data_YVY
# 
_chem_comp.id                                    YVY 
_chem_comp.name                                  "N-{3-[(prop-2-yn-1-yl)oxy]propanoyl}-D-phenylalanyl-N-[(3S)-6-(carbamoylamino)-2-oxohexan-3-yl]-L-phenylalaninamide" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C31 H39 N5 O6" 
_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                        577.671 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YVY 
_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        7MAV 
_chem_comp.pdbx_subcomponent_list                "YWD DPN PHE YWG" 
_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 
YVY C10  C1  C 0 1 N N N N N N 27.541 -5.719  27.079 8.378  -2.937 -1.251 C10  YWD 1  
YVY C01  C10 C 0 1 N N N N N N 25.908 -8.834  28.633 4.113  -0.702 -0.484 C01  YWD 2  
YVY C05  C12 C 0 1 N N N N N N 25.176 -7.602  29.140 5.138  -1.654 0.076  C05  YWD 3  
YVY C08  C15 C 0 1 N N N N N N 26.123 -6.440  28.815 6.286  -1.814 -0.923 C08  YWD 4  
YVY C11  C16 C 0 1 N N N N N N 28.293 -4.734  27.978 9.311  -3.878 -0.610 C11  YWD 5  
YVY C12  C17 C 0 1 N N N N N N 28.874 -3.962  28.667 10.055 -4.628 -0.098 C12  YWD 6  
YVY O03  O1  O 0 1 N N N N N N 26.816 -9.240  29.286 4.284  -0.200 -1.575 O03  YWD 7  
YVY O09  O2  O 0 1 N N N N N N 27.081 -6.803  27.842 7.258  -2.717 -0.391 O09  YWD 8  
YVY N02  N1  N 0 1 N N N N N N 25.532 -9.491  27.387 3.007  -0.407 0.228  N    DPN 9  
YVY C04  C11 C 0 1 N N R N N N 26.349 -10.625 27.051 2.011  0.518  -0.317 CA   DPN 10 
YVY C06  C13 C 0 1 N N N N N N 25.664 -11.996 27.204 0.667  0.230  0.301  C    DPN 11 
YVY O14  O3  O 0 1 N N N N N N 24.500 -12.082 26.954 0.552  -0.660 1.115  O    DPN 12 
YVY C07  C14 C 0 1 N N N N N N 26.696 -10.733 25.547 2.422  1.957  0.004  CB   DPN 13 
YVY C40  C29 C 0 1 Y N N N N N 27.484 -9.573  24.949 3.706  2.285  -0.714 CG   DPN 14 
YVY C39  C28 C 0 1 Y N N N N N 26.872 -8.675  24.088 4.922  2.040  -0.103 CD1  DPN 15 
YVY C41  C30 C 0 1 Y N N N N N 28.816 -9.407  25.278 3.668  2.825  -1.986 CD2  DPN 16 
YVY C38  C27 C 0 1 Y N N N N N 27.589 -7.606  23.572 6.099  2.336  -0.764 CE1  DPN 17 
YVY C42  C31 C 0 1 Y N N N N N 29.536 -8.343  24.755 4.845  3.125  -2.645 CE2  DPN 18 
YVY C37  C26 C 0 1 Y N N N N N 28.924 -7.444  23.903 6.061  2.876  -2.036 CZ   DPN 19 
YVY N13  N2  N 0 1 N N N N N N 26.442 -13.188 27.568 -0.408 0.963  -0.052 N    PHE 20 
YVY C15  C2  C 0 1 N N S N N N 25.840 -14.524 27.615 -1.714 0.683  0.548  CA   PHE 21 
YVY C16  C18 C 0 1 N N N N N N 25.750 -15.172 28.986 -2.805 1.149  -0.382 C    PHE 22 
YVY O19  O4  O 0 1 N N N N N N 26.068 -14.459 29.859 -2.519 1.664  -1.442 O    PHE 23 
YVY C17  C3  C 0 1 N N N N N N 26.598 -15.402 26.594 -1.832 1.423  1.882  CB   PHE 24 
YVY C24  C7  C 0 1 Y N N N N N 26.674 -14.769 25.182 -0.820 0.871  2.853  CG   PHE 25 
YVY C23  C19 C 0 1 Y N N N N N 25.565 -14.762 24.360 0.445  1.424  2.922  CD1  PHE 26 
YVY C25  C20 C 0 1 Y N N N N N 27.838 -14.183 24.737 -1.159 -0.184 3.679  CD2  PHE 27 
YVY C22  C6  C 0 1 Y N N N N N 25.618 -14.188 23.090 1.373  0.917  3.813  CE1  PHE 28 
YVY C26  C8  C 0 1 Y N N N N N 27.902 -13.606 23.469 -0.232 -0.690 4.570  CE2  PHE 29 
YVY C21  C5  C 0 1 Y N N N N N 26.789 -13.608 22.643 1.036  -0.142 4.634  CZ   PHE 30 
YVY C20  C4  C 0 1 N N S N N N 24.997 -17.278 30.389 -5.158 1.445  -0.940 C20  YWG 31 
YVY C28  C9  C 0 1 N N N N N N 26.301 -17.218 31.161 -6.435 0.647  -0.669 C28  YWG 32 
YVY C27  C21 C 0 1 N N N N N N 23.662 -16.722 30.966 -5.423 2.911  -0.710 C27  YWG 33 
YVY C29  C22 C 0 1 N N N N N N 22.778 -15.779 30.138 -6.213 3.702  -1.721 C29  YWG 34 
YVY C31  C23 C 0 1 N N N N N N 27.110 -18.392 30.581 -6.202 -0.823 -1.022 C31  YWG 35 
YVY C32  C24 C 0 1 N N N N N N 28.362 -18.540 31.438 -7.479 -1.621 -0.751 C32  YWG 36 
YVY C34  C25 C 0 1 N N N N N N 29.068 -19.901 33.424 -8.250 -3.926 -0.930 C34  YWG 37 
YVY N18  N3  N 0 1 N N N N N N 25.229 -16.558 29.116 -4.098 0.993  -0.036 N18  YWG 38 
YVY N33  N4  N 0 1 N N N N N N 28.013 -19.348 32.596 -7.256 -3.029 -1.089 N33  YWG 39 
YVY N35  N5  N 0 1 N N N N N N 30.479 -19.660 33.118 -8.045 -5.221 -1.241 N35  YWG 40 
YVY O30  O5  O 0 1 N N N N N N 23.237 -17.090 32.001 -5.003 3.451  0.285  O30  YWG 41 
YVY O36  O6  O 0 1 N N N N N N 28.782 -20.584 34.336 -9.331 -3.566 -0.506 O36  YWG 42 
YVY H102 H1  H 0 0 N N N N N N 28.218 -6.086  26.294 8.885  -1.991 -1.436 H102 YWD 43 
YVY H101 H2  H 0 0 N N N N N N 26.684 -5.209  26.615 8.033  -3.355 -2.197 H101 YWD 44 
YVY H051 H13 H 0 0 N N N N N N 24.214 -7.478  28.620 5.526  -1.259 1.015  H051 YWD 45 
YVY H052 H14 H 0 0 N N N N N N 25.001 -7.671  30.224 4.674  -2.624 0.254  H052 YWD 46 
YVY H082 H17 H 0 0 N N N N N N 26.646 -6.138  29.735 5.898  -2.209 -1.862 H082 YWD 47 
YVY H081 H18 H 0 0 N N N N N N 25.532 -5.594  28.435 6.750  -0.844 -1.101 H081 YWD 48 
YVY H121 H19 H 0 0 N N N N N N 29.393 -3.272  29.282 10.721 -5.299 0.359  H121 YWD 49 
YVY H021 H34 H 0 0 N N N N N N 24.772 -9.180  26.816 2.871  -0.809 1.100  H    DPN 50 
YVY H041 H12 H 0 0 N N N N N N 27.281 -10.619 27.636 1.949  0.391  -1.398 HA   DPN 51 
YVY H071 H16 H 0 0 N N N N N N 27.289 -11.649 25.405 1.638  2.640  -0.322 HB2  DPN 52 
YVY H072 H15 H 0 0 N N N N N N 25.751 -10.818 24.991 2.571  2.061  1.079  HB3  DPN 53 
YVY H391 H31 H 0 0 N N N N N N 25.835 -8.808  23.819 4.951  1.618  0.891  HD1  DPN 54 
YVY H411 H32 H 0 0 N N N N N N 29.298 -10.108 25.944 2.718  3.012  -2.465 HD2  DPN 55 
YVY H381 H30 H 0 0 N N N N N N 27.107 -6.900  22.912 7.049  2.141  -0.289 HE1  DPN 56 
YVY H421 H33 H 0 0 N N N N N N 30.577 -8.217  25.014 4.815  3.546  -3.639 HE2  DPN 57 
YVY H371 H29 H 0 0 N N N N N N 29.486 -6.616  23.496 6.981  3.107  -2.553 HZ   DPN 58 
YVY H131 H35 H 0 0 N N N N N N 27.411 -13.085 27.790 -0.316 1.676  -0.704 H    PHE 59 
YVY H151 H3  H 0 0 N N N N N N 24.810 -14.432 27.241 -1.814 -0.389 0.717  HA   PHE 60 
YVY H171 H5  H 0 0 N N N N N N 27.623 -15.560 26.962 -1.644 2.485  1.726  HB2  PHE 61 
YVY H172 H4  H 0 0 N N N N N N 26.083 -16.371 26.516 -2.835 1.287  2.286  HB3  PHE 62 
YVY H231 H20 H 0 0 N N N N N N 24.644 -15.207 24.705 0.708  2.251  2.280  HD1  PHE 63 
YVY H251 H21 H 0 0 N N N N N N 28.709 -14.170 25.376 -2.149 -0.613 3.628  HD2  PHE 64 
YVY H221 H8  H 0 0 N N N N N N 24.744 -14.197 22.456 2.362  1.349  3.866  HE1  PHE 65 
YVY H261 H9  H 0 0 N N N N N N 28.823 -13.156 23.129 -0.497 -1.515 5.216  HE2  PHE 66 
YVY H211 H7  H 0 0 N N N N N N 26.837 -13.161 21.661 1.761  -0.538 5.330  HZ   PHE 67 
YVY H201 H6  H 0 0 N N N N N N 24.817 -18.335 30.143 -4.845 1.291  -1.973 H201 YWG 68 
YVY H281 H10 H 0 0 N N N N N N 26.817 -16.262 30.990 -6.698 0.731  0.385  H281 YWG 69 
YVY H282 H11 H 0 0 N N N N N N 26.127 -17.353 32.239 -7.247 1.043  -1.279 H282 YWG 70 
YVY H1   H22 H 0 1 N N N N N N 21.838 -15.590 30.677 -7.207 3.268  -1.825 H1   YWG 71 
YVY H2   H23 H 0 1 N N N N N N 23.307 -14.828 29.978 -6.301 4.735  -1.385 H2   YWG 72 
YVY H3   H24 H 0 1 N N N N N N 22.556 -16.244 29.166 -5.701 3.675  -2.683 H3   YWG 73 
YVY H311 H25 H 0 0 N N N N N N 26.515 -19.316 30.620 -5.939 -0.906 -2.077 H311 YWG 74 
YVY H312 H26 H 0 0 N N N N N N 27.389 -18.179 29.539 -5.390 -1.219 -0.412 H312 YWG 75 
YVY H322 H27 H 0 0 N N N N N N 29.155 -19.037 30.860 -7.743 -1.538 0.304  H322 YWG 76 
YVY H321 H28 H 0 0 N N N N N N 28.712 -17.549 31.764 -8.292 -1.225 -1.360 H321 YWG 77 
YVY H181 H36 H 0 0 N N N N N N 25.017 -17.047 28.270 -4.327 0.581  0.812  H181 YWG 78 
YVY H331 H37 H 0 0 N N N N N N 27.054 -19.521 32.820 -6.394 -3.316 -1.427 H331 YWG 79 
YVY H352 H38 H 0 0 N N N N N N 31.191 -20.076 33.684 -8.760 -5.866 -1.126 H352 YWG 80 
YVY H351 H39 H 0 0 N N N N N N 30.731 -19.080 32.343 -7.182 -5.508 -1.579 H351 YWG 81 
# 
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 
YVY C21 C22  DOUB Y N 1  
YVY C21 C26  SING Y N 2  
YVY C22 C23  SING Y N 3  
YVY C26 C25  DOUB Y N 4  
YVY C38 C37  DOUB Y N 5  
YVY C38 C39  SING Y N 6  
YVY C37 C42  SING Y N 7  
YVY C39 C40  DOUB Y N 8  
YVY C23 C24  DOUB Y N 9  
YVY C25 C24  SING Y N 10 
YVY C42 C41  DOUB Y N 11 
YVY C40 C41  SING Y N 12 
YVY C40 C07  SING N N 13 
YVY C24 C17  SING N N 14 
YVY C07 C04  SING N N 15 
YVY C17 C15  SING N N 16 
YVY O14 C06  DOUB N N 17 
YVY C04 C06  SING N N 18 
YVY C04 N02  SING N N 19 
YVY C10 O09  SING N N 20 
YVY C10 C11  SING N N 21 
YVY C06 N13  SING N N 22 
YVY N02 C01  SING N N 23 
YVY N13 C15  SING N N 24 
YVY C15 C16  SING N N 25 
YVY O09 C08  SING N N 26 
YVY C11 C12  TRIP N N 27 
YVY C01 C05  SING N N 28 
YVY C01 O03  DOUB N N 29 
YVY C08 C05  SING N N 30 
YVY C16 N18  SING N N 31 
YVY C16 O19  DOUB N N 32 
YVY N18 C20  SING N N 33 
YVY C29 C27  SING N N 34 
YVY C20 C27  SING N N 35 
YVY C20 C28  SING N N 36 
YVY C31 C28  SING N N 37 
YVY C31 C32  SING N N 38 
YVY C27 O30  DOUB N N 39 
YVY C32 N33  SING N N 40 
YVY N33 C34  SING N N 41 
YVY N35 C34  SING N N 42 
YVY C34 O36  DOUB N N 43 
YVY C10 H102 SING N N 44 
YVY C10 H101 SING N N 45 
YVY C15 H151 SING N N 46 
YVY C17 H172 SING N N 47 
YVY C17 H171 SING N N 48 
YVY C20 H201 SING N N 49 
YVY C21 H211 SING N N 50 
YVY C22 H221 SING N N 51 
YVY C26 H261 SING N N 52 
YVY C28 H281 SING N N 53 
YVY C28 H282 SING N N 54 
YVY C04 H041 SING N N 55 
YVY C05 H051 SING N N 56 
YVY C05 H052 SING N N 57 
YVY C07 H072 SING N N 58 
YVY C07 H071 SING N N 59 
YVY C08 H082 SING N N 60 
YVY C08 H081 SING N N 61 
YVY C12 H121 SING N N 62 
YVY C23 H231 SING N N 63 
YVY C25 H251 SING N N 64 
YVY C29 H1   SING N N 65 
YVY C29 H2   SING N N 66 
YVY C29 H3   SING N N 67 
YVY C31 H311 SING N N 68 
YVY C31 H312 SING N N 69 
YVY C32 H322 SING N N 70 
YVY C32 H321 SING N N 71 
YVY C37 H371 SING N N 72 
YVY C38 H381 SING N N 73 
YVY C39 H391 SING N N 74 
YVY C41 H411 SING N N 75 
YVY C42 H421 SING N N 76 
YVY N02 H021 SING N N 77 
YVY N13 H131 SING N N 78 
YVY N18 H181 SING N N 79 
YVY N33 H331 SING N N 80 
YVY N35 H352 SING N N 81 
YVY N35 H351 SING N N 82 
# 
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 
YVY SMILES           ACDLabs              12.01 "CC(=O)C(CCCNC(N)=O)NC(=O)C(NC(=O)C(Cc1ccccc1)NC(=O)CCOCC#C)Cc1ccccc1"                                                                                                                                                                           
YVY InChI            InChI                1.03  "InChI=1S/C31H39N5O6/c1-3-18-42-19-16-28(38)34-26(20-23-11-6-4-7-12-23)29(39)36-27(21-24-13-8-5-9-14-24)30(40)35-25(22(2)37)15-10-17-33-31(32)41/h1,4-9,11-14,25-27H,10,15-21H2,2H3,(H,34,38)(H,35,40)(H,36,39)(H3,32,33,41)/t25-,26+,27-/m0/s1" 
YVY InChIKey         InChI                1.03  VYPOUUBVMAOAGP-VJGNERBWSA-N                                                                                                                                                                                                                      
YVY SMILES_CANONICAL CACTVS               3.385 "CC(=O)[C@H](CCCNC(N)=O)NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@@H](Cc2ccccc2)NC(=O)CCOCC#C"                                                                                                                                                              
YVY SMILES           CACTVS               3.385 "CC(=O)[CH](CCCNC(N)=O)NC(=O)[CH](Cc1ccccc1)NC(=O)[CH](Cc2ccccc2)NC(=O)CCOCC#C"                                                                                                                                                                  
YVY SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(=O)[C@H](CCCNC(=O)N)NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@@H](Cc2ccccc2)NC(=O)CCOCC#C"                                                                                                                                                              
YVY SMILES           "OpenEye OEToolkits" 2.0.7 "CC(=O)C(CCCNC(=O)N)NC(=O)C(Cc1ccccc1)NC(=O)C(Cc2ccccc2)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 
YVY "SYSTEMATIC NAME" ACDLabs              12.01 "N-{3-[(prop-2-yn-1-yl)oxy]propanoyl}-D-phenylalanyl-N-[(3S)-6-(carbamoylamino)-2-oxohexan-3-yl]-L-phenylalaninamide"                                                                   
YVY "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{R})-~{N}-[(2~{S})-1-[[(3~{S})-6-(aminocarbonylamino)-2-oxidanylidene-hexan-3-yl]amino]-1-oxidanylidene-3-phenyl-propan-2-yl]-3-phenyl-2-(3-prop-2-ynoxypropanoylamino)propanamide" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
YVY "Create component"         2021-04-01 RCSB 
YVY "Modify subcomponent list" 2021-04-01 RCSB 
YVY "Initial release"          2022-10-12 RCSB 
YVY "Modify PCM"               2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            YVY 
_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               C29 
_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      ? 
# 
