data_YVD
# 
_chem_comp.id                                    YVD 
_chem_comp.name                                  "4-fluoro-D-phenylalanyl-N-{(2R)-5-ethoxy-5-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]pentan-2-yl}-4-fluoro-L-phenylalaninamide" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C29 H36 F2 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                        558.617 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YVD 
_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        7MAZ 
_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 
YVD C10  C1  C 0 1 N N N N N N -8.154  -10.564 17.701 4.401  3.780  -0.155 C10  YVD 1  
YVD C13  C2  C 0 1 N N N N N N -10.019 -15.015 19.477 4.780  0.093  0.271  C13  YVD 2  
YVD C15  C3  C 0 1 N N N N N N -11.315 -17.264 18.921 5.826  -1.736 -1.037 C15  YVD 3  
YVD C20  C4  C 0 1 N N N N N N -13.177 -18.494 18.168 7.106  -3.455 -2.079 C20  YVD 4  
YVD C21  C5  C 0 1 N N N N N N -14.496 -17.716 18.387 6.991  -4.459 -3.228 C21  YVD 5  
YVD C22  C6  C 0 1 N N N N N N -9.926  -10.146 16.186 5.423  5.298  1.275  C22  YVD 6  
YVD C24  C7  C 0 1 Y N N N N N -13.270 -12.001 26.895 -3.015 -4.373 1.072  C24  YVD 7  
YVD C26  C8  C 0 1 Y N N N N N -14.396 -12.316 24.576 -2.221 -2.556 -0.273 C26  YVD 8  
YVD C28  C9  C 0 1 Y N N N N N -11.897 -13.113 25.022 -0.796 -3.529 1.388  C28  YVD 9  
YVD C01  C10 C 0 1 N N N N N N -12.600 -9.718  21.519 -2.430 -0.046 1.143  C01  YVD 10 
YVD C04  C11 C 0 1 N N S N N N -12.317 -12.174 22.074 -0.032 -0.372 0.860  C04  YVD 11 
YVD C05  C12 C 0 1 N N N N N N -12.992 -13.404 22.671 0.090  -1.637 0.009  C05  YVD 12 
YVD C07  C13 C 0 1 N N R N N N -10.175 -13.526 19.218 3.528  0.960  0.418  C07  YVD 13 
YVD C08  C14 C 0 1 N N N N N N -8.888  -12.727 18.779 3.763  2.017  1.498  C08  YVD 14 
YVD C09  C15 C 0 1 N N S N N N -9.285  -11.262 18.298 4.862  2.978  1.041  C09  YVD 15 
YVD C14  C16 C 0 1 N N N N N N -11.404 -15.807 19.514 4.592  -0.882 -0.892 C14  YVD 16 
YVD C18  C17 C 0 1 N N N N N N -11.937 -12.575 20.673 1.133  0.540  0.573  C18  YVD 17 
YVD C23  C18 C 0 1 N N N N N N -10.286 -11.271 17.173 5.137  4.042  2.129  C23  YVD 18 
YVD C25  C19 C 0 1 Y N N N N N -14.469 -11.837 25.998 -3.227 -3.440 0.070  C25  YVD 19 
YVD C27  C20 C 0 1 Y N N N N N -13.107 -12.961 24.114 -1.006 -2.602 0.384  C27  YVD 20 
YVD C29  C21 C 0 1 Y N N N N N -11.971 -12.628 26.449 -1.799 -4.414 1.732  C29  YVD 21 
YVD C31  C22 C 0 1 N N R N N N -13.428 -8.451  21.307 -3.717 0.662  0.808  C31  YVD 22 
YVD C33  C23 C 0 1 N N N N N N -14.217 -8.032  22.560 -4.280 0.107  -0.502 C33  YVD 23 
YVD C34  C24 C 0 1 Y N N N N N -11.637 -6.874  26.147 -7.738 2.347  -1.631 C34  YVD 24 
YVD C35  C25 C 0 1 Y N N N N N -11.966 -5.814  25.100 -6.484 2.741  -2.067 C35  YVD 25 
YVD C36  C26 C 0 1 Y N N N N N -12.823 -6.191  23.899 -5.366 2.016  -1.701 C36  YVD 26 
YVD C37  C27 C 0 1 Y N N N N N -13.331 -7.618  23.756 -5.500 0.897  -0.900 C37  YVD 27 
YVD C38  C28 C 0 1 Y N N N N N -13.000 -8.673  24.816 -6.751 0.503  -0.464 C38  YVD 28 
YVD C39  C29 C 0 1 Y N N N N N -12.152 -8.297  26.014 -7.870 1.230  -0.825 C39  YVD 29 
YVD F30  F1  F 0 1 N N N N N N -13.390 -11.545 28.131 -3.997 -5.238 1.407  F30  YVD 30 
YVD F40  F2  F 0 1 N N N N N N -10.882 -6.526  27.189 -8.831 3.056  -1.989 F40  YVD 31 
YVD N02  N1  N 0 1 N N N N N N -13.167 -11.007 21.928 -1.283 0.317  0.535  N02  YVD 32 
YVD N06  N2  N 0 1 N N N N N N -10.591 -13.090 20.512 2.392  0.116  0.798  N06  YVD 33 
YVD N11  N3  N 0 1 N N N N N N -8.538  -9.886  16.439 4.727  5.075  0.003  N11  YVD 34 
YVD N32  N4  N 0 1 N N N N N N -12.498 -7.449  20.876 -4.689 0.448  1.889  N32  YVD 35 
YVD O03  O1  O 0 1 N N N N N N -11.463 -9.667  21.315 -2.426 -0.944 1.959  O03  YVD 36 
YVD O12  O2  O 0 1 N N N N N N -7.087  -10.485 18.121 3.825  3.322  -1.119 O12  YVD 37 
YVD O16  O3  O 0 1 N N N N N N -12.313 -18.201 19.230 5.887  -2.669 -1.999 O16  YVD 38 
YVD O17  O4  O 0 1 N N N N N N -10.442 -17.627 18.220 6.759  -1.580 -0.285 O17  YVD 39 
YVD O19  O5  O 0 1 N N N N N N -12.696 -12.454 19.796 0.937  1.656  0.140  O19  YVD 40 
YVD H1   H1  H 0 1 N N N N N N -9.395  -15.443 18.679 5.642  0.730  0.076  H1   YVD 41 
YVD H131 H2  H 0 0 N N N N N N -9.516  -15.148 20.446 4.944  -0.467 1.192  H131 YVD 42 
YVD H202 H3  H 0 0 N N N N N N -13.382 -19.574 18.142 7.255  -3.991 -1.142 H202 YVD 43 
YVD H201 H4  H 0 0 N N N N N N -12.717 -18.186 17.218 7.953  -2.793 -2.258 H201 YVD 44 
YVD H212 H5  H 0 0 N N N N N N -15.191 -17.932 17.562 7.906  -5.048 -3.288 H212 YVD 45 
YVD H211 H6  H 0 0 N N N N N N -14.950 -18.026 19.340 6.144  -5.120 -3.049 H211 YVD 46 
YVD H213 H7  H 0 0 N N N N N N -14.285 -16.637 18.415 6.842  -3.923 -4.165 H213 YVD 47 
YVD H222 H8  H 0 0 N N N N N N -10.532 -9.249  16.379 5.035  6.190  1.766  H222 YVD 48 
YVD H221 H9  H 0 0 N N N N N N -10.078 -10.475 15.147 6.495  5.396  1.106  H221 YVD 49 
YVD H261 H10 H 0 0 N N N N N N -15.235 -12.204 23.906 -2.386 -1.828 -1.054 H261 YVD 50 
YVD H281 H11 H 0 0 N N N N N N -10.990 -13.565 24.648 0.153  -3.562 1.903  H281 YVD 51 
YVD H041 H12 H 0 0 N N N N N N -11.414 -11.929 22.652 -0.030 -0.643 1.916  H041 YVD 52 
YVD H051 H13 H 0 0 N N N N N N -13.978 -13.589 22.220 -0.002 -1.376 -1.046 H051 YVD 53 
YVD H052 H14 H 0 0 N N N N N N -12.368 -14.304 22.568 1.059  -2.102 0.185  H052 YVD 54 
YVD H071 H15 H 0 0 N N N N N N -10.968 -13.361 18.473 3.313  1.451  -0.531 H071 YVD 55 
YVD H081 H16 H 0 0 N N N N N N -8.395  -13.259 17.952 2.841  2.574  1.668  H081 YVD 56 
YVD H082 H17 H 0 0 N N N N N N -8.197  -12.654 19.632 4.069  1.529  2.424  H082 YVD 57 
YVD H091 H18 H 0 0 N N N N N N -9.684  -10.700 19.155 5.773  2.428  0.804  H091 YVD 58 
YVD H141 H19 H 0 0 N N N N N N -12.145 -15.239 18.931 3.730  -1.520 -0.697 H141 YVD 59 
YVD H142 H20 H 0 0 N N N N N N -11.736 -15.877 20.560 4.429  -0.322 -1.813 H142 YVD 60 
YVD H232 H21 H 0 0 N N N N N N -11.296 -11.102 17.574 6.005  3.774  2.731  H232 YVD 61 
YVD H231 H22 H 0 0 N N N N N N -10.254 -12.242 16.656 4.259  4.189  2.757  H231 YVD 62 
YVD H251 H23 H 0 0 N N N N N N -15.372 -11.379 26.374 -4.176 -3.404 -0.443 H251 YVD 63 
YVD H291 H24 H 0 0 N N N N N N -11.132 -12.725 27.122 -1.635 -5.138 2.517  H291 YVD 64 
YVD H311 H25 H 0 0 N N N N N N -14.151 -8.647  20.501 -3.526 1.730  0.698  H311 YVD 65 
YVD H331 H26 H 0 0 N N N N N N -14.859 -7.179  22.294 -3.525 0.185  -1.284 H331 YVD 66 
YVD H332 H27 H 0 0 N N N N N N -14.844 -8.880  22.872 -4.554 -0.939 -0.364 H332 YVD 67 
YVD H351 H28 H 0 0 N N N N N N -11.595 -4.806  25.210 -6.380 3.615  -2.693 H351 YVD 68 
YVD H361 H29 H 0 0 N N N N N N -13.069 -5.450  23.153 -4.388 2.323  -2.041 H361 YVD 69 
YVD H381 H30 H 0 0 N N N N N N -13.370 -9.682  24.710 -6.854 -0.372 0.161  H381 YVD 70 
YVD H391 H31 H 0 0 N N N N N N -11.916 -9.034  26.767 -8.847 0.922  -0.484 H391 YVD 71 
YVD H021 H32 H 0 0 N N N N N N -14.148 -11.082 22.108 -1.287 1.035  -0.118 H021 YVD 72 
YVD H061 H33 H 0 0 N N N N N N -9.967  -13.139 21.292 2.546  -0.747 1.212  H061 YVD 73 
YVD H111 H34 H 0 0 N N N N N N -7.931  -9.340  15.862 4.523  5.773  -0.640 H111 YVD 74 
YVD H322 H35 H 0 0 N N N N N N -12.983 -6.589  20.719 -5.539 0.966  1.719  H322 YVD 75 
YVD H321 H36 H 0 0 N N N N N N -11.802 -7.315  21.581 -4.883 -0.535 2.011  H321 YVD 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 
YVD C22 N11  SING N N 1  
YVD C22 C23  SING N N 2  
YVD N11 C10  SING N N 3  
YVD C23 C09  SING N N 4  
YVD C10 O12  DOUB N N 5  
YVD C10 C09  SING N N 6  
YVD C20 C21  SING N N 7  
YVD C20 O16  SING N N 8  
YVD O17 C15  DOUB N N 9  
YVD C09 C08  SING N N 10 
YVD C08 C07  SING N N 11 
YVD C15 O16  SING N N 12 
YVD C15 C14  SING N N 13 
YVD C07 C13  SING N N 14 
YVD C07 N06  SING N N 15 
YVD C13 C14  SING N N 16 
YVD O19 C18  DOUB N N 17 
YVD N06 C18  SING N N 18 
YVD C18 C04  SING N N 19 
YVD N32 C31  SING N N 20 
YVD C31 C01  SING N N 21 
YVD C31 C33  SING N N 22 
YVD O03 C01  DOUB N N 23 
YVD C01 N02  SING N N 24 
YVD N02 C04  SING N N 25 
YVD C04 C05  SING N N 26 
YVD C33 C37  SING N N 27 
YVD C05 C27  SING N N 28 
YVD C37 C36  DOUB Y N 29 
YVD C37 C38  SING Y N 30 
YVD C36 C35  SING Y N 31 
YVD C27 C26  DOUB Y N 32 
YVD C27 C28  SING Y N 33 
YVD C26 C25  SING Y N 34 
YVD C38 C39  DOUB Y N 35 
YVD C28 C29  DOUB Y N 36 
YVD C35 C34  DOUB Y N 37 
YVD C25 C24  DOUB Y N 38 
YVD C39 C34  SING Y N 39 
YVD C34 F40  SING N N 40 
YVD C29 C24  SING Y N 41 
YVD C24 F30  SING N N 42 
YVD C13 H1   SING N N 43 
YVD C13 H131 SING N N 44 
YVD C20 H202 SING N N 45 
YVD C20 H201 SING N N 46 
YVD C21 H212 SING N N 47 
YVD C21 H211 SING N N 48 
YVD C21 H213 SING N N 49 
YVD C22 H222 SING N N 50 
YVD C22 H221 SING N N 51 
YVD C26 H261 SING N N 52 
YVD C28 H281 SING N N 53 
YVD C04 H041 SING N N 54 
YVD C05 H051 SING N N 55 
YVD C05 H052 SING N N 56 
YVD C07 H071 SING N N 57 
YVD C08 H081 SING N N 58 
YVD C08 H082 SING N N 59 
YVD C09 H091 SING N N 60 
YVD C14 H141 SING N N 61 
YVD C14 H142 SING N N 62 
YVD C23 H232 SING N N 63 
YVD C23 H231 SING N N 64 
YVD C25 H251 SING N N 65 
YVD C29 H291 SING N N 66 
YVD C31 H311 SING N N 67 
YVD C33 H331 SING N N 68 
YVD C33 H332 SING N N 69 
YVD C35 H351 SING N N 70 
YVD C36 H361 SING N N 71 
YVD C38 H381 SING N N 72 
YVD C39 H391 SING N N 73 
YVD N02 H021 SING N N 74 
YVD N06 H061 SING N N 75 
YVD N11 H111 SING N N 76 
YVD N32 H322 SING N N 77 
YVD N32 H321 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 
YVD SMILES           ACDLabs              12.01 "Fc1ccc(cc1)CC(N)C(=O)NC(Cc1ccc(F)cc1)C(=O)NC(CC1CCNC1=O)CCC(=O)OCC"                                                                                                                                                                 
YVD InChI            InChI                1.03  "InChI=1S/C29H36F2N4O5/c1-2-40-26(36)12-11-23(17-20-13-14-33-27(20)37)34-29(39)25(16-19-5-9-22(31)10-6-19)35-28(38)24(32)15-18-3-7-21(30)8-4-18/h3-10,20,23-25H,2,11-17,32H2,1H3,(H,33,37)(H,34,39)(H,35,38)/t20-,23+,24+,25-/m0/s1" 
YVD InChIKey         InChI                1.03  WOTTZMBQRDTTCI-KTJVCJKDSA-N                                                                                                                                                                                                          
YVD SMILES_CANONICAL CACTVS               3.385 "CCOC(=O)CC[C@H](C[C@@H]1CCNC1=O)NC(=O)[C@H](Cc2ccc(F)cc2)NC(=O)[C@H](N)Cc3ccc(F)cc3"                                                                                                                                                
YVD SMILES           CACTVS               3.385 "CCOC(=O)CC[CH](C[CH]1CCNC1=O)NC(=O)[CH](Cc2ccc(F)cc2)NC(=O)[CH](N)Cc3ccc(F)cc3"                                                                                                                                                     
YVD SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CCOC(=O)CC[C@H](C[C@@H]1CCNC1=O)NC(=O)[C@H](Cc2ccc(cc2)F)NC(=O)[C@@H](Cc3ccc(cc3)F)N"                                                                                                                                               
YVD SMILES           "OpenEye OEToolkits" 2.0.7 "CCOC(=O)CCC(CC1CCNC1=O)NC(=O)C(Cc2ccc(cc2)F)NC(=O)C(Cc3ccc(cc3)F)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 
YVD "SYSTEMATIC NAME" ACDLabs              12.01 "4-fluoro-D-phenylalanyl-N-{(2R)-5-ethoxy-5-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]pentan-2-yl}-4-fluoro-L-phenylalaninamide"                                                     
YVD "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "ethyl (4~{R})-4-[[(2~{S})-2-[[(2~{R})-2-azanyl-3-(4-fluorophenyl)propanoyl]amino]-3-(4-fluorophenyl)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 
YVD "Create component" 2021-04-01 RCSB 
YVD "Initial release"  2022-10-12 RCSB 
YVD "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            YVD 
_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      ? 
# 
