data_LF7
# 
_chem_comp.id                                    LF7 
_chem_comp.name                                  
;2-{[(1r,3s,5R,7S)-3-hydroxytricyclo[3.3.1.1~3,7~]decan-1-yl]amino}-1-{(2S)-2-[(E)-iminomethyl]pyrrolidin-1-yl}ethan-1-o
ne
;
_chem_comp.type                                  NON-POLYMER 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C17 H27 N3 O2" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         "Vildagliptin, bound form" 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2012-12-11 
_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                        305.415 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     LF7 
_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        3W2T 
_chem_comp.pdbx_subcomponent_list                ? 
_chem_comp.pdbx_processing_site                  PDBJ 
_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 
LF7 O20 O1  O 0 1 N N N N N N 57.170 63.046 35.588 2.171  -1.640 -0.448 O20 LF7 1  
LF7 C14 C1  C 0 1 N N N N N N 56.787 64.063 36.173 2.072  -0.440 -0.302 C14 LF7 2  
LF7 N15 N1  N 0 1 N N N N N N 57.158 64.278 37.488 3.178  0.329  -0.276 N15 LF7 3  
LF7 C19 C2  C 0 1 N N N N N N 57.117 65.673 37.947 3.204  1.793  -0.100 C19 LF7 4  
LF7 C18 C3  C 0 1 N N N N N N 58.027 65.703 39.164 4.611  2.099  0.469  C18 LF7 5  
LF7 C17 C4  C 0 1 N N N N N N 59.099 64.671 38.851 5.488  1.076  -0.299 C17 LF7 6  
LF7 C16 C5  C 0 1 N N S N N N 58.426 63.662 37.944 4.560  -0.153 -0.414 C16 LF7 7  
LF7 C20 C6  C 0 1 N N N N N N 58.063 62.488 38.810 4.872  -1.137 0.683  C20 LF7 8  
LF7 N2  N2  N 0 1 N N N N N N 56.854 62.375 39.196 5.302  -2.306 0.391  N2  LF7 9  
LF7 C13 C7  C 0 1 N N N N N N 55.833 65.043 35.492 0.712  0.192  -0.154 C13 LF7 10 
LF7 N12 N3  N 0 1 N N N N N N 55.102 64.461 34.358 -0.322 -0.850 -0.221 N12 LF7 11 
LF7 C7  C8  C 0 1 N N N N N N 53.800 63.776 34.475 -1.664 -0.270 -0.080 C7  LF7 12 
LF7 C8  C9  C 0 1 N N N N N N 53.840 62.743 35.623 -1.773 0.443  1.269  C8  LF7 13 
LF7 C1  C10 C 0 1 N N R N N N 52.489 62.035 35.786 -3.171 1.047  1.415  C1  LF7 14 
LF7 C2  C11 C 0 1 N N N N N N 51.365 63.066 36.011 -3.413 2.052  0.287  C2  LF7 15 
LF7 C10 C12 C 0 1 N N S N N N 51.298 64.055 34.840 -3.304 1.339  -1.062 C10 LF7 16 
LF7 C9  C13 C 0 1 N N N N N N 52.661 64.769 34.761 -1.906 0.735  -1.209 C9  LF7 17 
LF7 C5  C14 C 0 1 N N N N N N 51.034 63.285 33.528 -4.351 0.226  -1.137 C5  LF7 18 
LF7 C21 C15 C 0 1 N N N N N N 52.229 61.282 34.479 -4.218 -0.066 1.341  C21 LF7 19 
LF7 C3  C16 C 0 1 N N N N N N 52.169 62.264 33.308 -4.109 -0.779 -0.009 C3  LF7 20 
LF7 O4  O2  O 0 1 N N N N N N 51.940 61.464 32.151 -5.087 -1.818 -0.078 O4  LF7 21 
LF7 C6  C17 C 0 1 N N N N N N 53.491 63.030 33.162 -2.711 -1.383 -0.155 C6  LF7 22 
LF7 H1  H1  H 0 1 N N N N N N 57.492 66.350 37.165 3.065  2.293  -1.058 H1  LF7 23 
LF7 H2  H2  H 0 1 N N N N N N 56.092 65.961 38.222 2.433  2.103  0.606  H2  LF7 24 
LF7 H3  H3  H 0 1 N N N N N N 58.472 66.701 39.295 4.912  3.122  0.239  H3  LF7 25 
LF7 H4  H4  H 0 1 N N N N N N 57.473 65.427 40.073 4.647  1.917  1.543  H4  LF7 26 
LF7 H5  H5  H 0 1 N N N N N N 59.449 64.186 39.774 5.752  1.457  -1.286 H5  LF7 27 
LF7 H6  H6  H 0 1 N N N N N N 59.951 65.143 38.339 6.384  0.831  0.270  H6  LF7 28 
LF7 H7  H7  H 0 1 N N N N N N 59.074 63.370 37.105 4.692  -0.627 -1.386 H7  LF7 29 
LF7 H8  H8  H 0 1 N N N N N N 58.807 61.760 39.097 4.731  -0.856 1.717  H8  LF7 30 
LF7 H9  H9  H 0 1 N N N N N N 56.717 61.564 39.765 5.502  -2.940 1.098  H9  LF7 31 
LF7 H10 H10 H 0 1 N N N N N N 56.418 65.900 35.126 0.651  0.703  0.807  H10 LF7 32 
LF7 H11 H11 H 0 1 N N N N N N 55.101 65.390 36.236 0.556  0.911  -0.959 H11 LF7 33 
LF7 H12 H12 H 0 1 N N N N N N 55.724 63.792 33.950 -0.162 -1.563 0.474  H12 LF7 34 
LF7 H14 H14 H 0 1 N N N N N N 54.613 61.992 35.402 -1.600 -0.273 2.073  H14 LF7 35 
LF7 H15 H15 H 0 1 N N N N N N 54.089 63.260 36.561 -1.027 1.236  1.322  H15 LF7 36 
LF7 H16 H16 H 0 1 N N N N N N 52.529 61.330 36.630 -3.248 1.555  2.377  H16 LF7 37 
LF7 H17 H17 H 0 1 N N N N N N 51.563 63.619 36.941 -4.409 2.482  0.391  H17 LF7 38 
LF7 H18 H18 H 0 1 N N N N N N 50.403 62.539 36.095 -2.667 2.845  0.340  H18 LF7 39 
LF7 H19 H19 H 0 1 N N N N N N 50.498 64.790 35.012 -3.477 2.055  -1.866 H19 LF7 40 
LF7 H20 H20 H 0 1 N N N N N N 52.857 65.272 35.719 -1.160 1.528  -1.156 H20 LF7 41 
LF7 H21 H21 H 0 1 N N N N N N 52.627 65.516 33.955 -1.829 0.227  -2.170 H21 LF7 42 
LF7 H22 H22 H 0 1 N N N N N N 51.005 63.991 32.685 -5.347 0.656  -1.033 H22 LF7 43 
LF7 H23 H23 H 0 1 N N N N N N 50.071 62.757 33.597 -4.274 -0.282 -2.098 H23 LF7 44 
LF7 H24 H24 H 0 1 N N N N N N 51.272 60.745 34.553 -4.045 -0.781 2.145  H24 LF7 45 
LF7 H25 H25 H 0 1 N N N N N N 53.041 60.561 34.307 -5.214 0.365  1.445  H25 LF7 46 
LF7 H26 H26 H 0 1 N N N N N N 51.121 60.993 32.248 -5.999 -1.507 0.007  H26 LF7 47 
LF7 H27 H27 H 0 1 N N N N N N 54.303 62.321 32.943 -2.634 -1.891 -1.117 H27 LF7 48 
LF7 H28 H28 H 0 1 N N N N N N 53.406 63.755 32.339 -2.539 -2.099 0.649  H28 LF7 49 
# 
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 
LF7 O4  C3  SING N N 1  
LF7 C6  C3  SING N N 2  
LF7 C6  C7  SING N N 3  
LF7 C3  C5  SING N N 4  
LF7 C3  C21 SING N N 5  
LF7 C5  C10 SING N N 6  
LF7 N12 C7  SING N N 7  
LF7 N12 C13 SING N N 8  
LF7 C7  C9  SING N N 9  
LF7 C7  C8  SING N N 10 
LF7 C21 C1  SING N N 11 
LF7 C9  C10 SING N N 12 
LF7 C10 C2  SING N N 13 
LF7 C13 C14 SING N N 14 
LF7 O20 C14 DOUB N N 15 
LF7 C8  C1  SING N N 16 
LF7 C1  C2  SING N N 17 
LF7 C14 N15 SING N N 18 
LF7 N15 C16 SING N N 19 
LF7 N15 C19 SING N N 20 
LF7 C16 C20 SING N N 21 
LF7 C16 C17 SING N N 22 
LF7 C19 C18 SING N N 23 
LF7 C20 N2  DOUB N N 24 
LF7 C17 C18 SING N N 25 
LF7 C19 H1  SING N N 26 
LF7 C19 H2  SING N N 27 
LF7 C18 H3  SING N N 28 
LF7 C18 H4  SING N N 29 
LF7 C17 H5  SING N N 30 
LF7 C17 H6  SING N N 31 
LF7 C16 H7  SING N N 32 
LF7 C20 H8  SING N N 33 
LF7 N2  H9  SING N N 34 
LF7 C13 H10 SING N N 35 
LF7 C13 H11 SING N N 36 
LF7 N12 H12 SING N N 37 
LF7 C8  H14 SING N N 38 
LF7 C8  H15 SING N N 39 
LF7 C1  H16 SING N N 40 
LF7 C2  H17 SING N N 41 
LF7 C2  H18 SING N N 42 
LF7 C10 H19 SING N N 43 
LF7 C9  H20 SING N N 44 
LF7 C9  H21 SING N N 45 
LF7 C5  H22 SING N N 46 
LF7 C5  H23 SING N N 47 
LF7 C21 H24 SING N N 48 
LF7 C21 H25 SING N N 49 
LF7 O4  H26 SING N N 50 
LF7 C6  H27 SING N N 51 
LF7 C6  H28 SING N N 52 
# 
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 
LF7 SMILES           ACDLabs              12.01 "O=C(N1C(CCC1)\C=N)CNC24CC3CC(C2)CC(C3)(O)C4"                                                                                                                
LF7 InChI            InChI                1.03  "InChI=1S/C17H27N3O2/c18-9-14-2-1-3-20(14)15(21)10-19-16-5-12-4-13(6-16)8-17(22,7-12)11-16/h9,12-14,18-19,22H,1-8,10-11H2/b18-9+/t12-,13+,14-,16+,17-/m0/s1" 
LF7 InChIKey         InChI                1.03  LUWVSODOPBYGON-FEZPVXCISA-N                                                                                                                                  
LF7 SMILES_CANONICAL CACTVS               3.385 "OC12C[C@H]3C[C@@H](C1)CC(C3)(C2)NCC(=O)N4CCC[C@H]4C=N"                                                                                                      
LF7 SMILES           CACTVS               3.385 "OC12C[CH]3C[CH](C1)CC(C3)(C2)NCC(=O)N4CCC[CH]4C=N"                                                                                                          
LF7 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "[H]/N=C/[C@@H]1CCCN1C(=O)CNC23C[C@H]4C[C@@H](C2)CC(C4)(C3)O"                                                                                                
LF7 SMILES           "OpenEye OEToolkits" 1.7.6 "C1CC(N(C1)C(=O)CNC23CC4CC(C2)CC(C4)(C3)O)C=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 
LF7 "SYSTEMATIC NAME" ACDLabs              12.01 "2-{[(1r,3s,5R,7S)-3-hydroxytricyclo[3.3.1.1~3,7~]decan-1-yl]amino}-1-{(2S)-2-[(E)-iminomethyl]pyrrolidin-1-yl}ethan-1-one" 
LF7 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 "1-[(2S)-2-(iminomethyl)pyrrolidin-1-yl]-2-[[(5R,7S)-3-oxidanyl-1-adamantyl]amino]ethanone"                                 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
LF7 "Create component"   2012-12-11 PDBJ 
LF7 "Modify synonyms"    2012-12-13 PDBJ 
LF7 "Initial release"    2013-05-15 RCSB 
LF7 "Other modification" 2018-02-01 RCSB 
LF7 "Modify synonyms"    2020-06-05 PDBE 
LF7 "Modify PCM"         2024-09-27 PDBE 
# 
_pdbx_chem_comp_synonyms.ordinal      1 
_pdbx_chem_comp_synonyms.comp_id      LF7 
_pdbx_chem_comp_synonyms.name         "Vildagliptin, bound form" 
_pdbx_chem_comp_synonyms.provenance   ? 
_pdbx_chem_comp_synonyms.type         ? 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            LF7 
_pdbx_chem_comp_pcm.modified_residue_id                SER 
_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               C20 
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom   OG 
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession     ? 
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession      ? 
# 
