data_L5P
# 
_chem_comp.id                                    L5P 
_chem_comp.name                                  "(2S)-2-azanyl-6-[[(3R,4R)-3,4-bis(oxidanyl)-2-oxidanylidene-5-phosphonooxy-pentyl]amino]hexanoic acid" 
_chem_comp.type                                  "L-peptide linking" 
_chem_comp.pdbx_type                             ATOMP 
_chem_comp.formula                               "C11 H23 N2 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                     2014-11-17 
_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                        358.282 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     L5P 
_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        4WXY 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  RCSB 
_chem_comp.pdbx_pcm                              N 
# 
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 
L5P N   N1  N 0 1 N N N N N N 14.793 22.430 14.754 7.090  2.288  0.155  N   L5P 1  
L5P CA  C1  C 0 1 N N S N N N 14.146 23.107 15.859 7.371  0.872  0.426  CA  L5P 2  
L5P CB  C2  C 0 1 N N N N N N 13.894 24.562 15.506 6.275  0.006  -0.198 CB  L5P 3  
L5P CG  C3  C 0 1 N N N N N N 15.223 25.216 15.379 4.942  0.294  0.495  CG  L5P 4  
L5P CD  C4  C 0 1 N N N N N N 15.100 26.650 14.913 3.845  -0.572 -0.129 CD  L5P 5  
L5P CE  C5  C 0 1 N N N N N N 16.175 27.332 15.727 2.512  -0.284 0.564  CE  L5P 6  
L5P NZ  N2  N 0 1 N N N N N N 16.852 28.468 15.115 1.459  -1.115 -0.035 NZ  L5P 7  
L5P C1  C6  C 0 1 N N N N N N 12.824 22.513 16.265 8.705  0.502  -0.171 C1  L5P 8  
L5P O   O1  O 0 1 N N N N N N 12.055 22.076 15.410 9.185  1.183  -1.046 O   L5P 9  
L5P O4  O2  O 0 1 N N N N N N 19.684 28.824 14.977 -0.591 -2.483 -0.930 O4  L5P 10 
L5P C3  C7  C 0 1 N N N N N N 18.965 29.600 15.589 -0.891 -1.734 -0.033 C3  L5P 11 
L5P C2  C8  C 0 1 N N N N N N 17.655 29.140 16.143 0.162  -0.865 0.607  C2  L5P 12 
L5P C5  C9  C 0 1 N N R N N N 19.353 31.017 15.844 -2.317 -1.666 0.449  C5  L5P 13 
L5P O13 O3  O 0 1 N N N N N N 18.296 31.690 16.523 -3.010 -2.852 0.054  O13 L5P 14 
L5P C6  C10 C 0 1 N N R N N N 19.572 31.711 14.534 -3.006 -0.446 -0.166 C6  L5P 15 
L5P O14 O4  O 0 1 N N N N N N 20.784 31.218 13.977 -2.313 0.740  0.229  O14 L5P 16 
L5P C7  C11 C 0 1 N N N N N N 19.715 33.194 14.746 -4.454 -0.377 0.323  C7  L5P 17 
L5P O8  O5  O 0 1 N N N N N N 20.162 33.661 13.506 -5.130 0.693  -0.340 O8  L5P 18 
L5P P9  P1  P 0 1 N N N N N N 19.989 35.163 13.098 -6.675 1.056  -0.068 P9  L5P 19 
L5P O12 O6  O 0 1 N N N N N N 21.131 35.811 13.777 -7.607 -0.162 -0.556 O12 L5P 20 
L5P O11 O7  O 0 1 N N N N N N 20.057 35.050 11.624 -6.880 1.285  1.380  O11 L5P 21 
L5P O10 O8  O 0 1 N N N N N N 18.666 35.643 13.560 -7.064 2.389  -0.882 O10 L5P 22 
L5P H1  H1  H 0 1 N N N N N N 14.954 21.473 14.997 7.765  2.884  0.612  H1  L5P 23 
L5P H2  H2  H 0 1 N N N N N N 14.205 22.474 13.946 7.062  2.468  -0.837 H2  L5P 24 
L5P H4  H4  H 0 1 N N N N N N 14.815 23.081 16.732 7.397  0.706  1.503  H4  L5P 25 
L5P H5  H5  H 0 1 N N N N N N 13.309 25.047 16.301 6.190  0.238  -1.260 H5  L5P 26 
L5P H6  H6  H 0 1 N N N N N N 13.347 24.630 14.554 6.529  -1.046 -0.075 H6  L5P 27 
L5P H7  H7  H 0 1 N N N N N N 15.828 24.655 14.651 5.027  0.063  1.557  H7  L5P 28 
L5P H8  H8  H 0 1 N N N N N N 15.722 25.201 16.359 4.688  1.347  0.372  H8  L5P 29 
L5P H9  H9  H 0 1 N N N N N N 15.297 26.739 13.834 3.760  -0.340 -1.191 H9  L5P 30 
L5P H10 H10 H 0 1 N N N N N N 14.105 27.061 15.139 4.099  -1.624 -0.006 H10 L5P 31 
L5P H11 H11 H 0 1 N N N N N N 15.710 27.686 16.659 2.597  -0.515 1.626  H11 L5P 32 
L5P H12 H12 H 0 1 N N N N N N 16.940 26.578 15.963 2.258  0.769  0.441  H12 L5P 33 
L5P H13 H13 H 0 1 N N N N N N 17.447 28.149 14.377 1.404  -0.966 -1.031 H13 L5P 34 
L5P OXT HXT O 0 1 N Y N N N N 12.550 22.470 17.309 9.358  -0.585 0.269  OXT L5P 35 
L5P H16 H16 H 0 1 N N N N N N 17.099 30.011 16.520 0.231  -1.100 1.669  H16 L5P 36 
L5P H17 H17 H 0 1 N N N N N N 17.841 28.438 16.969 -0.108 0.184  0.484  H17 L5P 37 
L5P H18 H18 H 0 1 N N N N N N 20.278 31.048 16.438 -2.331 -1.582 1.535  H18 L5P 38 
L5P H19 H19 H 0 1 N N N N N N 18.137 31.268 17.359 -3.037 -2.992 -0.903 H19 L5P 39 
L5P H20 H20 H 0 1 N N N N N N 18.724 31.513 13.862 -2.992 -0.530 -1.252 H20 L5P 40 
L5P H21 H21 H 0 1 N N N N N N 20.836 30.279 14.113 -2.286 0.880  1.186  H21 L5P 41 
L5P H22 H22 H 0 1 N N N N N N 20.451 33.409 15.535 -4.957 -1.318 0.100  H22 L5P 42 
L5P H23 H23 H 0 1 N N N N N N 18.749 33.648 15.012 -4.467 -0.205 1.399  H23 L5P 43 
L5P H24 H24 H 0 1 N N N N N N 21.776 36.074 13.131 -7.523 -0.369 -1.497 H24 L5P 44 
L5P H25 H25 H 0 1 N N N N N N 18.102 35.790 12.810 -7.983 2.668  -0.765 H25 L5P 45 
L5P HXT H3  H 0 1 N Y N N N N 11.693 22.070 17.396 10.210 -0.782 -0.144 HXT L5P 46 
# 
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 
L5P O11 P9  DOUB N N 1  
L5P P9  O8  SING N N 2  
L5P P9  O10 SING N N 3  
L5P P9  O12 SING N N 4  
L5P O8  C7  SING N N 5  
L5P O14 C6  SING N N 6  
L5P C6  C7  SING N N 7  
L5P C6  C5  SING N N 8  
L5P N   CA  SING N N 9  
L5P CD  CG  SING N N 10 
L5P CD  CE  SING N N 11 
L5P O4  C3  DOUB N N 12 
L5P NZ  CE  SING N N 13 
L5P NZ  C2  SING N N 14 
L5P CG  CB  SING N N 15 
L5P O   C1  DOUB N N 16 
L5P CB  CA  SING N N 17 
L5P C3  C5  SING N N 18 
L5P C3  C2  SING N N 19 
L5P C5  O13 SING N N 20 
L5P CA  C1  SING N N 21 
L5P N   H1  SING N N 22 
L5P N   H2  SING N N 23 
L5P CA  H4  SING N N 24 
L5P CB  H5  SING N N 25 
L5P CB  H6  SING N N 26 
L5P CG  H7  SING N N 27 
L5P CG  H8  SING N N 28 
L5P CD  H9  SING N N 29 
L5P CD  H10 SING N N 30 
L5P CE  H11 SING N N 31 
L5P CE  H12 SING N N 32 
L5P NZ  H13 SING N N 33 
L5P C1  OXT SING N N 34 
L5P C2  H16 SING N N 35 
L5P C2  H17 SING N N 36 
L5P C5  H18 SING N N 37 
L5P O13 H19 SING N N 38 
L5P C6  H20 SING N N 39 
L5P O14 H21 SING N N 40 
L5P C7  H22 SING N N 41 
L5P C7  H23 SING N N 42 
L5P O12 H24 SING N N 43 
L5P O10 H25 SING N N 44 
L5P OXT HXT SING N N 45 
# 
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 
L5P SMILES           ACDLabs              12.01 "NC(C(O)=O)CCCCNCC(=O)C(O)C(COP(O)(O)=O)O"                                                                                                             
L5P InChI            InChI                1.03  "InChI=1S/C11H23N2O9P/c12-7(11(17)18)3-1-2-4-13-5-8(14)10(16)9(15)6-22-23(19,20)21/h7,9-10,13,15-16H,1-6,12H2,(H,17,18)(H2,19,20,21)/t7-,9+,10-/m0/s1" 
L5P InChIKey         InChI                1.03  FCAUVIWDSGPTCC-SFGNSQDASA-N                                                                                                                            
L5P SMILES_CANONICAL CACTVS               3.385 "N[C@@H](CCCCNCC(=O)[C@H](O)[C@H](O)CO[P](O)(O)=O)C(O)=O"                                                                                              
L5P SMILES           CACTVS               3.385 "N[CH](CCCCNCC(=O)[CH](O)[CH](O)CO[P](O)(O)=O)C(O)=O"                                                                                                  
L5P SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "C(CCNCC(=O)[C@@H]([C@@H](COP(=O)(O)O)O)O)C[C@@H](C(=O)O)N"                                                                                            
L5P SMILES           "OpenEye OEToolkits" 1.7.6 "C(CCNCC(=O)C(C(COP(=O)(O)O)O)O)CC(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 
L5P "SYSTEMATIC NAME" ACDLabs              12.01 "(2S)-2-amino-6-{[(3R,4R)-3,4-dihydroxy-2-oxo-5-(phosphonooxy)pentyl]amino}hexanoic acid (non-preferred name)" 
L5P "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "(2S)-2-azanyl-6-[[(3R,4R)-3,4-bis(oxidanyl)-2-oxidanylidene-5-phosphonooxy-pentyl]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 
L5P "Create component" 2014-11-17 RCSB 
L5P "Initial release"  2015-01-14 RCSB 
L5P "Modify PCM"       2024-09-27 PDBE 
# 
