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                    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                        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 
_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 
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 
LYV "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            LYV 
_pdbx_chem_comp_pcm.modified_residue_id                ? 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Non-standard residue" 
_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      ? 
# 
