data_YVP
# 
_chem_comp.id                                    YVP 
_chem_comp.name                                  "N-{3-[(prop-2-yn-1-yl)oxy]propanoyl}-D-phenylalanyl-N-[(3S)-6-carbamimidamido-2-oxohexan-3-yl]-L-phenylalaninamide" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C31 H40 N6 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                        576.686 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YVP 
_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        7MAU 
_chem_comp.pdbx_subcomponent_list                "YWD DPN PHE ARM" 
_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 
YVP C10  C1  C 0 1 N N N N N N 30.592 -2.380  7.274  8.369   2.934  1.253  C10  YWD 1  
YVP C01  C10 C 0 1 N N N N N N 30.286 -6.356  7.688  4.103   0.702  0.484  C01  YWD 2  
YVP C05  C12 C 0 1 N N N N N N 29.593 -5.565  8.793  5.128   1.655  -0.075 C05  YWD 3  
YVP C08  C15 C 0 1 N N N N N N 30.144 -4.132  8.806  6.276   1.812  0.924  C08  YWD 4  
YVP C11  C16 C 0 1 N N N N N N 32.025 -2.871  7.231  9.302   3.875  0.613  C11  YWD 5  
YVP C12  C17 C 0 1 N N N N N N 33.084 -3.362  7.281  10.047  4.625  0.103  C12  YWD 6  
YVP O03  O1  O 0 1 N N N N N N 31.207 -7.057  7.955  4.274   0.198  1.574  O03  YWD 7  
YVP O09  O2  O 0 1 N N N N N N 29.808 -3.494  7.608  7.248   2.716  0.394  O09  YWD 8  
YVP N02  N1  N 0 1 N N N N N N 29.791 -6.240  6.333  2.996   0.410  -0.227 N    DPN 9  
YVP C04  C11 C 0 1 N N R N N N 30.493 -6.992  5.351  2.000   -0.516 0.317  CA   DPN 10 
YVP C06  C13 C 0 1 N N N N N N 29.845 -8.370  5.130  0.655   -0.227 -0.299 C    DPN 11 
YVP O14  O3  O 0 1 N N N N N N 28.623 -8.454  5.185  0.541   0.666  -1.112 O    DPN 12 
YVP C07  C14 C 0 1 N N N N N N 30.224 -6.397  3.957  2.410   -1.954 -0.007 CB   DPN 13 
YVP C40  C29 C 0 1 Y N N N N N 31.176 -5.402  3.333  3.694   -2.284 0.709  CG   DPN 14 
YVP C39  C28 C 0 1 Y N N N N N 31.036 -5.128  1.983  4.909   -2.039 0.098  CD1  DPN 15 
YVP C41  C30 C 0 1 Y N N N N N 32.144 -4.778  4.085  3.656   -2.827 1.980  CD2  DPN 16 
YVP C38  C27 C 0 1 Y N N N N N 31.881 -4.220  1.367  6.087   -2.342 0.756  CE1  DPN 17 
YVP C42  C31 C 0 1 Y N N N N N 32.991 -3.869  3.471  4.834   -3.129 2.638  CE2  DPN 18 
YVP C37  C26 C 0 1 Y N N N N N 32.863 -3.591  2.119  6.049   -2.890 2.024  CZ   DPN 19 
YVP N13  N2  N 0 1 N N N N N N 30.652 -9.542  4.798  -0.420  -0.959 0.053  N    PHE 20 
YVP C15  C2  C 0 1 N N S N N N 29.996 -10.791 4.503  -1.727  -0.677 -0.546 CA   PHE 21 
YVP C16  C18 C 0 1 N N N N N N 30.010 -11.894 5.517  -2.817  -1.144 0.384  C    PHE 22 
YVP O19  O4  O 0 1 N N N N N N 30.535 -11.763 6.540  -2.530  -1.661 1.443  O    PHE 23 
YVP C17  C3  C 0 1 N N N N N N 30.644 -11.294 3.161  -1.845  -1.414 -1.882 CB   PHE 24 
YVP C24  C7  C 0 1 Y N N N N N 30.670 -10.206 2.074  -0.834  -0.861 -2.852 CG   PHE 25 
YVP C23  C19 C 0 1 Y N N N N N 29.514 -10.025 1.339  0.431   -1.414 -2.923 CD1  PHE 26 
YVP C25  C20 C 0 1 Y N N N N N 31.779 -9.403  1.830  -1.173  0.196  -3.676 CD2  PHE 27 
YVP C22  C6  C 0 1 Y N N N N N 29.453 -9.047  0.362  1.359   -0.907 -3.813 CE1  PHE 28 
YVP C26  C8  C 0 1 Y N N N N N 31.725 -8.410  0.861  -0.245  0.703  -4.567 CE2  PHE 29 
YVP C21  C5  C 0 1 Y N N N N N 30.557 -8.237  0.121  1.022   0.154  -4.633 CZ   PHE 30 
YVP N18  N3  N 0 1 N N N N N N 29.280 -13.072 5.094  -4.110  -0.986 0.039  N    ARM 31 
YVP C20  C4  C 0 1 N N S N N N 29.109 -14.258 5.920  -5.170  -1.440 0.943  CA   ARM 32 
YVP C28  C9  C 0 1 N N N N N N 30.303 -14.597 6.797  -6.446  -0.641 0.674  CB   ARM 33 
YVP C31  C23 C 0 1 N N N N N N 30.250 -16.121 6.982  -6.212  0.829  1.030  CG   ARM 34 
YVP C32  C24 C 0 1 N N N N N N 31.498 -16.645 7.693  -7.489  1.628  0.761  CD   ARM 35 
YVP N33  N4  N 0 1 N N N N N N 31.696 -15.966 8.960  -7.265  3.035  1.102  NE   ARM 36 
YVP C34  C25 C 0 1 N N N N N N 30.956 -16.342 10.157 -8.278  3.951  0.942  CZ   ARM 37 
YVP N35  N5  N 0 1 N N N N N N 30.112 -17.274 10.157 -8.068  5.272  1.261  NH1  ARM 38 
YVP N36  N6  N 0 1 N N N N N N 31.207 -15.609 11.388 -9.438  3.567  0.487  NH2  ARM 39 
YVP C27  C21 C 0 1 N N N N N N 27.821 -14.009 6.764  -5.436  -2.905 0.710  C    ARM 40 
YVP O30  O5  O 0 1 N N N N N N 27.581 -14.656 7.716  -5.016  -3.444 -0.286 O    ARM 41 
YVP C29  C22 C 0 1 N N N N N N 26.803 -12.918 6.383  -6.225  -3.697 1.720  CM   ARM 42 
YVP H102 H2  H 0 0 N N N N N N 30.294 -1.985  6.292  8.876   1.986  1.436  H102 YWD 43 
YVP H101 H1  H 0 0 N N N N N N 30.481 -1.593  8.035  8.025   3.350  2.200  H101 YWD 44 
YVP H051 H14 H 0 0 N N N N N N 29.786 -6.043  9.765  5.515   1.262  -1.015 H051 YWD 45 
YVP H052 H13 H 0 0 N N N N N N 28.509 -5.541  8.605  4.664   2.625  -0.250 H052 YWD 46 
YVP H082 H18 H 0 0 N N N N N N 29.708 -3.579  9.651  5.889   2.205  1.864  H082 YWD 47 
YVP H081 H17 H 0 0 N N N N N N 31.239 -4.161  8.912  6.740   0.841  1.100  H081 YWD 48 
YVP H121 H19 H 0 0 N N N N N N 34.045 -3.807  7.326  10.713  5.297  -0.354 H121 YWD 49 
YVP H021 H34 H 0 0 N N N N N N 29.005 -5.667  6.102  2.859   0.813  -1.098 H    DPN 50 
YVP H041 H12 H 0 0 N N N N N N 31.571 -7.079  5.553  1.939   -0.391 1.398  HA   DPN 51 
YVP H071 H16 H 0 0 N N N N N N 30.162 -7.247  3.262  1.626   -2.638 0.318  HB2  DPN 52 
YVP H072 H15 H 0 0 N N N N N N 29.245 -5.898  4.015  2.557   -2.056 -1.083 HB3  DPN 53 
YVP H391 H31 H 0 0 N N N N N N 30.267 -5.623  1.409  4.939   -1.612 -0.893 HD1  DPN 54 
YVP H411 H32 H 0 0 N N N N N N 32.243 -4.993  5.139  2.706   -3.014 2.460  HD2  DPN 55 
YVP H381 H30 H 0 0 N N N N N N 31.777 -4.004  0.314  7.036   -2.152 0.278  HE1  DPN 56 
YVP H421 H33 H 0 0 N N N N N N 33.756 -3.374  4.050  4.804   -3.553 3.631  HE2  DPN 57 
YVP H371 H29 H 0 0 N N N N N N 33.530 -2.883  1.650  6.969   -3.127 2.538  HZ   DPN 58 
YVP H131 H35 H 0 0 N N N N N N 31.650 -9.478  4.776  -0.328  -1.673 0.703  H    PHE 59 
YVP H151 H3  H 0 0 N N N N N N 28.942 -10.573 4.275  -1.826  0.396  -0.713 HA   PHE 60 
YVP H171 H5  H 0 0 N N N N N N 31.677 -11.612 3.366  -1.658  -2.477 -1.728 HB2  PHE 61 
YVP H172 H4  H 0 0 N N N N N N 30.063 -12.151 2.788  -2.849  -1.277 -2.284 HB3  PHE 62 
YVP H231 H20 H 0 0 N N N N N N 28.654 -10.650 1.528  0.694   -2.243 -2.283 HD1  PHE 63 
YVP H251 H21 H 0 0 N N N N N N 32.686 -9.552  2.397  -2.162  0.626  -3.624 HD2  PHE 64 
YVP H221 H8  H 0 0 N N N N N N 28.549 -8.913  -0.213 2.347   -1.339 -3.868 HE1  PHE 65 
YVP H261 H9  H 0 0 N N N N N N 32.581 -7.777  0.682  -0.510  1.529  -5.210 HE2  PHE 66 
YVP H211 H7  H 0 0 N N N N N N 30.509 -7.473  -0.641 1.747   0.551  -5.328 HZ   PHE 67 
YVP H181 H36 H 0 0 N N N N N N 28.870 -13.070 4.182  -4.339  -0.573 -0.808 H    ARM 68 
YVP H201 H6  H 0 0 N N N N N N 28.913 -15.120 5.265  -4.856  -1.287 1.976  HA   ARM 69 
YVP H281 H11 H 0 0 N N N N N N 30.224 -14.088 7.769  -6.710  -0.722 -0.380 HB2  ARM 70 
YVP H282 H10 H 0 0 N N N N N N 31.240 -14.301 6.303  -7.258  -1.037 1.283  HB3  ARM 71 
YVP H311 H26 H 0 0 N N N N N N 30.175 -16.598 5.994  -5.948  0.910  2.084  HG2  ARM 72 
YVP H312 H25 H 0 0 N N N N N N 29.364 -16.377 7.581  -5.400  1.225  0.420  HG3  ARM 73 
YVP H321 H27 H 0 0 N N N N N N 31.382 -17.723 7.877  -7.753  1.547  -0.294 HD2  ARM 74 
YVP H322 H28 H 0 0 N N N N N N 32.376 -16.475 7.052  -8.301  1.232  1.370  HD3  ARM 75 
YVP H331 H37 H 0 0 N N N N N N 32.359 -15.219 9.013  -6.402  3.321  1.440  HE   ARM 76 
YVP H5   H39 H 0 1 N N N N N N 29.931 -17.785 9.317  -8.782  5.918  1.148  HH1  ARM 77 
YVP H361 H40 H 0 0 N N N N N N 30.648 -15.946 12.145 -10.152 4.213  0.374  HH22 ARM 78 
YVP H1   H22 H 0 1 N N N N N N 25.972 -12.923 7.104  -7.285  -3.652 1.469  HM1  ARM 79 
YVP H2   H23 H 0 1 N N N N N N 27.296 -11.935 6.399  -5.893  -4.735 1.707  HM2  ARM 80 
YVP H3   H24 H 0 1 N N N N N N 26.414 -13.116 5.374  -6.069  -3.278 2.714  HM3  ARM 81 
YVP H351 H38 H 0 0 N N N N N N 29.622 -17.504 10.997 -7.205  5.557  1.600  H351 ARM 82 
# 
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 
YVP C21 C22  DOUB Y N 1  
YVP C21 C26  SING Y N 2  
YVP C22 C23  SING Y N 3  
YVP C26 C25  DOUB Y N 4  
YVP C23 C24  DOUB Y N 5  
YVP C38 C39  DOUB Y N 6  
YVP C38 C37  SING Y N 7  
YVP C25 C24  SING Y N 8  
YVP C39 C40  SING Y N 9  
YVP C24 C17  SING N N 10 
YVP C37 C42  DOUB Y N 11 
YVP C17 C15  SING N N 12 
YVP C40 C07  SING N N 13 
YVP C40 C41  DOUB Y N 14 
YVP C42 C41  SING Y N 15 
YVP C07 C04  SING N N 16 
YVP C15 N13  SING N N 17 
YVP C15 C16  SING N N 18 
YVP N13 C06  SING N N 19 
YVP N18 C16  SING N N 20 
YVP N18 C20  SING N N 21 
YVP C06 O14  DOUB N N 22 
YVP C06 C04  SING N N 23 
YVP C04 N02  SING N N 24 
YVP C16 O19  DOUB N N 25 
YVP C20 C27  SING N N 26 
YVP C20 C28  SING N N 27 
YVP N02 C01  SING N N 28 
YVP C29 C27  SING N N 29 
YVP C27 O30  DOUB N N 30 
YVP C28 C31  SING N N 31 
YVP C31 C32  SING N N 32 
YVP C11 C10  SING N N 33 
YVP C11 C12  TRIP N N 34 
YVP C10 O09  SING N N 35 
YVP O09 C08  SING N N 36 
YVP C01 O03  DOUB N N 37 
YVP C01 C05  SING N N 38 
YVP C32 N33  SING N N 39 
YVP C05 C08  SING N N 40 
YVP N33 C34  SING N N 41 
YVP C34 N35  SING N N 42 
YVP C34 N36  DOUB N N 43 
YVP C10 H101 SING N N 44 
YVP C10 H102 SING N N 45 
YVP C15 H151 SING N N 46 
YVP C17 H172 SING N N 47 
YVP C17 H171 SING N N 48 
YVP C20 H201 SING N N 49 
YVP C21 H211 SING N N 50 
YVP C22 H221 SING N N 51 
YVP C26 H261 SING N N 52 
YVP C28 H282 SING N N 53 
YVP C28 H281 SING N N 54 
YVP C04 H041 SING N N 55 
YVP C05 H052 SING N N 56 
YVP C05 H051 SING N N 57 
YVP C07 H072 SING N N 58 
YVP C07 H071 SING N N 59 
YVP C08 H081 SING N N 60 
YVP C08 H082 SING N N 61 
YVP C12 H121 SING N N 62 
YVP C23 H231 SING N N 63 
YVP C25 H251 SING N N 64 
YVP C29 H1   SING N N 65 
YVP C29 H2   SING N N 66 
YVP C29 H3   SING N N 67 
YVP C31 H312 SING N N 68 
YVP C31 H311 SING N N 69 
YVP C32 H321 SING N N 70 
YVP C32 H322 SING N N 71 
YVP C37 H371 SING N N 72 
YVP C38 H381 SING N N 73 
YVP C39 H391 SING N N 74 
YVP C41 H411 SING N N 75 
YVP C42 H421 SING N N 76 
YVP N02 H021 SING N N 77 
YVP N13 H131 SING N N 78 
YVP N18 H181 SING N N 79 
YVP N33 H331 SING N N 80 
YVP N35 H351 SING N N 81 
YVP N35 H5   SING N N 82 
YVP N36 H361 SING N N 83 
# 
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 
YVP SMILES           ACDLabs              12.01 "CC(=O)C(CCCNC(=N)N)NC(=O)C(NC(=O)C(Cc1ccccc1)NC(=O)CCOCC#C)Cc1ccccc1"                                                                                                                                                                           
YVP InChI            InChI                1.03  "InChI=1S/C31H40N6O5/c1-3-18-42-19-16-28(39)35-26(20-23-11-6-4-7-12-23)29(40)37-27(21-24-13-8-5-9-14-24)30(41)36-25(22(2)38)15-10-17-34-31(32)33/h1,4-9,11-14,25-27H,10,15-21H2,2H3,(H,35,39)(H,36,41)(H,37,40)(H4,32,33,34)/t25-,26+,27-/m0/s1" 
YVP InChIKey         InChI                1.03  JNSZEVHYEISGKR-VJGNERBWSA-N                                                                                                                                                                                                                      
YVP SMILES_CANONICAL CACTVS               3.385 "CC(=O)[C@H](CCCNC(N)=N)NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@@H](Cc2ccccc2)NC(=O)CCOCC#C"                                                                                                                                                              
YVP SMILES           CACTVS               3.385 "CC(=O)[CH](CCCNC(N)=N)NC(=O)[CH](Cc1ccccc1)NC(=O)[CH](Cc2ccccc2)NC(=O)CCOCC#C"                                                                                                                                                                  
YVP SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "[H]/N=C(/N)\NCCC[C@@H](C(=O)C)NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@@H](Cc2ccccc2)NC(=O)CCOCC#C"                                                                                                                                                       
YVP SMILES           "OpenEye OEToolkits" 2.0.7 "CC(=O)C(CCCNC(=N)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 
YVP "SYSTEMATIC NAME" ACDLabs              12.01 "N-{3-[(prop-2-yn-1-yl)oxy]propanoyl}-D-phenylalanyl-N-[(3S)-6-carbamimidamido-2-oxohexan-3-yl]-L-phenylalaninamide"                                                               
YVP "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{R})-~{N}-[(2~{S})-1-[[(3~{S})-6-carbamimidamido-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 
YVP "Create component"         2021-04-01 RCSB 
YVP "Modify subcomponent list" 2021-04-01 RCSB 
YVP "Initial release"          2022-10-12 RCSB 
YVP "Modify PCM"               2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            YVP 
_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      ? 
# 
