data_YVM
# 
_chem_comp.id                                    YVM 
_chem_comp.name                                  "4-fluoro-N-{3-[(prop-2-yn-1-yl)oxy]propanoyl}-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                               "C35 H43 F N4 O7" 
_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                        650.737 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YVM 
_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        7MB2 
_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 
YVM C10  C1  C 0 1 N N N N N N 21.298 -10.112 30.074 -5.518 3.881  -0.069 C10  YVM 1  
YVM C13  C2  C 0 1 N N N N N N 22.658 -15.061 29.277 -6.091 0.244  -0.665 C13  YVM 2  
YVM C15  C3  C 0 1 N N N N N N 24.171 -16.909 30.128 -7.363 -1.551 0.479  C15  YVM 3  
YVM C20  C4  C 0 1 N N N N N N 25.654 -18.489 31.197 -8.836 -3.214 1.340  C20  YVM 4  
YVM C21  C5  C 0 1 N N N N N N 27.115 -18.338 31.720 -8.891 -4.254 2.462  C21  YVM 5  
YVM C22  C6  C 0 1 N N N N N N 23.352 -9.501  31.031 -5.063 5.348  -1.811 C22  YVM 6  
YVM C24  C7  C 0 1 Y N N N N N 26.165 -12.850 21.282 1.348  -4.797 -0.934 C24  YVM 7  
YVM C26  C8  C 0 1 Y N N N N N 27.423 -12.736 23.571 0.483  -3.071 0.481  C26  YVM 8  
YVM C28  C9  C 0 1 Y N N N N N 25.045 -13.764 23.441 -0.717 -3.719 -1.486 C28  YVM 9  
YVM C01  C10 C 0 1 N N N N N N 25.569 -9.956  26.474 1.119  -0.453 -0.561 C01  YVM 10 
YVM C04  C11 C 0 1 N N S N N N 25.368 -12.490 26.206 -1.311 -0.575 -0.703 C04  YVM 11 
YVM C05  C12 C 0 1 N N N N N N 26.248 -13.622 25.751 -1.671 -1.908 -0.044 C05  YVM 12 
YVM C07  C13 C 0 1 N N R N N N 23.032 -13.520 29.204 -4.781 1.036  -0.665 C07  YVM 13 
YVM C08  C14 C 0 1 N N N N N N 21.859 -12.625 29.551 -4.849 2.134  -1.728 C08  YVM 14 
YVM C09  C15 C 0 1 N N S N N N 22.448 -11.266 29.897 -5.917 3.158  -1.337 C09  YVM 15 
YVM C14  C16 C 0 1 N N N N N N 23.967 -15.845 29.044 -6.073 -0.771 0.479  C14  YVM 16 
YVM C18  C17 C 0 1 N N N N N N 24.906 -12.726 27.645 -2.433 0.408  -0.493 C18  YVM 17 
YVM C23  C18 C 0 1 N N N N N N 23.377 -11.093 30.827 -6.009 4.277  -2.399 C23  YVM 18 
YVM C25  C19 C 0 1 Y N N N N N 27.365 -12.462 22.079 1.460  -4.005 0.193  C25  YVM 19 
YVM C27  C20 C 0 1 Y N N N N N 26.239 -13.373 24.253 -0.606 -2.927 -0.358 C27  YVM 20 
YVM C29  C21 C 0 1 Y N N N N N 24.977 -13.504 21.951 0.259  -4.654 -1.774 C29  YVM 21 
YVM C30  C22 C 0 1 N N R N N N 26.445 -8.708  26.624 2.382  0.088  0.057  C30  YVM 22 
YVM C32  C23 C 0 1 N N N N N N 27.325 -8.568  25.415 2.416  -0.271 1.544  C32  YVM 23 
YVM C33  C24 C 0 1 Y N N N N N 24.853 -7.389  21.693 5.820  1.555  3.371  C33  YVM 24 
YVM C34  C25 C 0 1 Y N N N N N 25.234 -6.341  22.725 4.613  2.231  3.324  C34  YVM 25 
YVM C35  C26 C 0 1 Y N N N N N 26.062 -6.737  23.959 3.512  1.640  2.733  C35  YVM 26 
YVM C36  C27 C 0 1 Y N N N N N 26.479 -8.158  24.171 3.617  0.373  2.188  C36  YVM 27 
YVM C37  C28 C 0 1 Y N N N N N 26.079 -9.242  23.154 4.821  -0.303 2.235  C37  YVM 28 
YVM C38  C29 C 0 1 Y N N N N N 25.277 -8.860  21.896 5.923  0.286  2.826  C38  YVM 29 
YVM C40  C30 C 0 1 N N N N N N 26.188 -6.498  27.739 4.723  0.152  -0.616 C40  YVM 30 
YVM C41  C31 C 0 1 N N N N N N 25.373 -5.208  28.009 5.919  -0.453 -1.306 C41  YVM 31 
YVM C43  C32 C 0 1 N N N N N N 24.480 -5.460  29.210 7.120  0.484  -1.160 C43  YVM 32 
YVM C45  C33 C 0 1 N N N N N N 24.614 -5.852  31.554 9.435  0.710  -1.738 C45  YVM 33 
YVM C46  C34 C 0 1 N N N N N N 25.535 -6.914  32.249 10.535 0.029  -2.440 C46  YVM 34 
YVM C47  C35 C 0 1 N N N N N N 26.228 -7.763  32.782 11.412 -0.515 -3.000 C47  YVM 35 
YVM F39  F1  F 0 1 N N N N N N 24.145 -7.038  20.622 6.897  2.134  3.944  F39  YVM 36 
YVM N02  N1  N 0 1 N N N N N N 26.195 -11.256 26.232 -0.082 -0.049 -0.102 N02  YVM 37 
YVM N06  N2  N 0 1 N N N N N N 23.538 -13.238 27.838 -3.666 0.135  -0.964 N06  YVM 38 
YVM N11  N3  N 0 1 N N N N N N 21.847 -9.022  30.718 -5.049 5.105  -0.364 N11  YVM 39 
YVM N31  N4  N 0 1 N N N N N N 25.650 -7.543  26.874 3.545  -0.501 -0.614 N31  YVM 40 
YVM O03  O1  O 0 1 N N N N N N 24.375 -9.946  26.607 1.183  -1.251 -1.472 O03  YVM 41 
YVM O12  O2  O 0 1 N N N N N N 20.213 -10.171 29.592 -5.613 3.424  1.050  O12  YVM 42 
YVM O16  O3  O 0 1 N N N N N N 25.441 -17.544 30.155 -7.571 -2.504 1.401  O16  YVM 43 
YVM O17  O4  O 0 1 N N N N N N 23.208 -17.220 30.853 -8.209 -1.318 -0.351 O17  YVM 44 
YVM O19  O5  O 0 1 N N N N N N 25.660 -12.536 28.598 -2.227 1.446  0.101  O19  YVM 45 
YVM O42  O6  O 0 1 N N N N N N 27.282 -6.619  28.198 4.822  1.227  -0.062 O42  YVM 46 
YVM O44  O7  O 0 1 N N N N N N 25.284 -5.359  30.374 8.253  -0.090 -1.814 O44  YVM 47 
YVM H131 H1  H 0 0 N N N N N N 21.923 -15.310 28.498 -6.929 0.928  -0.531 H131 YVM 48 
YVM H1   H2  H 0 1 N N N N N N 22.241 -15.304 30.266 -6.198 -0.280 -1.615 H1   YVM 49 
YVM H201 H3  H 0 0 N N N N N N 24.946 -18.301 32.018 -8.926 -3.715 0.376  H201 YVM 50 
YVM H202 H4  H 0 0 N N N N N N 25.503 -19.507 30.809 -9.656 -2.507 1.460  H202 YVM 51 
YVM H211 H5  H 0 0 N N N N N N 27.293 -19.064 32.527 -8.071 -4.961 2.342  H211 YVM 52 
YVM H212 H6  H 0 0 N N N N N N 27.820 -18.525 30.897 -8.801 -3.753 3.426  H212 YVM 53 
YVM H213 H7  H 0 0 N N N N N N 27.263 -17.318 32.105 -9.841 -4.787 2.416  H213 YVM 54 
YVM H221 H8  H 0 0 N N N N N N 24.056 -9.018  30.337 -4.060 5.232  -2.223 H221 YVM 55 
YVM H222 H9  H 0 0 N N N N N N 23.624 -9.246  32.066 -5.444 6.346  -2.024 H222 YVM 56 
YVM H241 H10 H 0 0 N N N N N N 26.145 -12.662 20.219 2.113  -5.525 -1.161 H241 YVM 57 
YVM H261 H11 H 0 0 N N N N N N 28.304 -12.477 24.139 0.570  -2.452 1.363  H261 YVM 58 
YVM H281 H12 H 0 0 N N N N N N 24.210 -14.244 23.930 -1.568 -3.606 -2.143 H281 YVM 59 
YVM H041 H13 H 0 0 N N N N N N 24.502 -12.373 25.537 -1.156 -0.727 -1.771 H041 YVM 60 
YVM H052 H14 H 0 0 N N N N N N 25.818 -14.602 26.005 -1.738 -1.774 1.035  H052 YVM 61 
YVM H051 H15 H 0 0 N N N N N N 27.262 -13.546 26.172 -2.630 -2.256 -0.428 H051 YVM 62 
YVM H071 H16 H 0 0 N N N N N N 23.839 -13.337 29.929 -4.630 1.488  0.315  H071 YVM 63 
YVM H082 H17 H 0 0 N N N N N N 21.179 -12.538 28.691 -3.881 2.629  -1.801 H082 YVM 64 
YVM H081 H18 H 0 0 N N N N N N 21.310 -13.033 30.413 -5.104 1.692  -2.691 H081 YVM 65 
YVM H091 H19 H 0 0 N N N N N N 22.932 -10.962 28.957 -6.883 2.670  -1.210 H091 YVM 66 
YVM H141 H20 H 0 0 N N N N N N 23.921 -16.337 28.061 -5.235 -1.455 0.345  H141 YVM 67 
YVM H142 H21 H 0 0 N N N N N N 24.814 -15.144 29.064 -5.965 -0.247 1.429  H142 YVM 68 
YVM H232 H22 H 0 0 N N N N N N 23.115 -11.619 31.757 -7.027 4.657  -2.478 H232 YVM 69 
YVM H231 H23 H 0 0 N N N N N N 24.362 -11.436 30.477 -5.648 3.927  -3.367 H231 YVM 70 
YVM H251 H24 H 0 0 N N N N N N 28.200 -11.982 21.590 2.310  -4.118 0.850  H251 YVM 71 
YVM H291 H25 H 0 0 N N N N N N 24.102 -13.779 21.380 0.172  -5.272 -2.655 H291 YVM 72 
YVM H301 H26 H 0 0 N N N N N N 27.100 -8.874  27.492 2.408  1.171  -0.056 H301 YVM 73 
YVM H322 H27 H 0 0 N N N N N N 27.821 -9.529  25.215 1.508  0.091  2.026  H322 YVM 74 
YVM H321 H28 H 0 0 N N N N N N 28.085 -7.796  25.607 2.481  -1.353 1.656  H321 YVM 75 
YVM H341 H29 H 0 0 N N N N N N 24.923 -5.315  22.592 4.531  3.221  3.749  H341 YVM 76 
YVM H351 H30 H 0 0 N N N N N N 26.345 -5.983  24.679 2.570  2.167  2.696  H351 YVM 77 
YVM H371 H31 H 0 0 N N N N N N 26.361 -10.271 23.323 4.902  -1.293 1.811  H371 YVM 78 
YVM H381 H32 H 0 0 N N N N N N 25.015 -9.611  21.165 6.864  -0.242 2.862  H381 YVM 79 
YVM H411 H33 H 0 0 N N N N N N 26.056 -4.372  28.221 6.152  -1.416 -0.851 H411 YVM 80 
YVM H412 H34 H 0 0 N N N N N N 24.757 -4.965  27.131 5.695  -0.595 -2.363 H412 YVM 81 
YVM H431 H35 H 0 0 N N N N N N 23.676 -4.710  29.243 6.887  1.447  -1.615 H431 YVM 82 
YVM H432 H36 H 0 0 N N N N N N 24.040 -6.466  29.145 7.344  0.626  -0.103 H432 YVM 83 
YVM H451 H37 H 0 0 N N N N N N 24.422 -5.019  32.246 9.707  0.857  -0.692 H451 YVM 84 
YVM H452 H38 H 0 0 N N N N N N 23.660 -6.319  31.270 9.250  1.678  -2.204 H452 YVM 85 
YVM H471 H39 H 0 0 N N N N N N 26.831 -8.501  33.246 12.197 -1.000 -3.501 H471 YVM 86 
YVM H021 H40 H 0 0 N N N N N N 27.182 -11.314 26.084 -0.133 0.589  0.627  H021 YVM 87 
YVM H061 H41 H 0 0 N N N N N N 22.949 -13.396 27.046 -3.814 -0.659 -1.501 H061 YVM 88 
YVM H111 H42 H 0 0 N N N N N N 21.415 -8.147  30.937 -4.740 5.747  0.296  H111 YVM 89 
YVM H311 H43 H 0 0 N N N N N N 24.743 -7.448  26.463 3.466  -1.360 -1.056 H311 YVM 90 
# 
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 
YVM F39 C33  SING N N 1  
YVM C24 C29  DOUB Y N 2  
YVM C24 C25  SING Y N 3  
YVM C33 C38  DOUB Y N 4  
YVM C33 C34  SING Y N 5  
YVM C38 C37  SING Y N 6  
YVM C29 C28  SING Y N 7  
YVM C25 C26  DOUB Y N 8  
YVM C34 C35  DOUB Y N 9  
YVM C37 C36  DOUB Y N 10 
YVM C28 C27  DOUB Y N 11 
YVM C26 C27  SING Y N 12 
YVM C35 C36  SING Y N 13 
YVM C36 C32  SING N N 14 
YVM C27 C05  SING N N 15 
YVM C32 C30  SING N N 16 
YVM C05 C04  SING N N 17 
YVM C04 N02  SING N N 18 
YVM C04 C18  SING N N 19 
YVM N02 C01  SING N N 20 
YVM C01 O03  DOUB N N 21 
YVM C01 C30  SING N N 22 
YVM C30 N31  SING N N 23 
YVM N31 C40  SING N N 24 
YVM C18 N06  SING N N 25 
YVM C18 O19  DOUB N N 26 
YVM C40 C41  SING N N 27 
YVM C40 O42  DOUB N N 28 
YVM N06 C07  SING N N 29 
YVM C41 C43  SING N N 30 
YVM C14 C13  SING N N 31 
YVM C14 C15  SING N N 32 
YVM C07 C13  SING N N 33 
YVM C07 C08  SING N N 34 
YVM C43 O44  SING N N 35 
YVM C08 C09  SING N N 36 
YVM O12 C10  DOUB N N 37 
YVM C09 C10  SING N N 38 
YVM C09 C23  SING N N 39 
YVM C10 N11  SING N N 40 
YVM C15 O16  SING N N 41 
YVM C15 O17  DOUB N N 42 
YVM O16 C20  SING N N 43 
YVM O44 C45  SING N N 44 
YVM N11 C22  SING N N 45 
YVM C23 C22  SING N N 46 
YVM C20 C21  SING N N 47 
YVM C45 C46  SING N N 48 
YVM C46 C47  TRIP N N 49 
YVM C13 H131 SING N N 50 
YVM C13 H1   SING N N 51 
YVM C20 H201 SING N N 52 
YVM C20 H202 SING N N 53 
YVM C21 H211 SING N N 54 
YVM C21 H212 SING N N 55 
YVM C21 H213 SING N N 56 
YVM C22 H221 SING N N 57 
YVM C22 H222 SING N N 58 
YVM C24 H241 SING N N 59 
YVM C26 H261 SING N N 60 
YVM C28 H281 SING N N 61 
YVM C04 H041 SING N N 62 
YVM C05 H052 SING N N 63 
YVM C05 H051 SING N N 64 
YVM C07 H071 SING N N 65 
YVM C08 H082 SING N N 66 
YVM C08 H081 SING N N 67 
YVM C09 H091 SING N N 68 
YVM C14 H141 SING N N 69 
YVM C14 H142 SING N N 70 
YVM C23 H232 SING N N 71 
YVM C23 H231 SING N N 72 
YVM C25 H251 SING N N 73 
YVM C29 H291 SING N N 74 
YVM C30 H301 SING N N 75 
YVM C32 H322 SING N N 76 
YVM C32 H321 SING N N 77 
YVM C34 H341 SING N N 78 
YVM C35 H351 SING N N 79 
YVM C37 H371 SING N N 80 
YVM C38 H381 SING N N 81 
YVM C41 H411 SING N N 82 
YVM C41 H412 SING N N 83 
YVM C43 H431 SING N N 84 
YVM C43 H432 SING N N 85 
YVM C45 H451 SING N N 86 
YVM C45 H452 SING N N 87 
YVM C47 H471 SING N N 88 
YVM N02 H021 SING N N 89 
YVM N06 H061 SING N N 90 
YVM N11 H111 SING N N 91 
YVM N31 H311 SING N N 92 
# 
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 
YVM SMILES           ACDLabs              12.01 "Fc1ccc(cc1)CC(NC(=O)CCOCC#C)C(=O)NC(Cc1ccccc1)C(=O)NC(CC1CCNC1=O)CCC(=O)OCC"                                                                                                                                                                                    
YVM InChI            InChI                1.03  "InChI=1S/C35H43FN4O7/c1-3-19-46-20-17-31(41)39-29(22-25-10-12-27(36)13-11-25)35(45)40-30(21-24-8-6-5-7-9-24)34(44)38-28(14-15-32(42)47-4-2)23-26-16-18-37-33(26)43/h1,5-13,26,28-30H,4,14-23H2,2H3,(H,37,43)(H,38,44)(H,39,41)(H,40,45)/t26-,28+,29+,30-/m0/s1" 
YVM InChIKey         InChI                1.03  AMUUPQIKCDYOIG-XQVPNCLKSA-N                                                                                                                                                                                                                                      
YVM SMILES_CANONICAL CACTVS               3.385 "CCOC(=O)CC[C@H](C[C@@H]1CCNC1=O)NC(=O)[C@H](Cc2ccccc2)NC(=O)[C@@H](Cc3ccc(F)cc3)NC(=O)CCOCC#C"                                                                                                                                                                  
YVM SMILES           CACTVS               3.385 "CCOC(=O)CC[CH](C[CH]1CCNC1=O)NC(=O)[CH](Cc2ccccc2)NC(=O)[CH](Cc3ccc(F)cc3)NC(=O)CCOCC#C"                                                                                                                                                                        
YVM 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](Cc3ccc(cc3)F)NC(=O)CCOCC#C"                                                                                                                                                                  
YVM SMILES           "OpenEye OEToolkits" 2.0.7 "CCOC(=O)CCC(CC1CCNC1=O)NC(=O)C(Cc2ccccc2)NC(=O)C(Cc3ccc(cc3)F)NC(=O)CCOCC#C"                                                                                                                                                                                    
# 
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 
YVM "SYSTEMATIC NAME" ACDLabs              12.01 "4-fluoro-N-{3-[(prop-2-yn-1-yl)oxy]propanoyl}-D-phenylalanyl-N-{(2R)-5-ethoxy-5-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]pentan-2-yl}-L-phenylalaninamide"                                        
YVM "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "ethyl (4~{R})-4-[[(2~{S})-2-[[(2~{R})-3-(4-fluorophenyl)-2-(3-prop-2-ynoxypropanoylamino)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 
YVM "Create component" 2021-04-01 RCSB 
YVM "Initial release"  2022-10-12 RCSB 
YVM "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            YVM 
_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      ? 
# 
