197.167 233.566 0.493  -1.641 1.358  H2  YF5 29 
YF5 HZ1 H16 H 0 1 N N N N N N 251.654 196.462 233.060 1.848  1.283  -0.324 HZ1 YF5 30 
YF5 HZ2 H17 H 0 1 N N N N N N 250.972 195.675 234.524 1.837  0.380  1.210  HZ2 YF5 31 
YF5 OXT O6  O 0 1 N Y N N Y Y ?       ?       ?       -5.893 1.568  -0.410 OXT YF5 32 
YF5 HXT H7  H 0 1 N Y N N Y Y ?       ?       ?       -6.702 1.955  -0.047 HXT YF5 33 
YF5 HZ9 H1  H 0 1 N N N N N N 247.374 196.150 232.570 6.110  1.739  1.009  HZ9 YF5 34 
YF5 HZ8 H23 H 0 1 N N N N N N 245.858 195.674 231.879 7.785  1.612  0.951  HZ8 YF5 35 
YF5 HZ3 H24 H 0 1 N N N N N N 250.924 193.526 233.336 3.106  -1.460 0.137  HZ3 YF5 36 
YF5 HZ4 H18 H 0 1 N N N N N N 251.578 194.331 231.869 3.117  -0.557 -1.397 HZ4 YF5 37 
YF5 HZ5 H19 H 0 1 N N N N N N 249.741 195.971 231.934 4.347  1.295  -0.299 HZ5 YF5 38 
YF5 HZ6 H20 H 0 1 N N N N N N 249.096 195.202 233.424 4.335  0.392  1.236  HZ6 YF5 39 
YF5 HZ7 H21 H 0 1 N N N N N N 249.107 193.385 231.200 5.471  -1.255 -0.758 HZ7 YF5 40 
YF5 HZ0 H22 H 0 1 N N N N N N 245.733 193.908 230.678 8.742  -0.210 -0.119 HZ0 YF5 41 
# 
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 
YF5 NZ5 CZ4 DOUB N N 1  
YF5 CZ4 NZ3 SING N N 2  
YF5 CZ4 NZ6 SING N N 3  
YF5 NZ3 CZ2 SING N N 4  
YF5 CZ2 CZ1 SING N N 5  
YF5 CZ1 CZ  SING N N 6  
YF5 CZ  CE  SING N N 7  
YF5 CE  N   SING N N 8  
YF5 CE  CD  SING N N 9  
YF5 CD  O3  SING N N 10 
YF5 CD  CG  SING N N 11 
YF5 CG  CB  SING N N 12 
YF5 O2  CB  SING N N 13 
YF5 CB  CA  SING N N 14 
YF5 O1  CA  SING N N 15 
YF5 CA  C   SING N N 16 
YF5 C   O   DOUB N N 17 
YF5 CA  HA1 SING N N 18 
YF5 CG  HG1 SING N N 19 
YF5 CG  HG2 SING N N 20 
YF5 CE  HE  SING N N 21 
YF5 O1  HO1 SING N N 22 
YF5 CB  HB  SING N N 23 
YF5 O2  HO2 SING N N 24 
YF5 CD  HD  SING N N 25 
YF5 O3  HO3 SING N N 26 
YF5 N   H   SING N N 27 
YF5 N   H2  SING N N 28 
YF5 CZ  HZ1 SING N N 29 
YF5 CZ  HZ2 SING N N 30 
YF5 C   OXT SING N N 31 
YF5 OXT HXT SING N N 32 
YF5 NZ6 HZ9 SING N N 33 
YF5 NZ6 HZ8 SING N N 34 
YF5 CZ1 HZ3 SING N N 35 
YF5 CZ1 HZ4 SING N N 36 
YF5 CZ2 HZ5 SING N N 37 
YF5 CZ2 HZ6 SING N N 38 
YF5 NZ3 HZ7 SING N N 39 
YF5 NZ5 HZ0 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 
YF5 InChI            InChI                1.06  "InChI=1S/C10H22N4O5/c11-5(2-1-3-14-10(12)13)6(15)4-7(16)8(17)9(18)19/h5-8,15-17H,1-4,11H2,(H,18,19)(H4,12,13,14)/t5-,6+,7+,8-/m1/s1" 
YF5 InChIKey         InChI                1.06  GRIHTJROSVTQAL-VGRMVHKJSA-N                                                                                                           
YF5 SMILES_CANONICAL CACTVS               3.385 "N[C@H](CCCNC(N)=N)[C@@H](O)C[C@H](O)[C@@H](O)C(O)=O"                                                                                 
YF5 SMILES           CACTVS               3.385 "N[CH](CCCNC(N)=N)[CH](O)C[CH](O)[CH](O)C(O)=O"                                                                                       
YF5 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "[H]/N=C(\N)/NCCC[C@H]([C@H](C[C@@H]([C@H](C(=O)O)O)O)O)N"                                                                            
YF5 SMILES           "OpenEye OEToolkits" 2.0.7 "C(CC(C(CC(C(C(=O)O)O)O)O)N)CNC(=N)N"                                                                                                 
# 
_pdbx_chem_comp_identifier.comp_id           YF5 
_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~{R},3~{S},5~{S},6~{R})-6-azanyl-9-carbamimidamido-2,3,5-tris(oxidanyl)nonanoic acid" 
# 
loop_
_pdbx_chem_comp_synonyms.ordinal 
_pdbx_chem_comp_synonyms.comp_id 
_pdbx_chem_comp_synonyms.name 
_pdbx_chem_comp_synonyms.provenance 
_pdbx_chem_comp_synonyms.type 
1 YF5 "(2R,3S,5S,6R)-6-azanyl-9-carbamimidamido-2,3,5-tris(oxidanyl)nonanoic acid" PDB ? 
2 YF5 AGA                                                                          PDB ? 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
YF5 "Create component"         2023-12-04 PDBE 
YF5 "Modify backbone"          2024-01-15 PDBE 
YF5 "Modify linking type"      2024-01-15 PDBE 
YF5 "Modify name"              2024-01-15 PDBE 
YF5 "Modify leaving atom flag" 2024-01-18 PDBE 
YF5 "Initial release"          2024-07-24 RCSB 
YF5 "Modify PCM"               2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            YF5 
_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 and backbone" 
_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      ? 
# 
