data_XPL # _chem_comp.id XPL _chem_comp.name "N~6~-[(3R,5R)-5-amino-3-methyl-D-prolyl]-L-lysine" _chem_comp.type "L-PEPTIDE LINKING" _chem_comp.pdbx_type ATOMP _chem_comp.formula "C12 H24 N4 O3" _chem_comp.mon_nstd_parent_comp_id PYL _chem_comp.pdbx_synonyms "4-amino reduced pyrrolysine" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2014-07-30 _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 272.344 _chem_comp.one_letter_code O _chem_comp.three_letter_code XPL _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 1L2Q _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 XPL C C C 0 1 N N N Y N Y 20.008 90.748 89.668 6.314 0.450 -0.033 C XPL 1 XPL N N N 0 1 N N N Y Y N 18.299 92.300 89.090 5.278 -1.737 0.177 N XPL 2 XPL O O O 0 1 N N N Y N Y 20.909 91.577 89.794 7.014 0.138 0.902 O XPL 3 XPL CA CA C 0 1 N N S Y N N 18.844 90.999 88.724 5.121 -0.394 -0.396 CA XPL 4 XPL CB CB C 0 1 N N N N N N 19.329 90.987 87.269 3.850 0.252 0.160 CB XPL 5 XPL CD CD C 0 1 N N N N N N 21.235 89.310 86.927 1.357 0.110 0.243 CD XPL 6 XPL CE CE C 0 1 N N N N N N 22.024 89.815 85.713 0.134 -0.678 -0.231 CE XPL 7 XPL CG CG C 0 1 N N N N N N 19.736 89.593 86.775 2.628 -0.536 -0.313 CG XPL 8 XPL NZ NZ N 0 1 N N N N N N 23.458 89.367 85.723 -1.082 -0.060 0.302 NZ XPL 9 XPL OXT OXT O 0 1 N Y N Y N Y 19.963 89.612 90.352 6.598 1.553 -0.744 OXT XPL 10 XPL C2 C2 C 0 1 N N N N N N 24.375 89.776 84.840 -2.288 -0.587 0.013 C2 XPL 11 XPL N2 N2 N 0 1 N N N N N N 26.023 88.000 84.819 -4.658 -0.910 0.501 N2 XPL 12 XPL O2 O2 O 0 1 N N N N N N 24.172 90.664 84.039 -2.367 -1.574 -0.687 O2 XPL 13 XPL N3 N3 N 0 1 N N N N N N 28.327 87.302 84.930 -7.041 -0.684 0.144 N3 XPL 14 XPL CA2 CA2 C 0 1 N N R N N N 25.797 89.376 85.285 -3.539 0.049 0.561 CA2 XPL 15 XPL CB2 CB2 C 0 1 N N N N N N 26.257 90.827 87.302 -3.481 2.569 0.357 CB2 XPL 16 XPL CD2 CD2 C 0 1 N N N N N N 27.564 88.867 86.670 -5.481 1.179 -0.346 CD2 XPL 17 XPL CE2 CE2 C 0 1 N N R N N N 27.154 87.701 85.724 -5.708 -0.353 -0.378 CE2 XPL 18 XPL CG2 CG2 C 0 1 N N R N N N 26.176 89.452 86.748 -3.932 1.265 -0.305 CG2 XPL 19 XPL H HN H 0 1 N N N Y Y N 17.524 92.517 88.496 6.075 -2.210 -0.223 HN XPL 20 XPL H2 HNA H 0 1 N Y N Y Y N 17.993 92.277 90.042 5.350 -1.695 1.183 HNA XPL 21 XPL HA HA H 0 1 N N N Y N N 18.085 90.214 88.861 5.045 -0.469 -1.481 HA XPL 22 XPL HB HB H 0 1 N N N N N N 18.517 91.361 86.628 3.887 0.246 1.250 HB XPL 23 XPL HBA HBA H 0 1 N N N N N N 20.199 91.654 87.186 3.780 1.280 -0.196 HBA XPL 24 XPL HD HD H 0 1 N N N N N N 21.386 88.225 87.026 1.287 1.138 -0.113 HD XPL 25 XPL HDA HDA H 0 1 N N N N N N 21.605 89.816 87.831 1.394 0.104 1.332 HDA XPL 26 XPL HE HE H 0 1 N N N N N N 21.544 89.436 84.799 0.098 -0.673 -1.320 HE XPL 27 XPL HEA HEA H 0 1 N N N N N N 21.999 90.915 85.711 0.205 -1.706 0.125 HEA XPL 28 XPL HG HG H 0 1 N N N N N N 19.178 88.841 87.353 2.591 -0.530 -1.403 HG XPL 29 XPL HGA HGA H 0 1 N N N N N N 19.471 89.508 85.711 2.698 -1.564 0.042 HGA XPL 30 XPL HNZ HNZ H 0 1 N N N N N N 23.744 88.724 86.433 -1.019 0.730 0.862 HNZ XPL 31 XPL HXT HXT H 0 0 N Y N Y N Y 20.716 89.559 90.928 7.372 2.065 -0.470 HXT XPL 32 XPL HN2 HN2 H 0 1 N N N N N N 25.235 87.406 84.979 -4.345 -1.809 0.167 HN2 XPL 33 XPL HN3 HN3 H 0 1 N N N N N N 29.091 87.100 85.542 -7.179 -1.683 0.176 HN3 XPL 34 XPL HN3A HN3A H 0 0 N N N N N N 28.105 86.488 84.394 -7.186 -0.270 1.053 HN3A XPL 35 XPL HA2 HA2 H 0 1 N N N N N N 26.494 90.029 84.738 -3.375 0.363 1.592 HA2 XPL 36 XPL HB2 HB2 H 0 1 N N N N N N 26.537 90.779 88.365 -2.398 2.558 0.478 HB2 XPL 37 XPL HB2A HB2A H 0 0 N N N N N N 27.015 91.401 86.749 -3.768 3.413 -0.271 HB2A XPL 38 XPL HB2B HB2B H 0 0 N N N N N N 25.279 91.320 87.203 -3.955 2.664 1.334 HB2B XPL 39 XPL HD2 HD2 H 0 1 N N N N N N 27.941 88.520 87.644 -5.874 1.651 -1.246 HD2 XPL 40 XPL HD2A HD2A H 0 0 N N N N N N 28.296 89.552 86.217 -5.920 1.620 0.548 HD2A XPL 41 XPL HE2 HE2 H 0 1 N N N N N N 26.866 86.852 86.361 -5.594 -0.734 -1.393 HE2 XPL 42 XPL HG2 HG2 H 0 1 N N N N N N 25.516 88.816 87.356 -3.514 1.175 -1.307 HG2 XPL 43 # 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 XPL CA C SING N N 1 XPL C O DOUB N N 2 XPL C OXT SING N N 3 XPL CA N SING N N 4 XPL N H SING N N 5 XPL N H2 SING N N 6 XPL CB CA SING N N 7 XPL CA HA SING N N 8 XPL CG CB SING N N 9 XPL CB HB SING N N 10 XPL CB HBA SING N N 11 XPL CE CD SING N N 12 XPL CG CD SING N N 13 XPL CD HD SING N N 14 XPL CD HDA SING N N 15 XPL CE NZ SING N N 16 XPL CE HE SING N N 17 XPL CE HEA SING N N 18 XPL CG HG SING N N 19 XPL CG HGA SING N N 20 XPL C2 NZ SING N N 21 XPL NZ HNZ SING N N 22 XPL OXT HXT SING N N 23 XPL O2 C2 DOUB N N 24 XPL C2 CA2 SING N N 25 XPL N2 CA2 SING N N 26 XPL N2 CE2 SING N N 27 XPL N2 HN2 SING N N 28 XPL N3 CE2 SING N N 29 XPL N3 HN3 SING N N 30 XPL N3 HN3A SING N N 31 XPL CA2 CG2 SING N N 32 XPL CA2 HA2 SING N N 33 XPL CG2 CB2 SING N N 34 XPL CB2 HB2 SING N N 35 XPL CB2 HB2A SING N N 36 XPL CB2 HB2B SING N N 37 XPL CE2 CD2 SING N N 38 XPL CD2 CG2 SING N N 39 XPL CD2 HD2 SING N N 40 XPL CD2 HD2A SING N N 41 XPL CE2 HE2 SING N N 42 XPL CG2 HG2 SING N N 43 # 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 XPL SMILES ACDLabs 12.01 "O=C(NCCCCC(C(=O)O)N)C1NC(N)CC1C" XPL InChI InChI 1.03 "InChI=1S/C12H24N4O3/c1-7-6-9(14)16-10(7)11(17)15-5-3-2-4-8(13)12(18)19/h7-10,16H,2-6,13-14H2,1H3,(H,15,17)(H,18,19)/t7-,8+,9-,10-/m1/s1" XPL InChIKey InChI 1.03 BUXWWMHLAXRADI-UTINFBMNSA-N XPL SMILES_CANONICAL CACTVS 3.385 "C[C@@H]1C[C@H](N)N[C@H]1C(=O)NCCCC[C@H](N)C(O)=O" XPL SMILES CACTVS 3.385 "C[CH]1C[CH](N)N[CH]1C(=O)NCCCC[CH](N)C(O)=O" XPL SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C[C@@H]1C[C@@H](N[C@H]1C(=O)NCCCC[C@@H](C(=O)O)N)N" XPL SMILES "OpenEye OEToolkits" 1.7.6 "CC1CC(NC1C(=O)NCCCCC(C(=O)O)N)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 XPL "SYSTEMATIC NAME" ACDLabs 12.01 "N~6~-[(3R,5R)-5-amino-3-methyl-D-prolyl]-L-lysine" XPL "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(2S)-2-azanyl-6-[[(2R,3R,5R)-5-azanyl-3-methyl-pyrrolidin-2-yl]carbonylamino]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 XPL "Create component" 2014-07-30 RCSB XPL "Modify synonyms" 2020-06-05 PDBE XPL "Modify backbone" 2023-11-03 PDBE XPL "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id XPL _pdbx_chem_comp_synonyms.name "4-amino reduced pyrrolysine" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id XPL _pdbx_chem_comp_pcm.modified_residue_id PYL _pdbx_chem_comp_pcm.type Amination _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 ? #