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                    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                        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 
_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 
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 
RF9 "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            RF9 
_pdbx_chem_comp_pcm.modified_residue_id                LYS 
_pdbx_chem_comp_pcm.type                               Carboxyethylation 
_pdbx_chem_comp_pcm.category                           "Named protein modification" 
_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      ? 
# 
