data_PE1 # _chem_comp.id PE1 _chem_comp.name "N~2~-({3-HYDROXY-2-METHYL-5-[(PHOSPHONOOXY)METHYL]PYRIDIN-4-YL}METHYL)-L-LYSINE" _chem_comp.type "L-PEPTIDE LINKING" _chem_comp.pdbx_type ATOMP _chem_comp.formula "C14 H24 N3 O7 P" _chem_comp.mon_nstd_parent_comp_id LYS _chem_comp.pdbx_synonyms "PYRIDOXYL-GLUTAMIC ACID-5'-MONOPHOSPHATE" _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2004-11-12 _chem_comp.pdbx_modified_date 2020-06-17 _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 377.330 _chem_comp.one_letter_code K _chem_comp.three_letter_code PE1 _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 1WCB _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # # 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.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 PE1 N1 N1 N 0 1 Y N N 4.725 62.607 -10.008 1.398 -3.639 0.375 N1 PE1 1 PE1 C2 C2 C 0 1 Y N N 4.563 61.278 -9.696 0.180 -3.788 -0.108 C2 PE1 2 PE1 C2A C2A C 0 1 N N N 5.748 60.496 -9.169 -0.482 -5.141 -0.060 C2A PE1 3 PE1 C3 C3 C 0 1 Y N N 3.246 60.715 -9.901 -0.498 -2.711 -0.660 C3 PE1 4 PE1 O3 O3 O 0 1 N N N 3.022 59.416 -9.609 -1.754 -2.868 -1.156 O3 PE1 5 PE1 C4 C4 C 0 1 Y N N 2.175 61.550 -10.421 0.124 -1.467 -0.697 C4 PE1 6 PE1 C4A C4A C 0 1 N N N 0.810 60.895 -10.619 -0.576 -0.271 -1.287 C4A PE1 7 PE1 C5 C5 C 0 1 Y N N 2.453 62.939 -10.725 1.404 -1.356 -0.179 C5 PE1 8 PE1 C6 C6 C 0 1 Y N N 3.738 63.432 -10.501 2.016 -2.475 0.355 C6 PE1 9 PE1 C5A C5A C 0 1 N N N 1.390 63.903 -11.288 2.122 -0.031 -0.197 C5A PE1 10 PE1 O4P O4P O 0 1 N N N 2.012 64.741 -12.294 3.415 -0.181 0.391 O4P PE1 11 PE1 P P P 0 1 N N N 1.234 66.026 -12.900 4.459 1.036 0.539 P PE1 12 PE1 O1P O1P O 0 1 N N N 0.630 66.739 -11.744 3.814 2.153 1.264 O1P PE1 13 PE1 O2P O2P O 0 1 N N N 0.159 65.471 -13.893 5.752 0.538 1.359 O2P PE1 14 PE1 O3P O3P O 0 1 N N N 2.252 66.821 -13.699 4.910 1.536 -0.924 O3P PE1 15 PE1 N N N 0 1 N N N 0.489 59.951 -9.509 -1.333 0.421 -0.236 N PE1 16 PE1 CA CA C 0 1 N N S -0.789 59.199 -9.733 -2.031 1.596 -0.775 CA PE1 17 PE1 C C C 0 1 N N N -1.021 58.276 -8.522 -1.093 2.776 -0.787 C PE1 18 PE1 O O O 0 1 N N N 0.136 58.123 -7.822 -1.517 3.966 -1.242 O PE1 19 PE1 CB CB C 0 1 N N N -0.763 58.393 -11.044 -3.243 1.916 0.101 CB PE1 20 PE1 CG CG C 0 1 N N N 0.421 57.439 -11.090 -4.253 0.770 0.013 CG PE1 21 PE1 CD CD C 0 1 N N N -0.045 56.022 -11.347 -5.466 1.091 0.890 CD PE1 22 PE1 CE CE C 0 1 N N N 0.343 55.568 -12.737 -6.475 -0.056 0.802 CE PE1 23 PE1 OXT OXT O 0 1 N Y N -2.167 57.733 -8.193 0.040 2.651 -0.386 OXT PE1 24 PE1 NZ NZ N 0 1 N N N 0.377 54.091 -12.831 -7.639 0.252 1.644 NZ PE1 25 PE1 H6 H6 H 0 1 N N N 3.961 64.467 -10.715 3.013 -2.394 0.761 H6 PE1 26 PE1 H2A1 H2A1 H 0 0 N N N 6.626 61.156 -9.110 -1.035 -5.242 0.874 H2A1 PE1 27 PE1 H2A2 H2A2 H 0 0 N N N 5.514 60.107 -8.167 -1.168 -5.240 -0.901 H2A2 PE1 28 PE1 H2A3 H2A3 H 0 0 N N N 5.965 59.657 -9.847 0.279 -5.919 -0.118 H2A3 PE1 29 PE1 H3 H3 H 0 1 N N N 2.116 59.200 -9.797 -2.455 -2.720 -0.507 H3 PE1 30 PE1 H4A1 H4A1 H 0 0 N N N 0.039 61.679 -10.655 0.162 0.410 -1.711 H4A1 PE1 31 PE1 H4A2 H4A2 H 0 0 N N N 0.814 60.341 -11.569 -1.259 -0.599 -2.071 H4A2 PE1 32 PE1 H H H 0 1 N N N 1.236 59.292 -9.425 -1.980 -0.207 0.217 H PE1 33 PE1 H5A1 H5A1 H 0 0 N N N 0.570 63.327 -11.741 2.228 0.311 -1.227 H5A1 PE1 34 PE1 H5A2 H5A2 H 0 0 N N N 0.992 64.531 -10.477 1.547 0.701 0.371 H5A2 PE1 35 PE1 H2P H2P H 0 1 N N N -0.709 65.692 -13.576 6.424 1.222 1.486 H2P PE1 36 PE1 H3P H3P H 0 1 N N N 2.348 67.686 -13.319 5.341 0.854 -1.457 H3P PE1 37 PE1 HA HA H 0 1 N N N -1.620 59.918 -9.785 -2.363 1.386 -1.792 HA PE1 38 PE1 HB1C HB1C H 0 0 N N N -1.693 57.812 -11.124 -2.922 2.039 1.135 HB1C PE1 39 PE1 HB2C HB2C H 0 0 N N N -0.692 59.091 -11.891 -3.709 2.839 -0.246 HB2C PE1 40 PE1 HB HB H 0 1 N N N -0.021 57.567 -7.068 -0.880 4.693 -1.229 HB PE1 41 PE1 HG1C HG1C H 0 0 N N N 1.102 57.747 -11.897 -4.575 0.648 -1.021 HG1C PE1 42 PE1 HG2C HG2C H 0 0 N N N 0.952 57.476 -10.127 -3.787 -0.152 0.361 HG2C PE1 43 PE1 HD1C HD1C H 0 0 N N N 0.417 55.352 -10.607 -5.144 1.213 1.924 HD1C PE1 44 PE1 HD2C HD2C H 0 0 N N N -1.140 55.979 -11.247 -5.931 2.013 0.543 HD2C PE1 45 PE1 HE1C HE1C H 0 0 N N N -0.391 55.956 -13.459 -6.797 -0.178 -0.232 HE1C PE1 46 PE1 HE2C HE2C H 0 0 N N N 1.340 55.965 -12.978 -6.009 -0.978 1.150 HE2C PE1 47 PE1 HZ1N HZ1N H 0 0 N N N 0.636 53.821 -13.759 -8.321 -0.490 1.603 HZ1N PE1 48 PE1 HZ2N HZ2N H 0 0 N N N 1.046 53.731 -12.181 -7.359 0.434 2.596 HZ2N PE1 49 # # 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 PE1 N1 C2 SING Y N 1 PE1 N1 C6 DOUB Y N 2 PE1 C2 C2A SING N N 3 PE1 C2 C3 DOUB Y N 4 PE1 C3 O3 SING N N 5 PE1 C3 C4 SING Y N 6 PE1 C4 C4A SING N N 7 PE1 C4 C5 DOUB Y N 8 PE1 C4A N SING N N 9 PE1 C5 C6 SING Y N 10 PE1 C5 C5A SING N N 11 PE1 C5A O4P SING N N 12 PE1 O4P P SING N N 13 PE1 P O1P DOUB N N 14 PE1 P O2P SING N N 15 PE1 P O3P SING N N 16 PE1 N CA SING N N 17 PE1 CA C SING N N 18 PE1 CA CB SING N N 19 PE1 C O SING N N 20 PE1 C OXT DOUB N N 21 PE1 CB CG SING N N 22 PE1 CG CD SING N N 23 PE1 CD CE SING N N 24 PE1 CE NZ SING N N 25 PE1 C6 H6 SING N N 26 PE1 C2A H2A1 SING N N 27 PE1 C2A H2A2 SING N N 28 PE1 C2A H2A3 SING N N 29 PE1 O3 H3 SING N N 30 PE1 C4A H4A1 SING N N 31 PE1 C4A H4A2 SING N N 32 PE1 N H SING N N 33 PE1 C5A H5A1 SING N N 34 PE1 C5A H5A2 SING N N 35 PE1 O2P H2P SING N N 36 PE1 O3P H3P SING N N 37 PE1 CA HA SING N N 38 PE1 CB HB1C SING N N 39 PE1 CB HB2C SING N N 40 PE1 O HB SING N N 41 PE1 CG HG1C SING N N 42 PE1 CG HG2C SING N N 43 PE1 CD HD1C SING N N 44 PE1 CD HD2C SING N N 45 PE1 CE HE1C SING N N 46 PE1 CE HE2C SING N N 47 PE1 NZ HZ1N SING N N 48 PE1 NZ HZ2N SING N N 49 # # 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 PE1 SMILES ACDLabs 12.01 "O=C(O)C(NCc1c(cnc(c1O)C)COP(=O)(O)O)CCCCN" PE1 InChI InChI 1.03 "InChI=1S/C14H24N3O7P/c1-9-13(18)11(10(6-16-9)8-24-25(21,22)23)7-17-12(14(19)20)4-2-3-5-15/h6,12,17-18H,2-5,7-8,15H2,1H3,(H,19,20)(H2,21,22,23)/t12-/m0/s1" PE1 InChIKey InChI 1.03 GQMAOPRRHWJXFB-LBPRGKRZSA-N PE1 SMILES_CANONICAL CACTVS 3.385 "Cc1ncc(CO[P](O)(O)=O)c(CN[C@@H](CCCCN)C(O)=O)c1O" PE1 SMILES CACTVS 3.385 "Cc1ncc(CO[P](O)(O)=O)c(CN[CH](CCCCN)C(O)=O)c1O" PE1 SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 "Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H](CCCCN)C(=O)O)O" PE1 SMILES "OpenEye OEToolkits" 1.9.2 "Cc1c(c(c(cn1)COP(=O)(O)O)CNC(CCCCN)C(=O)O)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 PE1 "SYSTEMATIC NAME" ACDLabs 12.01 "N~2~-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)-L-lysine" PE1 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 "(2S)-6-azanyl-2-[[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylamino]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 PE1 "Create component" 2004-11-12 EBI PE1 "Modify descriptor" 2011-06-04 RCSB PE1 "Other modification" 2012-01-26 EBI PE1 "Modify name" 2012-01-31 EBI PE1 "Modify parent residue" 2012-01-31 EBI PE1 "Modify linking type" 2012-01-31 EBI PE1 "Other modification" 2012-01-31 EBI PE1 "Modify descriptor" 2014-09-05 RCSB PE1 "Modify one letter code" 2019-05-07 EBI PE1 "Modify synonyms" 2020-06-05 PDBE # _pdbx_chem_comp_synonyms.ordinal 1 _pdbx_chem_comp_synonyms.comp_id PE1 _pdbx_chem_comp_synonyms.name "PYRIDOXYL-GLUTAMIC ACID-5'-MONOPHOSPHATE" _pdbx_chem_comp_synonyms.provenance ? _pdbx_chem_comp_synonyms.type ? ##