data_LYV # _chem_comp.id LYV _chem_comp.name "O-phosphono-L-seryl-N-[(3S)-3-amino-3-carboxypropyl]glycinamide" _chem_comp.type "L-PEPTIDE LINKING" _chem_comp.pdbx_type ATOMP _chem_comp.formula "C9 H19 N4 O8 P" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2013-12-06 _chem_comp.pdbx_modified_date 2023-11-03 _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 342.243 _chem_comp.one_letter_code ? _chem_comp.three_letter_code LYV _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 4NGH _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_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 LYV N N N 0 1 N N N Y Y N -97.801 76.732 -11.399 6.559 -0.740 1.702 N LYV 1 LYV CA CA C 0 1 N N S Y N N -98.606 75.996 -10.441 6.400 -0.947 0.256 CA LYV 2 LYV C C C 0 1 N N N Y N Y -99.105 76.979 -9.410 7.714 -0.692 -0.435 C LYV 3 LYV O O O 0 1 N N N Y N Y -100.206 76.811 -8.931 8.570 -0.040 0.115 O LYV 4 LYV CB CB C 0 1 N N N N N N -97.684 74.871 -10.034 5.344 0.020 -0.284 CB LYV 5 LYV CG CG C 0 1 N N N N N N -98.174 73.743 -9.088 3.983 -0.320 0.326 CG LYV 6 LYV ND ND N 0 1 N N N N N N -98.124 72.299 -9.420 2.971 0.605 -0.191 ND LYV 7 LYV CE CE C 0 1 N N N N N N -97.753 71.369 -8.350 1.689 0.495 0.210 CE LYV 8 LYV CZ CZ C 0 1 N N N N N N -97.683 69.860 -8.525 0.649 1.447 -0.321 CZ LYV 9 LYV N1 N1 N 0 1 N N N N N N -97.881 69.122 -7.238 -0.655 1.122 0.262 N1 LYV 10 LYV C2 C2 C 0 1 N N N N N N -98.441 67.788 -7.009 -1.742 1.846 -0.070 C2 LYV 11 LYV OZ1 OZ1 O 0 1 N N N N N N -98.506 67.401 -5.822 -1.640 2.767 -0.853 OZ1 LYV 12 LYV C4 C4 C 0 1 N N S N N N -98.911 66.827 -8.063 -3.082 1.512 0.530 C4 LYV 13 LYV C5 C5 C 0 1 N N N N N N -97.773 66.007 -8.625 -3.693 0.323 -0.215 C5 LYV 14 LYV N6 N6 N 0 1 N N N N N N -99.634 67.447 -9.166 -3.974 2.673 0.414 N6 LYV 15 LYV O7 O7 O 0 1 N N N N N N -97.496 71.826 -7.243 1.373 -0.370 0.999 O7 LYV 16 LYV P P P 0 1 N N N N N N -96.063 65.214 -6.752 -5.820 -1.290 -0.092 P LYV 17 LYV O1 O1 O 0 1 N N N N N N -97.242 64.980 -7.848 -4.909 -0.068 0.426 O1 LYV 18 LYV O2 O2 O 0 1 N N N N N N -94.813 64.475 -7.211 -4.997 -2.517 -0.179 O2 LYV 19 LYV O3 O3 O 0 1 N N N N N N -95.722 66.705 -6.604 -7.034 -1.529 0.938 O3 LYV 20 LYV O4 O4 O 0 1 N N N N N N -96.498 64.659 -5.386 -6.412 -0.938 -1.547 O4 LYV 21 LYV H H1 H 0 1 N N N Y Y N -98.322 77.514 -11.741 6.853 0.204 1.902 H1 LYV 22 LYV H2 H2 H 0 1 N Y N Y Y N -96.966 77.056 -10.954 5.709 -0.967 2.195 H2 LYV 23 LYV HA H4 H 0 1 N N N Y N N -99.475 75.563 -10.957 6.083 -1.973 0.068 H4 LYV 24 LYV H6 H6 H 0 1 N N N N N N -97.358 74.381 -10.963 5.616 1.041 -0.018 H6 LYV 25 LYV H7 H7 H 0 1 N N N N N N -96.818 75.338 -9.542 5.289 -0.071 -1.368 H7 LYV 26 LYV H8 H8 H 0 1 N N N N N N -97.590 73.856 -8.163 3.710 -1.342 0.060 H8 LYV 27 LYV H9 H9 H 0 1 N N N N N N -99.232 73.965 -8.883 4.037 -0.229 1.411 H9 LYV 28 LYV H10 H10 H 0 1 N N N N N N -98.336 71.971 -10.341 3.224 1.297 -0.822 H10 LYV 29 LYV H11 H11 H 0 1 N N N N N N -98.466 69.551 -9.233 0.922 2.469 -0.056 H11 LYV 30 LYV H12 H12 H 0 1 N N N N N N -96.696 69.598 -8.933 0.594 1.357 -1.406 H12 LYV 31 LYV H13 H13 H 0 1 N N N N N N -97.589 69.610 -6.416 -0.735 0.386 0.889 H13 LYV 32 LYV H14 H14 H 0 1 N N N N N N -99.599 66.123 -7.571 -2.956 1.254 1.582 H14 LYV 33 LYV H15 H15 H 0 1 N N N N N N -98.132 65.553 -9.560 -3.902 0.609 -1.246 H15 LYV 34 LYV H16 H16 H 0 1 N N N N N N -96.951 66.703 -8.847 -2.992 -0.511 -0.205 H16 LYV 35 LYV H17 H17 H 0 1 N N N N N N -100.390 67.993 -8.805 -3.625 3.452 0.952 H17 LYV 36 LYV H18 H18 H 0 1 N N N N N N -99.013 68.038 -9.681 -4.108 2.931 -0.552 H18 LYV 37 LYV H20 H20 H 0 1 N N N N N N -94.810 66.846 -6.829 -7.625 -2.252 0.688 H20 LYV 38 LYV H21 H21 H 0 1 N N N N N N -95.898 63.974 -5.116 -6.963 -0.143 -1.566 H21 LYV 39 LYV OXT OXT O 0 1 N Y N Y N Y ? ? ? 7.935 -1.190 -1.663 OXT LYV 40 LYV HXT HXT H 0 1 N Y N Y N Y ? ? ? 8.793 -1.000 -2.066 HXT LYV 41 # 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 LYV N CA SING N N 1 LYV CA CB SING N N 2 LYV CA C SING N N 3 LYV CB CG SING N N 4 LYV ND CG SING N N 5 LYV ND CE SING N N 6 LYV C O DOUB N N 7 LYV N6 C4 SING N N 8 LYV C5 C4 SING N N 9 LYV C5 O1 SING N N 10 LYV CZ CE SING N N 11 LYV CZ N1 SING N N 12 LYV CE O7 DOUB N N 13 LYV C4 C2 SING N N 14 LYV O1 P SING N N 15 LYV N1 C2 SING N N 16 LYV O2 P DOUB N N 17 LYV C2 OZ1 DOUB N N 18 LYV P O3 SING N N 19 LYV P O4 SING N N 20 LYV N H SING N N 21 LYV N H2 SING N N 22 LYV CA HA SING N N 23 LYV CB H6 SING N N 24 LYV CB H7 SING N N 25 LYV CG H8 SING N N 26 LYV CG H9 SING N N 27 LYV ND H10 SING N N 28 LYV CZ H11 SING N N 29 LYV CZ H12 SING N N 30 LYV N1 H13 SING N N 31 LYV C4 H14 SING N N 32 LYV C5 H15 SING N N 33 LYV C5 H16 SING N N 34 LYV N6 H17 SING N N 35 LYV N6 H18 SING N N 36 LYV O3 H20 SING N N 37 LYV O4 H21 SING N N 38 LYV C OXT SING N N 39 LYV OXT HXT SING N N 40 # 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 LYV SMILES ACDLabs 12.01 "O=P(OCC(C(=O)NCC(=O)NCCC(C(=O)O)N)N)(O)O" LYV InChI InChI 1.03 "InChI=1S/C9H19N4O8P/c10-5(9(16)17)1-2-12-7(14)3-13-8(15)6(11)4-21-22(18,19)20/h5-6H,1-4,10-11H2,(H,12,14)(H,13,15)(H,16,17)(H2,18,19,20)/t5-,6-/m0/s1" LYV InChIKey InChI 1.03 OAHBGBOPVNAMDO-WDSKDSINSA-N LYV SMILES_CANONICAL CACTVS 3.385 "N[C@@H](CCNC(=O)CNC(=O)[C@@H](N)CO[P](O)(O)=O)C(O)=O" LYV SMILES CACTVS 3.385 "N[CH](CCNC(=O)CNC(=O)[CH](N)CO[P](O)(O)=O)C(O)=O" LYV SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C(CNC(=O)CNC(=O)[C@H](COP(=O)(O)O)N)[C@@H](C(=O)O)N" LYV SMILES "OpenEye OEToolkits" 1.7.6 "C(CNC(=O)CNC(=O)C(COP(=O)(O)O)N)C(C(=O)O)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 LYV "SYSTEMATIC NAME" ACDLabs 12.01 "O-phosphono-L-seryl-N-[(3S)-3-amino-3-carboxypropyl]glycinamide" LYV "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(2S)-2-azanyl-4-[2-[[(2S)-2-azanyl-3-phosphonooxy-propanoyl]amino]ethanoylamino]butanoic 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 LYV "Create component" 2013-12-06 RCSB LYV "Initial release" 2014-12-03 RCSB LYV "Modify backbone" 2023-11-03 PDBE #