data_LYR
# 
_chem_comp.id                                    LYR 
_chem_comp.name                                  "N~6~-[(2Z,4E,6E,8E)-3,7-DIMETHYL-9-(2,6,6-TRIMETHYLCYCLOHEX-1-EN-1-YL)NONA-2,4,6,8-TETRAENYL]LYSINE" 
_chem_comp.type                                  "L-PEPTIDE LINKING" 
_chem_comp.pdbx_type                             ATOMP 
_chem_comp.formula                               "C26 H42 N2 O2" 
_chem_comp.mon_nstd_parent_comp_id               LYS 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2005-03-17 
_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                        414.624 
_chem_comp.one_letter_code                       K 
_chem_comp.three_letter_code                     LYR 
_chem_comp.pdbx_model_coordinates_details        ? 
_chem_comp.pdbx_model_coordinates_missing_flag   Y 
_chem_comp.pdbx_ideal_coordinates_details        ? 
_chem_comp.pdbx_ideal_coordinates_missing_flag   N 
_chem_comp.pdbx_model_coordinates_db_code        ? 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_chem_comp.pdbx_pcm                              N 
# 
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 
LYR N    N    N 0 1 N N N N N N -4.945  -5.813 4.064  -6.763 0.638  3.659  N    LYR 1  
LYR CA   CA   C 0 1 N N S N N N -4.641  -5.120 5.320  -5.398 0.694  4.116  CA   LYR 2  
LYR C    C    C 0 1 N N N N N N -3.169  -5.640 5.622  -4.576 1.213  2.952  C    LYR 3  
LYR O    O    O 0 1 N N N N N N -2.607  -5.077 6.618  -5.003 1.420  1.823  O    LYR 4  
LYR OXT  OXT  O 0 1 N Y N N N N ?       ?      ?      -3.270 1.380  3.288  OXT  LYR 5  
LYR CB   CB   C 0 1 N N N N N N -5.636  -5.379 6.401  -4.876 -0.672 4.563  CB   LYR 6  
LYR CG   CG   C 0 1 N N N N N N -7.108  -4.861 6.011  -4.954 -1.769 3.493  CG   LYR 7  
LYR CD   CD   C 0 1 N N N N N N -8.145  -4.731 7.179  -4.473 -3.136 3.992  CD   LYR 8  
LYR CE   CE   C 0 1 N N N N N N -9.617  -4.341 6.747  -4.498 -4.212 2.904  CE   LYR 9  
LYR NZ   NZ   N 0 1 N N N N N N -9.660  -3.173 5.968  -3.676 -3.847 1.760  NZ   LYR 10 
LYR C1   C1   C 0 1 N N N N N N -9.746  -3.043 4.714  -3.756 -4.865 0.717  C1   LYR 11 
LYR C2   C2   C 0 1 N N N N N N -9.876  -1.701 3.936  -2.920 -4.495 -0.474 C2   LYR 12 
LYR C3   C3   C 0 1 N N N N N N -9.746  -1.485 2.680  -3.301 -4.363 -1.762 C3   LYR 13 
LYR C4   C4   C 0 1 N N N N N N -9.487  -2.653 1.685  -4.716 -4.545 -2.244 C4   LYR 14 
LYR C5   C5   C 0 1 N N N N N N -9.746  -0.144 2.160  -2.284 -4.014 -2.760 C5   LYR 15 
LYR C6   C6   C 0 1 N N N N N N -9.183  0.374  1.079  -1.278 -3.135 -2.609 C6   LYR 16 
LYR C7   C7   C 0 1 N N N N N N -8.233  -0.274 0.040  -1.069 -2.391 -1.380 C7   LYR 17 
LYR C80  C80  C 0 1 N N N N N N -7.886  0.374  -1.128 -0.107 -1.485 -1.098 C80  LYR 18 
LYR C8   C8   C 0 1 N N N N N N -8.449  1.716  -1.561 0.915  -1.165 -2.164 C8   LYR 19 
LYR C9   C9   C 0 1 N N N N N N -6.847  -0.274 -2.036 0.015  -0.787 0.182  C9   LYR 20 
LYR C10  C10  C 0 1 N N N N N N -6.329  0.331  -3.032 0.952  0.118  0.508  C10  LYR 21 
LYR C11  C11  C 0 1 N N N N N N -4.945  -0.015 -3.638 1.010  0.772  1.805  C11  LYR 22 
LYR C12  C12  C 0 1 N N N N N N -4.554  -1.269 -3.983 0.763  0.106  2.961  C12  LYR 23 
LYR C13  C13  C 0 1 N N N N N N -5.334  -2.611 -3.897 0.327  -1.336 3.073  C13  LYR 24 
LYR C14  C14  C 0 1 N N N N N N -3.169  -1.659 -4.460 0.903  0.758  4.322  C14  LYR 25 
LYR C15  C15  C 0 1 N N N N N N -2.088  -0.533 -4.070 1.637  2.091  4.314  C15  LYR 26 
LYR C16  C16  C 0 1 N N N N N N -2.651  0.808  -4.417 1.149  2.946  3.158  C16  LYR 27 
LYR C17  C17  C 0 1 N N N N N N -4.035  1.240  -3.854 1.398  2.270  1.782  C17  LYR 28 
LYR C18  C18  C 0 1 N N N N N N -3.732  1.889  -2.470 0.560  3.072  0.755  C18  LYR 29 
LYR C19  C19  C 0 1 N N N N N N -4.727  2.193  -4.806 2.893  2.412  1.414  C19  LYR 30 
LYR H    H    H 0 1 N N N N N N -4.647  -5.251 3.293  -7.012 1.103  2.802  H    LYR 31 
LYR H2   HN2  H 0 1 N Y N N N N -5.930  -5.971 4.000  -7.478 0.319  4.292  H2   LYR 32 
LYR HA   HA   H 0 1 N N N N N N -4.699  -4.023 5.255  -5.376 1.431  4.924  HA   LYR 33 
LYR HXT  HXT  H 0 1 N Y N N N N 0.879   -0.311 0.180  -2.686 1.680  2.560  HXT  LYR 34 
LYR HB2  HB1  H 0 1 N N N N N N -5.311  -4.832 7.298  -3.827 -0.576 4.876  HB2  LYR 35 
LYR HB3  HB2  H 0 1 N N N N N N -5.683  -6.463 6.581  -5.427 -1.002 5.453  HB3  LYR 36 
LYR HG2  HG1  H 0 1 N N N N N N -7.519  -5.629 5.340  -4.330 -1.459 2.646  HG2  LYR 37 
LYR HG3  HG2  H 0 1 N N N N N N -6.992  -3.860 5.569  -5.980 -1.843 3.115  HG3  LYR 38 
LYR HD2  HD1  H 0 1 N N N N N N -7.786  -3.908 7.814  -5.085 -3.466 4.840  HD2  LYR 39 
LYR HD3  HD2  H 0 1 N N N N N N -8.197  -5.706 7.685  -3.444 -3.043 4.362  HD3  LYR 40 
LYR HE2  HE1  H 0 1 N N N N N N -10.196 -4.154 7.663  -4.146 -5.165 3.311  HE2  LYR 41 
LYR HE3  HE2  H 0 1 N N N N N N -10.037 -5.169 6.156  -5.530 -4.360 2.569  HE3  LYR 42 
LYR HZ   HZ   H 0 1 N N N N N N -10.477 -2.704 6.303  -2.706 -3.752 2.057  HZ   LYR 43 
LYR H1   H1   H 0 1 N N N N N N -8.864  -3.571 4.283  -4.805 -5.045 0.473  H1   LYR 44 
LYR H11  1H1  H 0 1 N N N N N N -10.604 -3.677 4.391  -3.367 -5.807 1.121  H11  LYR 45 
LYR HC2  H2   H 0 1 N N N N N N -10.107 -0.834 4.537  -1.868 -4.339 -0.229 HC2  LYR 46 
LYR H41  1H4  H 0 1 N N N N N N -10.056 -2.479 0.760  -4.776 -5.382 -2.949 H41  LYR 47 
LYR H42  2H4  H 0 1 N N N N N N -9.808  -3.601 2.141  -5.072 -3.638 -2.745 H42  LYR 48 
LYR H43  3H4  H 0 1 N N N N N N -8.414  -2.704 1.450  -5.429 -4.753 -1.445 H43  LYR 49 
LYR H5   H5   H 0 1 N N N N N N -10.303 0.565  2.755  -2.373 -4.530 -3.716 H5   LYR 50 
LYR H6   H6   H 0 1 N N N N N N -9.424  1.410  0.892  -0.586 -2.963 -3.425 H6   LYR 51 
LYR H7   H7   H 0 1 N N N N N N -7.832  -1.258 0.235  -1.798 -2.610 -0.599 H7   LYR 52 
LYR H81  1H8  H 0 1 N N N N N N -8.008  2.004  -2.527 0.748  -1.733 -3.087 H81  LYR 53 
LYR H82  2H8  H 0 1 N N N N N N -8.206  2.477  -0.805 1.926  -1.409 -1.819 H82  LYR 54 
LYR H83  3H8  H 0 1 N N N N N N -9.541  1.639  -1.666 0.877  -0.103 -2.432 H83  LYR 55 
LYR H9   H9   H 0 1 N N N N N N -6.537  -1.287 -1.827 -0.726 -1.027 0.941  H9   LYR 56 
LYR H10  H10  H 0 1 N N N N N N -6.891  1.136  -3.482 1.728  0.414  -0.191 H10  LYR 57 
LYR H131 1H13 H 0 0 N N N N N N -5.991  -2.710 -4.774 0.850  -1.798 3.903  H131 LYR 58 
LYR H132 2H13 H 0 0 N N N N N N -5.941  -2.624 -2.980 0.567  -1.849 2.148  H132 LYR 59 
LYR H133 3H13 H 0 0 N N N N N N -4.622  -3.449 -3.877 -0.743 -1.368 3.242  H133 LYR 60 
LYR H141 1H14 H 0 0 N N N N N N -3.190  -1.762 -5.555 -0.103 0.900  4.737  H141 LYR 61 
LYR H142 2H14 H 0 0 N N N N N N -2.882  -2.610 -3.987 1.435  0.080  5.001  H142 LYR 62 
LYR H151 1H15 H 0 0 N N N N N N -1.153  -0.702 -4.623 1.472  2.609  5.265  H151 LYR 63 
LYR H152 2H15 H 0 0 N N N N N N -1.875  -0.579 -2.992 2.717  1.923  4.228  H152 LYR 64 
LYR H161 1H16 H 0 0 N N N N N N -2.820  0.745  -5.502 0.076  3.139  3.291  H161 LYR 65 
LYR H162 2H16 H 0 0 N N N N N N -1.926  1.548  -4.047 1.645  3.925  3.191  H162 LYR 66 
LYR H181 1H18 H 0 0 N N N N N N -4.087  1.225  -1.668 1.023  4.044  0.558  H181 LYR 67 
LYR H182 2H18 H 0 0 N N N N N N -4.247  2.858  -2.399 0.487  2.528  -0.191 H182 LYR 68 
LYR H183 3H18 H 0 0 N N N N N N -2.648  2.042  -2.366 -0.452 3.243  1.134  H183 LYR 69 
LYR H191 1H19 H 0 0 N N N N N N -4.143  2.271  -5.735 3.079  3.373  0.926  H191 LYR 70 
LYR H192 2H19 H 0 0 N N N N N N -4.807  3.185  -4.338 3.516  2.354  2.311  H192 LYR 71 
LYR H193 3H19 H 0 0 N N N N N N -5.734  1.815  -5.037 3.198  1.614  0.730  H193 LYR 72 
# 
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 
LYR N   CA   SING N N 1  
LYR N   H    SING N N 2  
LYR N   H2   SING N N 3  
LYR CA  C    SING N N 4  
LYR CA  CB   SING N N 5  
LYR CA  HA   SING N N 6  
LYR C   O    DOUB N N 7  
LYR C   OXT  SING N N 8  
LYR OXT HXT  SING N N 9  
LYR CB  CG   SING N N 10 
LYR CB  HB2  SING N N 11 
LYR CB  HB3  SING N N 12 
LYR CG  CD   SING N N 13 
LYR CG  HG2  SING N N 14 
LYR CG  HG3  SING N N 15 
LYR CD  CE   SING N N 16 
LYR CD  HD2  SING N N 17 
LYR CD  HD3  SING N N 18 
LYR CE  NZ   SING N N 19 
LYR CE  HE2  SING N N 20 
LYR CE  HE3  SING N N 21 
LYR NZ  C1   SING N N 22 
LYR NZ  HZ   SING N N 23 
LYR C1  C2   SING N N 24 
LYR C1  H1   SING N N 25 
LYR C1  H11  SING N N 26 
LYR C2  C3   DOUB N E 27 
LYR C2  HC2  SING N N 28 
LYR C3  C4   SING N N 29 
LYR C3  C5   SING N N 30 
LYR C4  H41  SING N N 31 
LYR C4  H42  SING N N 32 
LYR C4  H43  SING N N 33 
LYR C5  C6   DOUB N Z 34 
LYR C5  H5   SING N N 35 
LYR C6  C7   SING N N 36 
LYR C6  H6   SING N N 37 
LYR C7  C80  DOUB N E 38 
LYR C7  H7   SING N N 39 
LYR C80 C8   SING N N 40 
LYR C80 C9   SING N N 41 
LYR C8  H81  SING N N 42 
LYR C8  H82  SING N N 43 
LYR C8  H83  SING N N 44 
LYR C9  C10  DOUB N E 45 
LYR C9  H9   SING N N 46 
LYR C10 C11  SING N N 47 
LYR C10 H10  SING N N 48 
LYR C11 C12  DOUB N N 49 
LYR C11 C17  SING N N 50 
LYR C12 C13  SING N N 51 
LYR C12 C14  SING N N 52 
LYR C13 H131 SING N N 53 
LYR C13 H132 SING N N 54 
LYR C13 H133 SING N N 55 
LYR C14 C15  SING N N 56 
LYR C14 H141 SING N N 57 
LYR C14 H142 SING N N 58 
LYR C15 C16  SING N N 59 
LYR C15 H151 SING N N 60 
LYR C15 H152 SING N N 61 
LYR C16 C17  SING N N 62 
LYR C16 H161 SING N N 63 
LYR C16 H162 SING N N 64 
LYR C17 C18  SING N N 65 
LYR C17 C19  SING N N 66 
LYR C18 H181 SING N N 67 
LYR C18 H182 SING N N 68 
LYR C18 H183 SING N N 69 
LYR C19 H191 SING N N 70 
LYR C19 H192 SING N N 71 
LYR C19 H193 SING N N 72 
# 
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 
LYR SMILES           ACDLabs              10.04 "O=C(O)C(N)CCCCNC/C=C(/C=C\C=C(\C=C\C1=C(CCCC1(C)C)C)C)C"                                                                                                                                                      
LYR SMILES_CANONICAL CACTVS               3.341 "CC1=C(\C=C\C(C)=C\C=C/C(C)=C/CNCCCC[C@H](N)C(O)=O)C(C)(C)CCC1"                                                                                                                                                
LYR SMILES           CACTVS               3.341 "CC1=C(C=CC(C)=CC=CC(C)=CCNCCCC[CH](N)C(O)=O)C(C)(C)CCC1"                                                                                                                                                      
LYR SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 "CC1=C(C(CCC1)(C)C)C=C/C(=C/C=C\C(=C\CNCCCC[C@@H](C(=O)O)N)\C)/C"                                                                                                                                              
LYR SMILES           "OpenEye OEToolkits" 1.5.0 "CC1=C(C(CCC1)(C)C)C=CC(=CC=CC(=CCNCCCCC(C(=O)O)N)C)C"                                                                                                                                                         
LYR InChI            InChI                1.03  "InChI=1S/C26H42N2O2/c1-20(14-15-23-22(3)12-9-17-26(23,4)5)10-8-11-21(2)16-19-28-18-7-6-13-24(27)25(29)30/h8,10-11,14-16,24,28H,6-7,9,12-13,17-19,27H2,1-5H3,(H,29,30)/b11-8-,15-14+,20-10+,21-16+/t24-/m0/s1" 
LYR InChIKey         InChI                1.03  FSIGCSBKSBDRLV-GGOCYBHBSA-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 
LYR "SYSTEMATIC NAME" ACDLabs              10.04 "N~6~-[(2E,4Z,6E,8E)-3,7-dimethyl-9-(2,6,6-trimethylcyclohex-1-en-1-yl)nona-2,4,6,8-tetraen-1-yl]-L-lysine"             
LYR "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2S)-2-amino-6-[[(2E,4Z,6E)-3,7-dimethyl-9-(2,6,6-trimethyl-1-cyclohexenyl)nona-2,4,6,8-tetraenyl]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 
LYR "Create component"  2005-03-17 RCSB 
LYR "Modify descriptor" 2011-06-04 RCSB 
LYR "Modify PCM"        2024-09-27 PDBE 
# 
