data_LLP # _chem_comp.id LLP _chem_comp.name "(2S)-2-amino-6-[[3-hydroxy-2-methyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]hexanoic acid" _chem_comp.type "L-PEPTIDE LINKING" _chem_comp.pdbx_type ATOMP _chem_comp.formula "C14 H22 N3 O7 P" _chem_comp.mon_nstd_parent_comp_id LYS _chem_comp.pdbx_synonyms "N'-PYRIDOXYL-LYSINE-5'-MONOPHOSPHATE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 1999-07-08 _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 375.314 _chem_comp.one_letter_code K _chem_comp.three_letter_code LLP _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 ? _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 LLP N1 N1 N 0 1 Y N N N N N -28.372 -11.409 2.891 3.692 -2.911 -0.723 N1 LLP 1 LLP C2 C2 C 0 1 Y N N N N N -27.708 -12.569 3.117 2.555 -3.537 -0.497 C2 LLP 2 LLP "C2'" "C2'" C 0 1 N N N N N N -28.142 -13.864 2.427 2.461 -5.021 -0.741 "C2'" LLP 3 LLP C3 C3 C 0 1 Y N N N N N -26.633 -12.454 3.984 1.443 -2.846 -0.036 C3 LLP 4 LLP O3 O3 O 0 1 N N N N N N -25.895 -13.477 4.286 0.274 -3.495 0.196 O3 LLP 5 LLP C4 C4 C 0 1 Y N N N N N -26.278 -11.219 4.588 1.549 -1.463 0.186 C4 LLP 6 LLP "C4'" "C4'" C 0 1 N N N N N N -25.128 -11.145 5.497 0.396 -0.683 0.677 "C4'" LLP 7 LLP C5 C5 C 0 1 Y N N N N N -27.029 -10.061 4.305 2.780 -0.847 -0.069 C5 LLP 8 LLP C6 C6 C 0 1 Y N N N N N -28.093 -10.208 3.430 3.831 -1.614 -0.526 C6 LLP 9 LLP "C5'" "C5'" C 0 1 N N N N N N -26.695 -8.720 4.922 2.953 0.634 0.151 "C5'" LLP 10 LLP OP4 OP4 O 0 1 N N N N N N -25.333 -8.322 4.650 4.291 1.011 -0.181 OP4 LLP 11 LLP P P P 0 1 N N N N N N -24.616 -7.426 5.781 4.830 2.524 -0.065 P LLP 12 LLP OP1 OP1 O 0 1 N N N N N N -23.323 -6.868 5.254 3.952 3.422 -0.848 OP1 LLP 13 LLP OP2 OP2 O 0 1 N N N N N N -24.392 -8.287 6.992 4.822 2.979 1.480 OP2 LLP 14 LLP OP3 OP3 O 0 1 N N N N N N -25.517 -6.267 6.129 6.331 2.605 -0.640 OP3 LLP 15 LLP N N N 0 1 N N N Y Y N -18.964 -10.492 3.189 -7.060 0.437 1.475 N LLP 16 LLP CA CA C 0 1 N N S Y N N -18.994 -11.931 2.901 -6.483 1.102 0.299 CA LLP 17 LLP CB CB C 0 1 N N N N N N -20.427 -12.401 2.903 -5.288 0.293 -0.209 CB LLP 18 LLP CG CG C 0 1 N N N N N N -20.942 -12.716 4.318 -4.180 0.303 0.846 CG LLP 19 LLP CD CD C 0 1 N N N N N N -21.833 -11.664 4.928 -2.985 -0.507 0.338 CD LLP 20 LLP CE CE C 0 1 N N N N N N -22.902 -12.244 5.836 -1.877 -0.497 1.393 CE LLP 21 LLP NZ NZ N 0 1 N N N N N N -24.273 -12.098 5.273 -0.732 -1.271 0.907 NZ LLP 22 LLP C C C 0 1 N N N Y N Y -18.063 -12.161 1.735 -7.524 1.196 -0.786 C LLP 23 LLP O O O 0 1 N N N Y N Y -16.826 -12.095 2.005 -8.486 0.465 -0.765 O LLP 24 LLP OXT OXT O 0 1 N Y N Y N Y -18.442 -12.261 0.464 -7.382 2.090 -1.777 OXT LLP 25 LLP "H2'1" "H2'1" H 0 0 N N N N N N -29.011 -13.664 1.783 2.729 -5.557 0.169 "H2'1" LLP 26 LLP "H2'2" "H2'2" H 0 0 N N N N N N -27.313 -14.249 1.815 1.441 -5.278 -1.028 "H2'2" LLP 27 LLP "H2'3" "H2'3" H 0 0 N N N N N N -28.414 -14.611 3.187 3.145 -5.301 -1.543 "H2'3" LLP 28 LLP HO3 HO3 H 0 1 N N N N N N -25.212 -13.208 4.889 0.185 -3.836 1.096 HO3 LLP 29 LLP "H4'1" "H4'1" H 0 0 N N N N N N -25.007 -10.390 6.260 0.495 0.380 0.842 "H4'1" LLP 30 LLP H6 H6 H 0 1 N N N N N N -28.703 -9.353 3.179 4.783 -1.145 -0.725 H6 LLP 31 LLP "H5'1" "H5'1" H 0 0 N N N N N N -27.376 -7.960 4.510 2.254 1.180 -0.483 "H5'1" LLP 32 LLP "H5'2" "H5'2" H 0 0 N N N N N N -26.835 -8.786 6.011 2.757 0.871 1.196 "H5'2" LLP 33 LLP HOP2 HOP2 H 0 0 N N N N N N -23.464 -8.314 7.195 5.377 2.434 2.053 HOP2 LLP 34 LLP HOP3 HOP3 H 0 0 N N N N N N -25.071 -5.450 5.939 6.720 3.489 -0.602 HOP3 LLP 35 LLP H H H 0 1 N N N Y Y N -18.017 -10.171 3.190 -7.811 0.985 1.868 H LLP 36 LLP H2 HN2 H 0 1 N Y N Y Y N -19.481 -10.001 2.488 -7.374 -0.494 1.247 HN2 LLP 37 LLP HA HA H 0 1 N N N Y N N -18.519 -12.424 3.762 -6.153 2.104 0.574 HA LLP 38 LLP HB2 HB2 H 0 1 N N N N N N -21.057 -11.613 2.466 -5.599 -0.734 -0.399 HB2 LLP 39 LLP HB3 HB3 H 0 1 N N N N N N -20.500 -13.311 2.290 -4.915 0.737 -1.132 HB3 LLP 40 LLP HG2 HG2 H 0 1 N N N N N N -21.510 -13.657 4.271 -3.868 1.330 1.037 HG2 LLP 41 LLP HG3 HG3 H 0 1 N N N N N N -20.070 -12.846 4.976 -4.553 -0.141 1.769 HG3 LLP 42 LLP HD2 HD2 H 0 1 N N N N N N -21.209 -10.975 5.517 -3.296 -1.534 0.148 HD2 LLP 43 LLP HD3 HD3 H 0 1 N N N N N N -22.326 -11.109 4.116 -2.611 -0.063 -0.585 HD3 LLP 44 LLP HE2 HE2 H 0 1 N N N N N N -22.695 -13.314 5.985 -1.565 0.530 1.584 HE2 LLP 45 LLP HE3 HE3 H 0 1 N N N N N N -22.862 -11.724 6.804 -2.250 -0.940 2.316 HE3 LLP 46 LLP HXT HXT H 0 1 N Y N Y N Y -17.675 -12.269 -0.096 -8.075 2.113 -2.450 HXT LLP 47 # 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 LLP N1 C2 DOUB Y N 1 LLP N1 C6 SING Y N 2 LLP C2 "C2'" SING N N 3 LLP C2 C3 SING Y N 4 LLP C3 O3 SING N N 5 LLP C3 C4 DOUB Y N 6 LLP C4 "C4'" SING N N 7 LLP C4 C5 SING Y N 8 LLP "C4'" NZ DOUB N N 9 LLP C5 C6 DOUB Y N 10 LLP C5 "C5'" SING N N 11 LLP "C5'" OP4 SING N N 12 LLP OP4 P SING N N 13 LLP P OP1 DOUB N N 14 LLP P OP2 SING N N 15 LLP P OP3 SING N N 16 LLP N CA SING N N 17 LLP CA CB SING N N 18 LLP CA C SING N N 19 LLP CB CG SING N N 20 LLP CG CD SING N N 21 LLP CD CE SING N N 22 LLP CE NZ SING N N 23 LLP C O DOUB N N 24 LLP C OXT SING N N 25 LLP "C2'" "H2'1" SING N N 26 LLP "C2'" "H2'2" SING N N 27 LLP "C2'" "H2'3" SING N N 28 LLP O3 HO3 SING N N 29 LLP "C4'" "H4'1" SING N N 30 LLP C6 H6 SING N N 31 LLP "C5'" "H5'1" SING N N 32 LLP "C5'" "H5'2" SING N N 33 LLP OP2 HOP2 SING N N 34 LLP OP3 HOP3 SING N N 35 LLP N H SING N N 36 LLP N H2 SING N N 37 LLP CA HA SING N N 38 LLP CB HB2 SING N N 39 LLP CB HB3 SING N N 40 LLP CG HG2 SING N N 41 LLP CG HG3 SING N N 42 LLP CD HD2 SING N N 43 LLP CD HD3 SING N N 44 LLP CE HE2 SING N N 45 LLP CE HE3 SING N N 46 LLP OXT HXT SING N N 47 # 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 LLP SMILES ACDLabs 12.01 "n1c(C)c(O)c(\C=N\CCCCC(N)C(=O)O)c(c1)COP(=O)(O)O" LLP InChI InChI 1.03 "InChI=1S/C14H22N3O7P/c1-9-13(18)11(10(6-17-9)8-24-25(21,22)23)7-16-5-3-2-4-12(15)14(19)20/h6-7,12,18H,2-5,8,15H2,1H3,(H,19,20)(H2,21,22,23)/b16-7+/t12-/m0/s1" LLP InChIKey InChI 1.03 YQSOQJORMNSDJL-QFULYMJESA-N LLP SMILES_CANONICAL CACTVS 3.385 "Cc1ncc(CO[P](O)(O)=O)c(C=NCCCC[C@H](N)C(O)=O)c1O" LLP SMILES CACTVS 3.385 "Cc1ncc(CO[P](O)(O)=O)c(C=NCCCC[CH](N)C(O)=O)c1O" LLP SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/CCCCC(C(=O)O)N)O" LLP SMILES "OpenEye OEToolkits" 1.7.6 "Cc1c(c(c(cn1)COP(=O)(O)O)C=NCCCCC(C(=O)O)N)O" # 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 LLP "SYSTEMATIC NAME" ACDLabs 12.01 "(E)-N~6~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-lysine" LLP "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "2-azanyl-6-[(E)-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]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 LLP "Create component" 1999-07-08 RCSB LLP "Modify formula" 2015-10-26 RCSB LLP "Modify value order" 2015-10-26 RCSB LLP "Modify synonyms" 2021-03-01 PDBE LLP "Modify backbone" 2023-11-03 PDBE LLP "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id LLP _pdbx_chem_comp_synonyms.name "N'-PYRIDOXYL-LYSINE-5'-MONOPHOSPHATE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id LLP _pdbx_chem_comp_pcm.modified_residue_id LYS _pdbx_chem_comp_pcm.type "Pyridoxal phosphate" _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 PTM-0387 _pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ? #