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 2024-07-19 _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 # 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 #