data_YVG
# 
_chem_comp.id                                    YVG 
_chem_comp.name                                  "D-phenylalanyl-N-{(2R)-5-ethoxy-5-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]pentan-2-yl}-L-phenylalaninamide" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C29 H38 N4 O5" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2021-04-01 
_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                        522.636 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YVG 
_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        7MB0 
_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 
YVG C10  C1  C 0 1 N N N N N N 27.674 -10.574 4.849  4.094  3.634  -0.449 C10  YVG 1  
YVG C13  C2  C 0 1 N N N N N N 29.149 -15.220 3.829  4.349  -0.011 0.293  C13  YVG 2  
YVG C15  C3  C 0 1 N N N N N N 30.561 -17.066 4.805  5.279  -1.988 -0.879 C15  YVG 3  
YVG C20  C4  C 0 1 N N N N N N 32.332 -18.659 5.026  6.455  -3.844 -1.802 C20  YVG 4  
YVG C21  C5  C 0 1 N N N N N N 33.408 -18.936 6.095  6.266  -4.935 -2.858 C21  YVG 5  
YVG C22  C6  C 0 1 N N N N N N 29.363 -10.209 6.534  4.008  5.223  1.242  C22  YVG 6  
YVG C24  C7  C 0 1 Y N N N N N 32.563 -12.926 -4.004 -3.491 -4.175 1.711  C24  YVG 7  
YVG C26  C8  C 0 1 Y N N N N N 33.743 -12.740 -1.650 -2.626 -2.624 0.105  C26  YVG 8  
YVG C28  C9  C 0 1 Y N N N N N 31.406 -13.949 -1.864 -1.273 -3.309 1.958  C28  YVG 9  
YVG C01  C10 C 0 1 N N N N N N 32.008 -10.088 1.214  -2.854 0.094  1.055  C01  YVG 10 
YVG C04  C11 C 0 1 N N S N N N 31.818 -12.559 1.026  -0.451 -0.291 0.925  C04  YVG 11 
YVG C05  C12 C 0 1 N N N N N N 32.620 -13.736 0.481  -0.315 -1.685 0.311  C05  YVG 12 
YVG C07  C13 C 0 1 N N R N N N 29.521 -13.718 3.946  3.139  0.920  0.395  C07  YVG 13 
YVG C08  C14 C 0 1 N N N N N N 28.400 -12.748 4.281  3.449  2.053  1.376  C08  YVG 14 
YVG C09  C15 C 0 1 N N S N N N 28.893 -11.198 4.341  4.564  2.931  0.805  C09  YVG 15 
YVG C14  C16 C 0 1 N N N N N N 30.454 -16.024 3.710  4.088  -1.071 -0.779 C14  YVG 16 
YVG C18  C17 C 0 1 N N N N N N 31.364 -12.870 2.443  0.735  0.550  0.530  C18  YVG 17 
YVG C23  C18 C 0 1 N N N N N N 29.888 -11.175 5.478  4.899  4.083  1.782  C23  YVG 18 
YVG C25  C19 C 0 1 Y N N N N N 33.739 -12.468 -3.150 -3.654 -3.430 0.558  C25  YVG 19 
YVG C27  C20 C 0 1 Y N N N N N 32.595 -13.502 -1.022 -1.436 -2.563 0.805  C27  YVG 20 
YVG C29  C21 C 0 1 Y N N N N N 31.395 -13.662 -3.365 -2.301 -4.115 2.411  C29  YVG 21 
YVG C30  C22 C 0 1 N N R N N N 32.837 -8.801  1.257  -4.119 0.742  0.554  C30  YVG 22 
YVG C32  C23 C 0 1 N N N N N N 33.618 -8.565  -0.037 -4.640 -0.028 -0.660 C32  YVG 23 
YVG C33  C24 C 0 1 Y N N N N N 31.098 -7.604  -3.729 -8.024 2.006  -2.291 C33  YVG 24 
YVG C34  C25 C 0 1 Y N N N N N 31.570 -9.030  -3.457 -6.753 2.310  -2.740 C34  YVG 25 
YVG C35  C26 C 0 1 Y N N N N N 32.408 -9.344  -2.227 -5.657 1.651  -2.212 C35  YVG 26 
YVG C36  C27 C 0 1 Y N N N N N 32.776 -8.237  -1.252 -5.834 0.689  -1.236 C36  YVG 27 
YVG C37  C28 C 0 1 Y N N N N N 32.319 -6.817  -1.518 -7.106 0.384  -0.787 C37  YVG 28 
YVG C38  C29 C 0 1 Y N N N N N 31.485 -6.495  -2.757 -8.201 1.043  -1.315 C38  YVG 29 
YVG N02  N1  N 0 1 N N N N N N 32.651 -11.364 1.039  -1.681 0.339  0.438  N02  YVG 30 
YVG N06  N2  N 0 1 N N N N N N 30.023 -13.370 2.609  1.980  0.164  0.873  N06  YVG 31 
YVG N11  N3  N 0 1 N N N N N N 27.935 -10.021 6.216  3.795  4.916  -0.177 N11  YVG 32 
YVG N31  N4  N 0 1 N N N N N N 31.927 -7.698  1.546  -5.132 0.725  1.617  N31  YVG 33 
YVG O03  O1  O 0 1 N N N N N N 30.798 -10.045 1.328  -2.891 -0.648 2.014  O03  YVG 34 
YVG O12  O2  O 0 1 N N N N N N 26.623 -10.574 4.273  4.006  3.118  -1.543 O12  YVG 35 
YVG O16  O3  O 0 1 N N N N N N 31.831 -17.396 5.287  5.274  -3.001 -1.760 O16  YVG 36 
YVG O17  O4  O 0 1 N N N N N N 29.586 -17.561 5.288  6.239  -1.812 -0.166 O17  YVG 37 
YVG O19  O5  O 0 1 N N N N N N 32.069 -12.703 3.381  0.569  1.575  -0.097 O19  YVG 38 
YVG H1   H1  H 0 1 N N N N N N 28.528 -15.382 2.936  5.232  0.568  0.023  H1   YVG 39 
YVG H2   H2  H 0 1 N N N N N N 28.595 -15.538 4.724  4.514  -0.499 1.254  H2   YVG 40 
YVG H201 H3  H 0 0 N N N N N N 31.529 -19.407 5.093  6.607  -4.306 -0.826 H201 YVG 41 
YVG H202 H4  H 0 0 N N N N N N 32.779 -18.690 4.021  7.325  -3.239 -2.057 H202 YVG 42 
YVG H213 H5  H 0 0 N N N N N N 33.840 -19.934 5.931  7.153  -5.568 -2.890 H213 YVG 43 
YVG H212 H6  H 0 0 N N N N N N 34.201 -18.177 6.022  5.396  -5.541 -2.603 H212 YVG 44 
YVG H211 H7  H 0 0 N N N N N N 32.951 -18.894 7.095  6.114  -4.473 -3.834 H211 YVG 45 
YVG H222 H8  H 0 0 N N N N N N 29.480 -10.638 7.540  3.055  5.239  1.772  H222 YVG 46 
YVG H221 H9  H 0 0 N N N N N N 29.899 -9.250  6.479  4.515  6.182  1.350  H221 YVG 47 
YVG H241 H10 H 0 0 N N N N N N 32.559 -12.728 -5.066 -4.296 -4.801 2.067  H241 YVG 48 
YVG H261 H11 H 0 0 N N N N N N 34.561 -12.391 -1.038 -2.753 -2.042 -0.796 H261 YVG 49 
YVG H281 H12 H 0 0 N N N N N N 30.577 -14.465 -1.403 -0.343 -3.261 2.505  H281 YVG 50 
YVG H041 H13 H 0 0 N N N N N N 30.935 -12.398 0.390  -0.492 -0.374 2.011  H041 YVG 51 
YVG H051 H14 H 0 0 N N N N N N 32.143 -14.693 0.740  -0.364 -1.610 -0.775 H051 YVG 52 
YVG H052 H15 H 0 0 N N N N N N 33.650 -13.724 0.866  0.642  -2.119 0.603  H052 YVG 53 
YVG H071 H16 H 0 0 N N N N N N 30.326 -13.610 4.687  2.920  1.340  -0.587 H071 YVG 54 
YVG H082 H17 H 0 0 N N N N N N 27.618 -12.837 3.512  2.554  2.656  1.530  H082 YVG 55 
YVG H081 H18 H 0 0 N N N N N N 27.983 -13.021 5.261  3.771  1.631  2.328  H081 YVG 56 
YVG H091 H19 H 0 0 N N N N N N 29.269 -10.821 3.378  5.451  2.333  0.598  H091 YVG 57 
YVG H141 H20 H 0 0 N N N N N N 30.476 -16.528 2.732  3.205  -1.651 -0.509 H141 YVG 58 
YVG H142 H21 H 0 0 N N N N N N 31.308 -15.335 3.787  3.922  -0.583 -1.739 H142 YVG 59 
YVG H232 H22 H 0 0 N N N N N N 29.988 -12.182 5.908  5.954  4.351  1.721  H232 YVG 60 
YVG H231 H23 H 0 0 N N N N N N 30.867 -10.834 5.112  4.623  3.821  2.803  H231 YVG 61 
YVG H251 H24 H 0 0 N N N N N N 34.570 -11.951 -3.607 -4.584 -3.477 0.011  H251 YVG 62 
YVG H291 H25 H 0 0 N N N N N N 30.560 -13.981 -3.971 -2.174 -4.697 3.312  H291 YVG 63 
YVG H301 H26 H 0 0 N N N N N N 33.561 -8.891  2.080  -3.910 1.773  0.268  H301 YVG 64 
YVG H321 H27 H 0 0 N N N N N N 34.192 -9.477  -0.258 -3.856 -0.091 -1.415 H321 YVG 65 
YVG H322 H28 H 0 0 N N N N N N 34.311 -7.727  0.132  -4.932 -1.033 -0.355 H322 YVG 66 
YVG H331 H29 H 0 0 N N N N N N 30.497 -7.383  -4.599 -8.879 2.523  -2.700 H331 YVG 67 
YVG H341 H30 H 0 0 N N N N N N 31.307 -9.822  -4.143 -6.615 3.061  -3.503 H341 YVG 68 
YVG H351 H31 H 0 0 N N N N N N 32.742 -10.355 -2.046 -4.664 1.888  -2.564 H351 YVG 69 
YVG H371 H32 H 0 0 N N N N N N 32.584 -6.029  -0.829 -7.244 -0.368 -0.025 H371 YVG 70 
YVG H381 H33 H 0 0 N N N N N N 31.169 -5.479  -2.945 -9.194 0.805  -0.964 H381 YVG 71 
YVG H021 H34 H 0 0 N N N N N N 33.643 -11.428 0.929  -1.651 0.933  -0.328 H021 YVG 72 
YVG H061 H35 H 0 0 N N N N N N 29.431 -13.481 1.811  2.107  -0.615 1.437  H061 YVG 73 
YVG H111 H36 H 0 0 N N N N N N 27.255 -9.596  6.813  3.479  5.556  -0.834 H111 YVG 74 
YVG H311 H37 H 0 0 N N N N N N 31.435 -7.885  2.396  -5.343 -0.220 1.900  H311 YVG 75 
YVG H3   H38 H 0 1 N N N N N N 32.450 -6.851  1.644  -4.839 1.281  2.406  H3   YVG 76 
# 
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 
YVG C24 C29  DOUB Y N 1  
YVG C24 C25  SING Y N 2  
YVG C33 C34  DOUB Y N 3  
YVG C33 C38  SING Y N 4  
YVG C34 C35  SING Y N 5  
YVG C29 C28  SING Y N 6  
YVG C25 C26  DOUB Y N 7  
YVG C38 C37  DOUB Y N 8  
YVG C35 C36  DOUB Y N 9  
YVG C28 C27  DOUB Y N 10 
YVG C26 C27  SING Y N 11 
YVG C37 C36  SING Y N 12 
YVG C36 C32  SING N N 13 
YVG C27 C05  SING N N 14 
YVG C32 C30  SING N N 15 
YVG C05 C04  SING N N 16 
YVG C04 N02  SING N N 17 
YVG C04 C18  SING N N 18 
YVG N02 C01  SING N N 19 
YVG C01 C30  SING N N 20 
YVG C01 O03  DOUB N N 21 
YVG C30 N31  SING N N 22 
YVG C18 N06  SING N N 23 
YVG C18 O19  DOUB N N 24 
YVG N06 C07  SING N N 25 
YVG C14 C13  SING N N 26 
YVG C14 C15  SING N N 27 
YVG C13 C07  SING N N 28 
YVG C07 C08  SING N N 29 
YVG O12 C10  DOUB N N 30 
YVG C08 C09  SING N N 31 
YVG C09 C10  SING N N 32 
YVG C09 C23  SING N N 33 
YVG C15 O16  SING N N 34 
YVG C15 O17  DOUB N N 35 
YVG C10 N11  SING N N 36 
YVG C20 O16  SING N N 37 
YVG C20 C21  SING N N 38 
YVG C23 C22  SING N N 39 
YVG N11 C22  SING N N 40 
YVG C13 H1   SING N N 41 
YVG C13 H2   SING N N 42 
YVG C20 H201 SING N N 43 
YVG C20 H202 SING N N 44 
YVG C21 H213 SING N N 45 
YVG C21 H212 SING N N 46 
YVG C21 H211 SING N N 47 
YVG C22 H222 SING N N 48 
YVG C22 H221 SING N N 49 
YVG C24 H241 SING N N 50 
YVG C26 H261 SING N N 51 
YVG C28 H281 SING N N 52 
YVG C04 H041 SING N N 53 
YVG C05 H051 SING N N 54 
YVG C05 H052 SING N N 55 
YVG C07 H071 SING N N 56 
YVG C08 H082 SING N N 57 
YVG C08 H081 SING N N 58 
YVG C09 H091 SING N N 59 
YVG C14 H141 SING N N 60 
YVG C14 H142 SING N N 61 
YVG C23 H232 SING N N 62 
YVG C23 H231 SING N N 63 
YVG C25 H251 SING N N 64 
YVG C29 H291 SING N N 65 
YVG C30 H301 SING N N 66 
YVG C32 H321 SING N N 67 
YVG C32 H322 SING N N 68 
YVG C33 H331 SING N N 69 
YVG C34 H341 SING N N 70 
YVG C35 H351 SING N N 71 
YVG C37 H371 SING N N 72 
YVG C38 H381 SING N N 73 
YVG N02 H021 SING N N 74 
YVG N06 H061 SING N N 75 
YVG N11 H111 SING N N 76 
YVG N31 H311 SING N N 77 
YVG N31 H3   SING N N 78 
# 
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 
YVG SMILES           ACDLabs              12.01 "NC(Cc1ccccc1)C(=O)NC(Cc1ccccc1)C(=O)NC(CC1CCNC1=O)CCC(=O)OCC"                                                                                                                                                            
YVG InChI            InChI                1.03  "InChI=1S/C29H38N4O5/c1-2-38-26(34)14-13-23(19-22-15-16-31-27(22)35)32-29(37)25(18-21-11-7-4-8-12-21)33-28(36)24(30)17-20-9-5-3-6-10-20/h3-12,22-25H,2,13-19,30H2,1H3,(H,31,35)(H,32,37)(H,33,36)/t22-,23+,24+,25-/m0/s1" 
YVG InChIKey         InChI                1.03  OCJALNNRTNBTPO-LIONHTAISA-N                                                                                                                                                                                               
YVG SMILES_CANONICAL CACTVS               3.385 "CCOC(=O)CC[C@H](C[C@@H]1CCNC1=O)NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@H](N)Cc3ccccc3"                                                                                                                                           
YVG SMILES           CACTVS               3.385 "CCOC(=O)CC[CH](C[CH]1CCNC1=O)NC(=O)[CH](Cc2ccccc2)NC(=O)[CH](N)Cc3ccccc3"                                                                                                                                                
YVG SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CCOC(=O)CC[C@H](C[C@@H]1CCNC1=O)NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@@H](Cc3ccccc3)N"                                                                                                                                          
YVG SMILES           "OpenEye OEToolkits" 2.0.7 "CCOC(=O)CCC(CC1CCNC1=O)NC(=O)C(Cc2ccccc2)NC(=O)C(Cc3ccccc3)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 
YVG "SYSTEMATIC NAME" ACDLabs              12.01 "D-phenylalanyl-N-{(2R)-5-ethoxy-5-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]pentan-2-yl}-L-phenylalaninamide"                                                     
YVG "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "ethyl (4~{R})-4-[[(2~{S})-2-[[(2~{R})-2-azanyl-3-phenyl-propanoyl]amino]-3-phenyl-propanoyl]amino]-5-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]pentanoate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
YVG "Create component" 2021-04-01 RCSB 
YVG "Initial release"  2022-10-12 RCSB 
YVG "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            YVG 
_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      ? 
# 
