data_L3F
# 
_chem_comp.id                                    L3F 
_chem_comp.name                                  "(phenylmethyl) N-[(2S)-3-methyl-1-oxidanylidene-1-[[(2S)-1-oxidanyl-3-phenyl-propan-2-yl]amino]butan-2-yl]carbamate" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C22 H28 N2 O4" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "benzyl N-[(2S)-1-[[(2S)-1-hydroxy-3-phenylpropan-2-yl]amino]-3-methyl-1-oxobutan-2-yl]carbamate; calpain inhibitor III" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2022-06-14 
_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                        384.469 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     L3F 
_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        8A4X 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBE 
_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 
L3F N1  N1  N 0 1 N N N N N N 17.170 -24.605 -0.096 0.974  0.589  -0.028 N1  L3F 1  
L3F C4  C1  C 0 1 N N N N N N 16.000 -22.511 -0.549 -1.408 0.724  -0.473 C4  L3F 2  
L3F C5  C2  C 0 1 N N S N N N 14.422 -20.623 -0.734 -3.740 0.836  -1.170 C5  L3F 3  
L3F C6  C3  C 0 1 N N N N N N 13.151 -20.658 0.124  -5.065 0.363  -0.567 C6  L3F 4  
L3F C7  C4  C 0 1 Y N N N N N 12.808 -22.037 0.630  -4.933 -1.072 -0.128 C7  L3F 5  
L3F C8  C5  C 0 1 Y N N N N N 13.252 -22.464 1.875  -4.511 -1.366 1.155  C8  L3F 6  
L3F C10 C6  C 0 1 Y N N N N N 12.236 -24.609 1.543  -4.691 -3.706 0.679  C10 L3F 7  
L3F C13 C7  C 0 1 N N N N N N 14.862 -19.197 -1.020 -3.910 2.250  -1.729 C13 L3F 8  
L3F C15 C8  C 0 1 N N N N N N 16.793 -27.964 0.460  4.271  -0.618 0.923  C15 L3F 9  
L3F C17 C9  C 0 1 Y N N N N N 16.344 -28.868 -1.855 6.423  0.382  0.126  C17 L3F 10 
L3F C20 C10 C 0 1 Y N N N N N 13.707 -28.062 -1.745 6.997  -1.873 -1.367 C20 L3F 11 
L3F C21 C11 C 0 1 Y N N N N N 14.549 -27.833 -0.668 5.835  -1.816 -0.621 C21 L3F 12 
L3F N   N2  N 0 1 N N N N N N 15.493 -21.367 -0.073 -2.707 0.842  -0.132 N   L3F 13 
L3F C   C12 C 0 1 N N N N N N 18.995 -22.437 -0.984 0.674  2.056  2.451  C   L3F 14 
L3F O   O1  O 0 1 N N N N N N 15.705 -22.971 -1.649 -1.095 0.612  -1.640 O   L3F 15 
L3F C1  C13 C 0 1 N N N N N N 18.350 -22.488 0.387  -0.405 2.050  1.367  C1  L3F 16 
L3F C11 C14 C 0 1 Y N N N N N 11.786 -24.196 0.308  -5.118 -3.412 -0.602 C11 L3F 17 
L3F C12 C15 C 0 1 Y N N N N N 12.068 -22.918 -0.147 -5.239 -2.095 -1.006 C12 L3F 18 
L3F C14 C16 C 0 1 N N N N N N 17.046 -25.637 0.755  2.001  0.074  0.677  C14 L3F 19 
L3F C16 C17 C 0 1 Y N N N N N 15.879 -28.233 -0.709 5.545  -0.686 0.120  C16 L3F 20 
L3F C18 C18 C 0 1 Y N N N N N 15.499 -29.095 -2.930 7.589  0.322  -0.615 C18 L3F 21 
L3F C19 C19 C 0 1 Y N N N N N 14.181 -28.692 -2.875 7.876  -0.806 -1.361 C19 L3F 22 
L3F C2  C20 C 0 1 N N N N N N 19.295 -23.112 1.394  -0.168 3.215  0.404  C2  L3F 23 
L3F C3  C21 C 0 1 N N S N N N 17.004 -23.233 0.349  -0.345 0.730  0.595  C3  L3F 24 
L3F C9  C22 C 0 1 Y N N N N N 12.967 -23.742 2.327  -4.390 -2.683 1.559  C9  L3F 25 
L3F O1  O2  O 0 1 N N N N N N 13.868 -18.476 -1.739 -4.409 3.111  -0.703 O1  L3F 26 
L3F O2  O3  O 0 1 N N N N N N 16.556 -25.572 1.862  1.833  -0.273 1.829  O2  L3F 27 
L3F O3  O4  O 0 1 N N N N N N 17.549 -26.763 0.201  3.212  -0.056 0.105  O3  L3F 28 
L3F H20 H1  H 0 1 N N N N N N 17.381 -24.786 -1.057 1.109  0.869  -0.947 H20 L3F 29 
L3F H1  H2  H 0 1 N N N N N N 14.194 -21.108 -1.694 -3.445 0.161  -1.973 H1  L3F 30 
L3F H11 H3  H 0 1 N N N N N N 13.296 -19.995 0.990  -5.316 0.985  0.292  H11 L3F 31 
L3F H10 H4  H 0 1 N N N N N N 12.310 -20.290 -0.483 -5.853 0.442  -1.316 H10 L3F 32 
L3F H12 H5  H 0 1 N N N N N N 13.825 -21.793 2.497  -4.275 -0.567 1.843  H12 L3F 33 
L3F H14 H6  H 0 1 N N N N N N 12.017 -25.606 1.895  -4.596 -4.734 0.994  H14 L3F 34 
L3F H17 H7  H 0 1 N N N N N N 15.786 -19.221 -1.616 -2.946 2.621  -2.077 H17 L3F 35 
L3F H18 H8  H 0 1 N Y N N N N 15.054 -18.685 -0.066 -4.614 2.229  -2.561 H18 L3F 36 
L3F H21 H9  H 0 1 N N N N N N 16.194 -27.833 1.373  3.990  -1.621 1.243  H21 L3F 37 
L3F H22 H10 H 0 1 N N N N N N 17.482 -28.812 0.592  4.427  0.013  1.799  H22 L3F 38 
L3F H23 H11 H 0 1 N N N N N N 17.374 -29.188 -1.908 6.196  1.265  0.705  H23 L3F 39 
L3F H26 H12 H 0 1 N N N N N N 12.676 -27.745 -1.698 7.224  -2.756 -1.946 H26 L3F 40 
L3F H27 H13 H 0 1 N N N N N N 14.167 -27.338 0.213  5.153  -2.653 -0.618 H27 L3F 41 
L3F H9  H14 H 0 1 N N N N N N 15.867 -21.002 0.780  -2.957 0.931  0.801  H9  L3F 42 
L3F H3  H15 H 0 1 N N N N N N 19.952 -21.899 -0.920 0.631  2.996  3.001  H3  L3F 43 
L3F H2  H16 H 0 1 N N N N N N 19.174 -23.461 -1.343 0.506  1.226  3.137  H2  L3F 44 
L3F H4  H17 H 0 1 N N N N N N 18.327 -21.914 -1.684 1.655  1.951  1.988  H4  L3F 45 
L3F H5  H18 H 0 1 N N N N N N 18.150 -21.454 0.706  -1.386 2.155  1.830  H5  L3F 46 
L3F H15 H19 H 0 1 N N N N N N 11.211 -24.871 -0.308 -5.353 -4.211 -1.289 H15 L3F 47 
L3F H16 H20 H 0 1 N N N N N N 11.709 -22.604 -1.116 -5.574 -1.866 -2.007 H16 L3F 48 
L3F H24 H21 H 0 1 N N N N N N 15.874 -29.589 -3.814 8.275  1.155  -0.611 H24 L3F 49 
L3F H25 H22 H 0 1 N N N N N N 13.524 -28.869 -3.713 8.787  -0.853 -1.940 H25 L3F 50 
L3F H6  H23 H 0 1 N N N N N N 18.812 -23.141 2.382  0.813  3.110  -0.059 H6  L3F 51 
L3F H8  H24 H 0 1 N N N N N N 19.544 -24.136 1.077  -0.938 3.210  -0.368 H8  L3F 52 
L3F H7  H25 H 0 1 N N N N N N 20.215 -22.512 1.454  -0.212 4.155  0.954  H7  L3F 53 
L3F H   H26 H 0 1 N N N N N N 16.597 -23.239 1.371  -0.513 -0.100 1.281  H   L3F 54 
L3F H13 H27 H 0 1 N N N N N N 13.319 -24.060 3.297  -4.059 -2.912 2.561  H13 L3F 55 
L3F H19 H28 H 0 1 N N N N N N 14.173 -17.591 -1.901 -4.542 4.025  -0.988 H19 L3F 56 
# 
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 
L3F C18 C19 DOUB Y N 1  
L3F C18 C17 SING Y N 2  
L3F C19 C20 SING Y N 3  
L3F C17 C16 DOUB Y N 4  
L3F C20 C21 DOUB Y N 5  
L3F O1  C13 SING N N 6  
L3F O   C4  DOUB N N 7  
L3F C13 C5  SING N N 8  
L3F C   C1  SING N N 9  
L3F C5  N   SING N N 10 
L3F C5  C6  SING N N 11 
L3F C16 C21 SING Y N 12 
L3F C16 C15 SING N N 13 
L3F C4  N   SING N N 14 
L3F C4  C3  SING N N 15 
L3F C12 C11 DOUB Y N 16 
L3F C12 C7  SING Y N 17 
L3F N1  C3  SING N N 18 
L3F N1  C14 SING N N 19 
L3F C6  C7  SING N N 20 
L3F O3  C15 SING N N 21 
L3F O3  C14 SING N N 22 
L3F C11 C10 SING Y N 23 
L3F C3  C1  SING N N 24 
L3F C1  C2  SING N N 25 
L3F C7  C8  DOUB Y N 26 
L3F C14 O2  DOUB N N 27 
L3F C10 C9  DOUB Y N 28 
L3F C8  C9  SING Y N 29 
L3F N1  H20 SING N N 30 
L3F C5  H1  SING N N 31 
L3F C6  H11 SING N N 32 
L3F C6  H10 SING N N 33 
L3F C8  H12 SING N N 34 
L3F C10 H14 SING N N 35 
L3F C13 H17 SING N N 36 
L3F C13 H18 SING N N 37 
L3F C15 H21 SING N N 38 
L3F C15 H22 SING N N 39 
L3F C17 H23 SING N N 40 
L3F C20 H26 SING N N 41 
L3F C21 H27 SING N N 42 
L3F N   H9  SING N N 43 
L3F C   H3  SING N N 44 
L3F C   H2  SING N N 45 
L3F C   H4  SING N N 46 
L3F C1  H5  SING N N 47 
L3F C11 H15 SING N N 48 
L3F C12 H16 SING N N 49 
L3F C18 H24 SING N N 50 
L3F C19 H25 SING N N 51 
L3F C2  H6  SING N N 52 
L3F C2  H8  SING N N 53 
L3F C2  H7  SING N N 54 
L3F C3  H   SING N N 55 
L3F C9  H13 SING N N 56 
L3F O1  H19 SING N N 57 
# 
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 
L3F InChI            InChI                1.06  "InChI=1S/C22H28N2O4/c1-16(2)20(24-22(27)28-15-18-11-7-4-8-12-18)21(26)23-19(14-25)13-17-9-5-3-6-10-17/h3-12,16,19-20,25H,13-15H2,1-2H3,(H,23,26)(H,24,27)/t19-,20-/m0/s1" 
L3F InChIKey         InChI                1.06  VLFHBNSJHLMKMM-PMACEKPBSA-N                                                                                                                                                
L3F SMILES_CANONICAL CACTVS               3.385 "CC(C)[C@H](NC(=O)OCc1ccccc1)C(=O)N[C@H](CO)Cc2ccccc2"                                                                                                                     
L3F SMILES           CACTVS               3.385 "CC(C)[CH](NC(=O)OCc1ccccc1)C(=O)N[CH](CO)Cc2ccccc2"                                                                                                                       
L3F SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(C)[C@@H](C(=O)N[C@@H](Cc1ccccc1)CO)NC(=O)OCc2ccccc2"                                                                                                                   
L3F SMILES           "OpenEye OEToolkits" 2.0.7 "CC(C)C(C(=O)NC(Cc1ccccc1)CO)NC(=O)OCc2ccccc2"                                                                                                                             
# 
_pdbx_chem_comp_identifier.comp_id           L3F 
_pdbx_chem_comp_identifier.type              "SYSTEMATIC NAME" 
_pdbx_chem_comp_identifier.program           "OpenEye OEToolkits" 
_pdbx_chem_comp_identifier.program_version   2.0.7 
_pdbx_chem_comp_identifier.identifier        "(phenylmethyl) ~{N}-[(2~{S})-3-methyl-1-oxidanylidene-1-[[(2~{S})-1-oxidanyl-3-phenyl-propan-2-yl]amino]butan-2-yl]carbamate" 
# 
loop_
_pdbx_chem_comp_synonyms.ordinal 
_pdbx_chem_comp_synonyms.comp_id 
_pdbx_chem_comp_synonyms.name 
_pdbx_chem_comp_synonyms.provenance 
_pdbx_chem_comp_synonyms.type 
1 L3F "benzyl N-[(2S)-1-[[(2S)-1-hydroxy-3-phenylpropan-2-yl]amino]-3-methyl-1-oxobutan-2-yl]carbamate" AUTHOR ? 
2 L3F "calpain inhibitor III"                                                                           AUTHOR ? 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
L3F "Create component"         2022-06-14 PDBE 
L3F "Modify leaving atom flag" 2022-06-14 PDBE 
L3F "Modify descriptor"        2022-08-22 RCSB 
L3F "Initial release"          2023-07-05 RCSB 
L3F "Modify PCM"               2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            L3F 
_pdbx_chem_comp_pcm.modified_residue_id                CYS 
_pdbx_chem_comp_pcm.type                               None 
_pdbx_chem_comp_pcm.category                           "Covalent chemical modification" 
_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               C13 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   SG 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
