data_EXA # _chem_comp.id EXA _chem_comp.name "N~6~-[(R)-[(E)-(1-carboxyethylidene)amino]{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl]-L-lysine" _chem_comp.type "peptide linking" _chem_comp.pdbx_type ATOMP _chem_comp.formula "C17 H27 N4 O9 P" _chem_comp.mon_nstd_parent_comp_id LYS _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2017-03-01 _chem_comp.pdbx_modified_date 2023-11-27 _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 462.391 _chem_comp.one_letter_code K _chem_comp.three_letter_code EXA _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 5V12 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site RCSB # 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_n_terminal_atom_flag _chem_comp_atom.pdbx_backbone_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 EXA N N1 N 0 1 N N N N N N 32.591 -74.266 5.087 7.255 -0.035 1.745 N EXA 1 EXA CA C1 C 0 1 N N S N N N 32.244 -75.644 4.640 7.132 -0.832 0.517 CA EXA 2 EXA CB C2 C 0 1 N N N N N N 33.372 -76.627 4.951 5.988 -0.280 -0.336 CB EXA 3 EXA CG C3 C 0 1 N N N N N N 34.390 -76.703 3.815 4.662 -0.470 0.405 CG EXA 4 EXA CD C4 C 0 1 N N N N N N 35.360 -77.868 4.012 3.518 0.082 -0.448 CD EXA 5 EXA CE C5 C 0 1 N N N N N N 36.517 -77.820 3.016 2.193 -0.108 0.292 CE EXA 6 EXA NZ N2 N 0 1 N N N N N N 37.370 -79.016 3.153 1.094 0.422 -0.526 NZ EXA 7 EXA "C4'" C6 C 0 1 N N S N N N 38.744 -78.747 2.668 -0.197 0.257 0.154 "C4'" EXA 8 EXA C4 C7 C 0 1 Y N N N N N 39.719 -79.391 3.592 -0.992 1.532 0.040 C4 EXA 9 EXA C3 C8 C 0 1 Y N N N N N 39.385 -80.661 4.280 -0.353 2.765 -0.047 C3 EXA 10 EXA O3 O1 O 0 1 N N N N N N 38.187 -81.275 4.083 1.004 2.840 -0.032 O3 EXA 11 EXA C2 C9 C 0 1 Y N N N N N 40.398 -81.252 5.192 -1.120 3.915 -0.152 C2 EXA 12 EXA "C2'" C10 C 0 1 N N N N N N 40.101 -82.539 5.915 -0.442 5.258 -0.247 "C2'" EXA 13 EXA C5 C11 C 0 1 Y N N N N N 41.065 -78.823 3.888 -2.377 1.505 0.014 C5 EXA 14 EXA C6 C12 C 0 1 Y N N N N N 41.915 -79.484 4.772 -3.073 2.694 -0.092 C6 EXA 15 EXA N1 N3 N 0 1 Y N N N N N 41.588 -80.635 5.381 -2.437 3.847 -0.168 N1 EXA 16 EXA "C5'" C13 C 0 1 N N N N N N 41.547 -77.536 3.264 -3.115 0.194 0.099 "C5'" EXA 17 EXA OP4 O2 O 0 1 N N N N N N 40.607 -76.492 3.478 -4.523 0.436 0.052 OP4 EXA 18 EXA P P1 P 0 1 N N N N N N 40.804 -75.106 2.701 -5.618 -0.742 0.119 P EXA 19 EXA OP1 O3 O 0 1 N N N N N N 40.881 -75.379 1.219 -5.344 -1.732 -0.946 OP1 EXA 20 EXA OP2 O4 O 0 1 N N N N N N 39.625 -74.218 3.018 -5.542 -1.464 1.556 OP2 EXA 21 EXA OP3 O5 O 0 1 N N N N N N 42.102 -74.502 3.179 -7.089 -0.120 -0.091 OP3 EXA 22 EXA C C14 C 0 1 N N N N N N 30.960 -76.139 5.244 8.420 -0.758 -0.262 C EXA 23 EXA O O6 O 0 1 N N N N N N 29.977 -76.302 4.492 9.199 0.143 -0.056 O EXA 24 EXA N3 N4 N 0 1 N N N N N N 38.919 -79.207 1.295 -0.941 -0.840 -0.469 N3 EXA 25 EXA C7 C15 C 0 1 N N N N N N 38.854 -78.380 0.246 -1.163 -1.918 0.186 C7 EXA 26 EXA C8 C16 C 0 1 N N N N N N 39.094 -78.865 -1.112 -1.987 -2.994 -0.413 C8 EXA 27 EXA C9 C17 C 0 1 N N N N N N 38.563 -77.104 0.416 -0.585 -2.092 1.567 C9 EXA 28 EXA O10 O7 O 0 1 N N N N N N 40.010 -78.345 -1.786 -2.197 -4.015 0.208 O10 EXA 29 EXA O11 O8 O 0 1 N N N N N N 38.372 -79.778 -1.570 -2.504 -2.838 -1.647 O11 EXA 30 EXA OXT O9 O 0 1 N Y N N N N 30.694 -75.795 6.502 8.701 -1.692 -1.184 OXT EXA 31 EXA H H1 H 0 1 N N N N N N 31.837 -73.645 4.872 7.962 -0.418 2.355 H EXA 32 EXA H2 H2 H 0 1 N N N N N N 32.751 -74.266 6.074 7.449 0.932 1.531 H2 EXA 33 EXA HA H4 H 0 1 N N N N N N 32.115 -75.624 3.548 6.924 -1.870 0.777 HA EXA 34 EXA HB2 H5 H 0 1 N N N N N N 32.940 -77.626 5.109 6.152 0.781 -0.521 HB2 EXA 35 EXA HB3 H6 H 0 1 N N N N N N 33.885 -76.301 5.868 5.953 -0.814 -1.286 HB3 EXA 36 EXA HG2 H7 H 0 1 N N N N N N 34.961 -75.763 3.783 4.498 -1.531 0.590 HG2 EXA 37 EXA HG3 H8 H 0 1 N N N N N N 33.855 -76.840 2.864 4.697 0.064 1.355 HG3 EXA 38 EXA HD2 H9 H 0 1 N N N N N N 34.813 -78.813 3.877 3.682 1.143 -0.634 HD2 EXA 39 EXA HD3 H10 H 0 1 N N N N N N 35.767 -77.823 5.033 3.483 -0.452 -1.398 HD3 EXA 40 EXA HE2 H11 H 0 1 N N N N N N 37.121 -76.921 3.207 2.029 -1.169 0.478 HE2 EXA 41 EXA HE3 H12 H 0 1 N N N N N N 36.113 -77.780 1.994 2.228 0.426 1.242 HE3 EXA 42 EXA HZ1 H13 H 0 1 N N N N N N 36.975 -79.763 2.618 1.081 -0.012 -1.438 HZ1 EXA 43 EXA H15 H15 H 0 1 N N N N N N 38.912 -77.660 2.696 -0.026 0.028 1.206 H15 EXA 44 EXA H16 H16 H 0 1 N N N N N N 38.149 -82.070 4.601 1.411 2.792 -0.908 H16 EXA 45 EXA H17 H17 H 0 1 N N N N N N 40.961 -82.815 6.542 -0.262 5.500 -1.294 H17 EXA 46 EXA H18 H18 H 0 1 N N N N N N 39.212 -82.406 6.550 -1.082 6.020 0.197 H18 EXA 47 EXA H19 H19 H 0 1 N N N N N N 39.912 -83.336 5.181 0.507 5.224 0.287 H19 EXA 48 EXA H20 H20 H 0 1 N N N N N N 42.883 -79.050 4.977 -4.153 2.680 -0.113 H20 EXA 49 EXA H21 H21 H 0 1 N N N N N N 41.680 -77.686 2.182 -2.828 -0.440 -0.739 H21 EXA 50 EXA H22 H22 H 0 1 N N N N N N 42.509 -77.254 3.716 -2.864 -0.305 1.035 H22 EXA 51 EXA H23 H23 H 0 1 N N N N N N 39.163 -74.006 2.216 -5.711 -0.873 2.303 H23 EXA 52 EXA H24 H24 H 0 1 N N N N N N 42.701 -74.418 2.447 -7.800 -0.774 -0.062 H24 EXA 53 EXA H25 H25 H 0 1 N N N N N N 38.412 -76.901 1.487 -1.249 -1.632 2.299 H25 EXA 54 EXA H26 H26 H 0 1 N N N N N N 39.391 -76.486 0.039 -0.482 -3.155 1.787 H26 EXA 55 EXA H27 H27 H 0 1 N N N N N N 37.643 -76.861 -0.136 0.394 -1.615 1.614 H27 EXA 56 EXA H28 H28 H 0 1 N N N N N N 38.640 -79.978 -2.459 -3.035 -3.567 -1.996 H28 EXA 57 EXA HXT H29 H 0 1 N Y N N N N 29.754 -75.728 6.621 9.540 -1.602 -1.658 HXT EXA 58 # 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 EXA O10 C8 DOUB N N 1 EXA O11 C8 SING N N 2 EXA C8 C7 SING N N 3 EXA C7 C9 SING N N 4 EXA C7 N3 DOUB N N 5 EXA OP1 P DOUB N N 6 EXA N3 "C4'" SING N N 7 EXA "C4'" NZ SING N N 8 EXA "C4'" C4 SING N N 9 EXA P OP2 SING N N 10 EXA P OP3 SING N N 11 EXA P OP4 SING N N 12 EXA CE NZ SING N N 13 EXA CE CD SING N N 14 EXA "C5'" OP4 SING N N 15 EXA "C5'" C5 SING N N 16 EXA C4 C5 DOUB Y N 17 EXA C4 C3 SING Y N 18 EXA CG CD SING N N 19 EXA CG CB SING N N 20 EXA C5 C6 SING Y N 21 EXA O3 C3 SING N N 22 EXA C3 C2 DOUB Y N 23 EXA O C DOUB N N 24 EXA CA CB SING N N 25 EXA CA N SING N N 26 EXA CA C SING N N 27 EXA C6 N1 DOUB Y N 28 EXA C2 N1 SING Y N 29 EXA C2 "C2'" SING N N 30 EXA C OXT SING N N 31 EXA N H SING N N 32 EXA N H2 SING N N 33 EXA CA HA SING N N 34 EXA CB HB2 SING N N 35 EXA CB HB3 SING N N 36 EXA CG HG2 SING N N 37 EXA CG HG3 SING N N 38 EXA CD HD2 SING N N 39 EXA CD HD3 SING N N 40 EXA CE HE2 SING N N 41 EXA CE HE3 SING N N 42 EXA NZ HZ1 SING N N 43 EXA "C4'" H15 SING N N 44 EXA O3 H16 SING N N 45 EXA "C2'" H17 SING N N 46 EXA "C2'" H18 SING N N 47 EXA "C2'" H19 SING N N 48 EXA C6 H20 SING N N 49 EXA "C5'" H21 SING N N 50 EXA "C5'" H22 SING N N 51 EXA OP2 H23 SING N N 52 EXA OP3 H24 SING N N 53 EXA C9 H25 SING N N 54 EXA C9 H26 SING N N 55 EXA C9 H27 SING N N 56 EXA O11 H28 SING N N 57 EXA OXT HXT SING N N 58 # 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 EXA SMILES ACDLabs 12.01 "Oc1c(C(\N=C(/C)C(=O)O)NCCCCC(N)C(=O)O)c(cnc1C)COP(=O)(O)O" EXA InChI InChI 1.06 "InChI=1S/C17H27N4O9P/c1-9-14(22)13(11(7-20-9)8-30-31(27,28)29)15(21-10(2)16(23)24)19-6-4-3-5-12(18)17(25)26/h7,12,15,19,22H,3-6,8,18H2,1-2H3,(H,23,24)(H,25,26)(H2,27,28,29)/b21-10+/t12-,15+/m0/s1" EXA InChIKey InChI 1.06 AIKQXQJRQAGCPQ-GRNKCENMSA-N EXA SMILES_CANONICAL CACTVS 3.385 "Cc1ncc(CO[P](O)(O)=O)c([C@H](NCCCC[C@H](N)C(O)=O)N=C(C)C(O)=O)c1O" EXA SMILES CACTVS 3.385 "Cc1ncc(CO[P](O)(O)=O)c([CH](NCCCC[CH](N)C(O)=O)N=C(C)C(O)=O)c1O" EXA SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "Cc1c(c(c(cn1)COP(=O)(O)O)[C@H](NCCCC[C@@H](C(=O)O)N)/N=C(\C)/C(=O)O)O" EXA SMILES "OpenEye OEToolkits" 2.0.7 "Cc1c(c(c(cn1)COP(=O)(O)O)C(NCCCCC(C(=O)O)N)N=C(C)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 EXA "SYSTEMATIC NAME" ACDLabs 12.01 "N~6~-[(R)-[(E)-(1-carboxyethylidene)amino]{3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl]-L-lysine" EXA "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{S})-2-azanyl-6-[[(~{R})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]-[(~{E})-(1-oxidanyl-1-oxidanylidene-propan-2-ylidene)amino]methyl]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 EXA "Create component" 2017-03-01 RCSB EXA "Initial release" 2018-03-07 RCSB EXA "Modify atom id" 2023-02-02 PDBJ EXA "Modify atom id" 2023-02-07 RCSB EXA "Modify atom id" 2023-11-27 RCSB #