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 #