data_RF9 # _chem_comp.id RF9 _chem_comp.name "N~6~-[(1R)-1-carboxyethyl]-L-lysine" _chem_comp.type "L-peptide linking" _chem_comp.pdbx_type ATOMP _chem_comp.formula "C9 H18 N2 O4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2019-02-05 _chem_comp.pdbx_modified_date 2023-11-03 _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 218.250 _chem_comp.one_letter_code ? _chem_comp.three_letter_code RF9 _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 6NVA _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # 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 RF9 N N N 0 1 N N N Y Y N -24.326 -22.525 14.820 3.741 -0.583 -1.708 N RF9 1 RF9 CA CA C 0 1 N N S Y N N -24.351 -22.222 16.265 3.711 0.259 -0.505 CA RF9 2 RF9 C C C 0 1 N N N Y N Y -23.291 -23.096 16.899 4.948 0.005 0.318 C RF9 3 RF9 CB CB C 0 1 N N N N N N -25.737 -22.477 16.867 2.469 -0.077 0.322 CB RF9 4 RF9 CG CG C 0 1 N N N N N N -25.628 -22.821 18.353 1.213 0.298 -0.467 CG RF9 5 RF9 CD CD C 0 1 N N N N N N -26.723 -22.237 19.238 -0.029 -0.039 0.361 CD RF9 6 RF9 CE CE C 0 1 N N N N N N -27.811 -23.218 19.646 -1.285 0.337 -0.428 CE RF9 7 RF9 NZ NZ N 0 1 N N N N N N -27.758 -23.484 21.097 -2.477 0.014 0.366 NZ RF9 8 RF9 O O1 O 0 1 N N N Y N Y -23.308 -24.328 16.695 5.578 -1.014 0.161 OXT RF9 9 RF9 C1 C1 C 0 1 N N N N N N -28.522 -22.281 23.108 -4.033 1.838 -0.132 C1 RF9 10 RF9 CX1 CX1 C 0 1 N N R N N N -28.956 -23.053 21.861 -3.705 0.361 -0.361 CX1 RF9 11 RF9 CX2 CX2 C 0 1 N N N N N N -29.820 -24.180 22.353 -4.844 -0.490 0.139 CX2 RF9 12 RF9 O3 O3 O 0 1 N N N N N N -30.482 -24.833 21.509 -4.652 -1.303 1.012 O1 RF9 13 RF9 O2 O2 O 0 1 N N N N N N -29.878 -24.384 23.599 -6.071 -0.345 -0.386 O2 RF9 14 RF9 OXT OXT O 0 1 N Y N Y N Y -22.138 -22.496 17.153 5.348 0.910 1.225 O3 RF9 15 RF9 H H1 H 0 1 N N N Y Y N -23.411 -22.349 14.458 4.517 -0.336 -2.304 H1 RF9 16 RF9 H2 H2 H 0 1 N Y N Y Y N -24.562 -23.486 14.677 3.771 -1.562 -1.463 H2 RF9 17 RF9 HA H4 H 0 1 N N N Y N N -24.086 -21.166 16.423 3.679 1.309 -0.798 H4 RF9 18 RF9 H5 H5 H 0 1 N N N N N N -26.353 -21.573 16.750 2.456 -1.145 0.539 H5 RF9 19 RF9 H6 H6 H 0 1 N N N N N N -26.212 -23.315 16.337 2.492 0.483 1.257 H6 RF9 20 RF9 H7 H7 H 0 1 N N N N N N -25.659 -23.916 18.452 1.226 1.366 -0.684 H7 RF9 21 RF9 H8 H8 H 0 1 N N N N N N -24.660 -22.447 18.718 1.190 -0.262 -1.401 H8 RF9 22 RF9 H9 H9 H 0 1 N N N N N N -26.252 -21.850 20.153 -0.042 -1.107 0.578 H9 RF9 23 RF9 H10 H10 H 0 1 N N N N N N -27.198 -21.409 18.692 -0.006 0.522 1.295 H10 RF9 24 RF9 H11 H11 H 0 1 N N N N N N -28.793 -22.793 19.393 -1.271 1.405 -0.646 H11 RF9 25 RF9 H12 H12 H 0 1 N N N N N N -27.668 -24.163 19.101 -1.308 -0.224 -1.363 H12 RF9 26 RF9 H13 H13 H 0 1 N N N N N N -27.645 -24.469 21.227 -2.480 -0.959 0.636 H13 RF9 27 RF9 H15 H15 H 0 1 N N N N N N -29.412 -21.963 23.671 -4.179 2.016 0.934 H15 RF9 28 RF9 H16 H16 H 0 1 N N N N N N -27.899 -22.929 23.742 -3.209 2.454 -0.493 H16 RF9 29 RF9 H17 H17 H 0 1 N N N N N N -27.943 -21.395 22.808 -4.944 2.096 -0.672 H17 RF9 30 RF9 H18 H18 H 0 1 N N N N N N -29.564 -22.387 21.231 -3.559 0.183 -1.427 H18 RF9 31 RF9 H19 H19 H 0 1 N N N N N N -30.487 -25.091 23.777 -6.769 -0.913 -0.032 H19 RF9 32 RF9 HXT HXT H 0 1 N Y N Y N Y -21.438 -23.138 17.143 6.147 0.702 1.729 H20 RF9 33 # 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 RF9 N CA SING N N 1 RF9 CA CB SING N N 2 RF9 CA C SING N N 3 RF9 O C DOUB N N 4 RF9 CB CG SING N N 5 RF9 CG CD SING N N 6 RF9 CD CE SING N N 7 RF9 CE NZ SING N N 8 RF9 NZ CX1 SING N N 9 RF9 O3 CX2 DOUB N N 10 RF9 CX1 CX2 SING N N 11 RF9 CX1 C1 SING N N 12 RF9 CX2 O2 SING N N 13 RF9 C OXT SING N N 14 RF9 N H SING N N 15 RF9 N H2 SING N N 16 RF9 CA HA SING N N 17 RF9 CB H5 SING N N 18 RF9 CB H6 SING N N 19 RF9 CG H7 SING N N 20 RF9 CG H8 SING N N 21 RF9 CD H9 SING N N 22 RF9 CD H10 SING N N 23 RF9 CE H11 SING N N 24 RF9 CE H12 SING N N 25 RF9 NZ H13 SING N N 26 RF9 C1 H15 SING N N 27 RF9 C1 H16 SING N N 28 RF9 C1 H17 SING N N 29 RF9 CX1 H18 SING N N 30 RF9 O2 H19 SING N N 31 RF9 OXT HXT SING N N 32 # 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 RF9 SMILES ACDLabs 12.01 "NC(CCCCNC(C)C(O)=O)C(O)=O" RF9 InChI InChI 1.03 "InChI=1S/C9H18N2O4/c1-6(8(12)13)11-5-3-2-4-7(10)9(14)15/h6-7,11H,2-5,10H2,1H3,(H,12,13)(H,14,15)/t6-,7+/m1/s1" RF9 InChIKey InChI 1.03 XCYPSOHOIAZISD-RQJHMYQMSA-N RF9 SMILES_CANONICAL CACTVS 3.385 "C[C@@H](NCCCC[C@H](N)C(O)=O)C(O)=O" RF9 SMILES CACTVS 3.385 "C[CH](NCCCC[CH](N)C(O)=O)C(O)=O" RF9 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@H](C(=O)O)NCCCC[C@@H](C(=O)O)N" RF9 SMILES "OpenEye OEToolkits" 2.0.7 "CC(C(=O)O)NCCCCC(C(=O)O)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 RF9 "SYSTEMATIC NAME" ACDLabs 12.01 "N~6~-[(1R)-1-carboxyethyl]-L-lysine" RF9 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{S})-2-azanyl-6-[[(2~{R})-1-oxidanyl-1-oxidanylidene-propan-2-yl]amino]hexanoic acid" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site RF9 "Create component" 2019-02-05 RCSB RF9 "Initial release" 2019-02-27 RCSB RF9 "Modify backbone" 2023-11-03 PDBE #