data_YV6
# 
_chem_comp.id                                    YV6 
_chem_comp.name                                  "methyl (3S)-1-[N-(4-sulfanylbutanoyl)-L-valyl-3-hydroxy-L-phenylalanyl]-1,2-diazinane-3-carboxylate" 
_chem_comp.type                                  non-polymer 
_chem_comp.pdbx_type                             HETAIN 
_chem_comp.formula                               "C24 H36 N4 O6 S" 
_chem_comp.mon_nstd_parent_comp_id               ? 
_chem_comp.pdbx_synonyms                         ? 
_chem_comp.pdbx_formal_charge                    0 
_chem_comp.pdbx_initial_date                     2023-02-22 
_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                        508.631 
_chem_comp.one_letter_code                       ? 
_chem_comp.three_letter_code                     YV6 
_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        8G9Q 
_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_n_terminal_atom_flag 
_chem_comp_atom.pdbx_backbone_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 
YV6 C1  C1  C 0 1 N N N N N N -14.911 -7.676  -33.024 -6.935 3.249  -0.231 C1  YV6 1  
YV6 C10 C2  C 0 1 Y N N N N N -19.579 -5.303  -34.479 -0.988 1.304  -0.551 C10 YV6 2  
YV6 C11 C3  C 0 1 Y N N N N N -18.744 -5.571  -33.390 0.223  1.430  -1.206 C11 YV6 3  
YV6 C12 C4  C 0 1 Y N N N N N -17.909 -4.575  -32.893 1.060  2.493  -0.919 C12 YV6 4  
YV6 C13 C5  C 0 1 Y N N N N N -17.903 -3.317  -33.474 0.687  3.432  0.023  C13 YV6 5  
YV6 C14 C6  C 0 1 Y N N N N N -18.734 -3.047  -34.555 -0.528 3.308  0.681  C14 YV6 6  
YV6 C15 C7  C 0 1 Y N N N N N -19.566 -4.054  -35.064 -1.365 2.241  0.392  C15 YV6 7  
YV6 C16 C8  C 0 1 N N N N N N -21.182 -4.968  -38.211 0.846  -0.926 0.345  C16 YV6 8  
YV6 C17 C9  C 0 1 N N S N N N -22.299 -4.059  -38.646 2.227  -1.490 0.135  C17 YV6 9  
YV6 C18 C10 C 0 1 N N N N N N -22.369 -2.344  -36.958 4.458  -0.528 -0.049 C18 YV6 10 
YV6 C19 C11 C 0 1 N N N N N N -21.965 -0.941  -36.568 5.486  0.510  0.323  C19 YV6 11 
YV6 C2  C12 C 0 1 N N N N N N -16.527 -8.282  -34.775 -5.850 1.143  0.027  C2  YV6 12 
YV6 C20 C13 C 0 1 N N N N N N -21.923 -0.773  -35.047 6.788  0.231  -0.432 C20 YV6 13 
YV6 C21 C14 C 0 1 N N N N N N -21.172 0.509   -34.694 7.832  1.284  -0.054 C21 YV6 14 
YV6 C27 C15 C 0 1 N N N N N N -22.492 -4.072  -40.165 2.411  -2.729 1.014  C27 YV6 15 
YV6 C28 C16 C 0 1 N N N N N N -23.536 -3.068  -40.645 3.793  -3.334 0.760  C28 YV6 16 
YV6 C29 C17 C 0 1 N N N N N N -22.895 -5.486  -40.586 2.292  -2.331 2.487  C29 YV6 17 
YV6 C3  C18 C 0 1 N N S N N N -17.852 -8.873  -35.135 -5.320 -0.166 -0.500 C3  YV6 18 
YV6 C4  C19 C 0 1 N N N N N N -17.718 -10.376 -35.350 -6.474 -1.163 -0.643 C4  YV6 19 
YV6 C5  C20 C 0 1 N N N N N N -19.047 -10.958 -35.822 -5.927 -2.493 -1.171 C5  YV6 20 
YV6 C6  C21 C 0 1 N N N N N N -19.469 -10.226 -37.100 -4.850 -3.004 -0.207 C6  YV6 21 
YV6 C7  C22 C 0 1 N N N N N N -20.574 -8.036  -36.849 -2.560 -2.142 -0.185 C7  YV6 22 
YV6 C8  C23 C 0 1 N N S N N N -20.415 -6.571  -36.538 -1.571 -1.030 0.049  C8  YV6 23 
YV6 C9  C24 C 0 1 N N N N N N -20.478 -6.402  -35.014 -1.900 0.147  -0.871 C9  YV6 24 
YV6 N1  N1  N 0 1 N N N N N N -19.495 -8.802  -36.772 -3.875 -1.928 0.018  N1  YV6 25 
YV6 N2  N2  N 0 1 N N N N N N -18.347 -8.225  -36.377 -4.323 -0.703 0.437  N2  YV6 26 
YV6 N3  N3  N 0 1 N N N N N N -21.431 -5.743  -37.158 -0.218 -1.512 -0.240 N3  YV6 27 
YV6 N4  N4  N 0 1 N N N N N N -22.004 -2.725  -38.175 3.227  -0.482 0.497  N4  YV6 28 
YV6 O1  O1  O 0 1 N N N N N N -16.166 -8.249  -33.383 -6.449 2.008  -0.807 O1  YV6 29 
YV6 O2  O2  O 0 1 N N N N N N -15.745 -7.813  -35.585 -5.735 1.414  1.198  O2  YV6 30 
YV6 O3  O3  O 0 1 N N N N N N -21.670 -8.478  -37.166 -2.174 -3.230 -0.557 O3  YV6 31 
YV6 O4  O4  O 0 1 N N N N N N -18.726 -1.818  -35.123 -0.897 4.230  1.609  O4  YV6 32 
YV6 O5  O5  O 0 1 N N N N N N -20.093 -4.964  -38.771 0.691  0.056  1.040  O5  YV6 33 
YV6 O6  O6  O 0 1 N N N N N N -22.983 -3.089  -36.203 4.739  -1.403 -0.840 O6  YV6 34 
YV6 S1  S1  S 0 1 N N N N N N -20.953 0.684   -32.905 9.375  0.953  -0.948 S1  YV6 35 
YV6 H1  H1  H 0 1 N N N N N N -14.783 -7.726  -31.933 -7.672 3.027  0.541  H1  YV6 36 
YV6 H2  H2  H 0 1 N N N N N N -14.100 -8.234  -33.514 -6.101 3.796  0.209  H2  YV6 37 
YV6 H3  H3  H 0 1 N N N N N N -14.881 -6.626  -33.349 -7.396 3.855  -1.010 H3  YV6 38 
YV6 H4  H4  H 0 1 N N N N N N -18.747 -6.550  -32.935 0.516  0.697  -1.943 H4  YV6 39 
YV6 H5  H5  H 0 1 N N N N N N -17.264 -4.783  -32.052 2.006  2.589  -1.432 H5  YV6 40 
YV6 H6  H6  H 0 1 N N N N N N -17.253 -2.546  -33.087 1.341  4.262  0.247  H6  YV6 41 
YV6 H7  H7  H 0 1 N N N N N N -20.198 -3.851  -35.916 -2.311 2.142  0.903  H7  YV6 42 
YV6 H8  H8  H 0 1 N N N N N N -23.232 -4.409  -38.181 2.352  -1.766 -0.912 H8  YV6 43 
YV6 H9  H9  H 0 1 N N N N N N -20.967 -0.729  -36.979 5.116  1.500  0.056  H9  YV6 44 
YV6 H10 H10 H 0 1 N N N N N N -22.693 -0.230  -36.986 5.672  0.468  1.396  H10 YV6 45 
YV6 H11 H11 H 0 1 N N N N N N -22.950 -0.715  -34.657 7.157  -0.759 -0.165 H11 YV6 46 
YV6 H12 H12 H 0 1 N N N N N N -21.408 -1.635  -34.598 6.602  0.272  -1.505 H12 YV6 47 
YV6 H13 H13 H 0 1 N N N N N N -20.183 0.486   -35.174 7.462  2.274  -0.321 H13 YV6 48 
YV6 H14 H14 H 0 1 N N N N N N -21.742 1.371   -35.070 8.018  1.243  1.019  H14 YV6 49 
YV6 H15 H15 H 0 1 N N N N N N -21.530 -3.829  -40.640 1.643  -3.463 0.773  H15 YV6 50 
YV6 H16 H16 H 0 1 N N N N N N -23.239 -2.054  -40.338 4.562  -2.640 1.099  H16 YV6 51 
YV6 H17 H17 H 0 1 N N N N N N -23.610 -3.112  -41.742 3.884  -4.273 1.306  H17 YV6 52 
YV6 H18 H18 H 0 1 N N N N N N -24.512 -3.314  -40.201 3.917  -3.521 -0.307 H18 YV6 53 
YV6 H19 H19 H 0 1 N N N N N N -22.138 -6.203  -40.236 1.308  -1.900 2.668  H19 YV6 54 
YV6 H20 H20 H 0 1 N N N N N N -23.870 -5.737  -40.142 2.423  -3.213 3.113  H20 YV6 55 
YV6 H21 H21 H 0 1 N N N N N N -22.968 -5.535  -41.682 3.061  -1.597 2.728  H21 YV6 56 
YV6 H22 H22 H 0 1 N N N N N N -18.566 -8.692  -34.318 -4.856 -0.006 -1.472 H22 YV6 57 
YV6 H23 H23 H 0 1 N N N N N N -17.427 -10.855 -34.403 -6.941 -1.321 0.329  H23 YV6 58 
YV6 H24 H24 H 0 1 N N N N N N -16.946 -10.568 -36.110 -7.211 -0.768 -1.341 H24 YV6 59 
YV6 H25 H25 H 0 1 N N N N N N -19.811 -10.817 -35.044 -6.736 -3.221 -1.233 H25 YV6 60 
YV6 H26 H26 H 0 1 N N N N N N -18.929 -12.032 -36.031 -5.494 -2.343 -2.160 H26 YV6 61 
YV6 H27 H27 H 0 1 N N N N N N -20.467 -10.561 -37.418 -5.310 -3.285 0.740  H27 YV6 62 
YV6 H28 H28 H 0 1 N N N N N N -18.744 -10.418 -37.905 -4.347 -3.867 -0.643 H28 YV6 63 
YV6 H29 H29 H 0 1 N N N N N N -19.421 -6.246  -36.880 -1.627 -0.707 1.088  H29 YV6 64 
YV6 H30 H30 H 0 1 N N N N N N -21.516 -6.167  -34.734 -2.936 0.449  -0.718 H30 YV6 65 
YV6 H31 H31 H 0 1 N N N N N N -20.178 -7.352  -34.548 -1.757 -0.151 -1.909 H31 YV6 66 
YV6 H32 H32 H 0 1 N N N N N N -17.661 -8.325  -37.098 -4.697 -0.756 1.373  H32 YV6 67 
YV6 H33 H33 H 0 1 N N N N N N -22.356 -5.755  -36.779 -0.087 -2.253 -0.852 H33 YV6 68 
YV6 H34 H34 H 0 1 N N N N N N -21.521 -2.084  -38.771 3.002  0.219  1.129  H34 YV6 69 
YV6 H35 H35 H 0 1 N N N N N N -18.112 -1.259  -34.661 -1.394 4.976  1.247  H35 YV6 70 
YV6 H36 H36 H 0 1 N N N N N N -20.309 1.810   -32.820 10.186 1.939  -0.526 H36 YV6 71 
# 
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 
YV6 C28 C27 SING N N 1  
YV6 C29 C27 SING N N 2  
YV6 C27 C17 SING N N 3  
YV6 O5  C16 DOUB N N 4  
YV6 C17 C16 SING N N 5  
YV6 C17 N4  SING N N 6  
YV6 C16 N3  SING N N 7  
YV6 N4  C18 SING N N 8  
YV6 O3  C7  DOUB N N 9  
YV6 N3  C8  SING N N 10 
YV6 C6  N1  SING N N 11 
YV6 C6  C5  SING N N 12 
YV6 C18 C19 SING N N 13 
YV6 C18 O6  DOUB N N 14 
YV6 C7  N1  SING N N 15 
YV6 C7  C8  SING N N 16 
YV6 N1  N2  SING N N 17 
YV6 C19 C20 SING N N 18 
YV6 C8  C9  SING N N 19 
YV6 N2  C3  SING N N 20 
YV6 C5  C4  SING N N 21 
YV6 O2  C2  DOUB N N 22 
YV6 C4  C3  SING N N 23 
YV6 C3  C2  SING N N 24 
YV6 O4  C14 SING N N 25 
YV6 C15 C14 DOUB Y N 26 
YV6 C15 C10 SING Y N 27 
YV6 C20 C21 SING N N 28 
YV6 C9  C10 SING N N 29 
YV6 C2  O1  SING N N 30 
YV6 C21 S1  SING N N 31 
YV6 C14 C13 SING Y N 32 
YV6 C10 C11 DOUB Y N 33 
YV6 C13 C12 DOUB Y N 34 
YV6 C11 C12 SING Y N 35 
YV6 O1  C1  SING N N 36 
YV6 C1  H1  SING N N 37 
YV6 C1  H2  SING N N 38 
YV6 C1  H3  SING N N 39 
YV6 C11 H4  SING N N 40 
YV6 C12 H5  SING N N 41 
YV6 C13 H6  SING N N 42 
YV6 C15 H7  SING N N 43 
YV6 C17 H8  SING N N 44 
YV6 C19 H9  SING N N 45 
YV6 C19 H10 SING N N 46 
YV6 C20 H11 SING N N 47 
YV6 C20 H12 SING N N 48 
YV6 C21 H13 SING N N 49 
YV6 C21 H14 SING N N 50 
YV6 C27 H15 SING N N 51 
YV6 C28 H16 SING N N 52 
YV6 C28 H17 SING N N 53 
YV6 C28 H18 SING N N 54 
YV6 C29 H19 SING N N 55 
YV6 C29 H20 SING N N 56 
YV6 C29 H21 SING N N 57 
YV6 C3  H22 SING N N 58 
YV6 C4  H23 SING N N 59 
YV6 C4  H24 SING N N 60 
YV6 C5  H25 SING N N 61 
YV6 C5  H26 SING N N 62 
YV6 C6  H27 SING N N 63 
YV6 C6  H28 SING N N 64 
YV6 C8  H29 SING N N 65 
YV6 C9  H30 SING N N 66 
YV6 C9  H31 SING N N 67 
YV6 N2  H32 SING N N 68 
YV6 N3  H33 SING N N 69 
YV6 N4  H34 SING N N 70 
YV6 O4  H35 SING N N 71 
YV6 S1  H36 SING N N 72 
# 
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 
YV6 SMILES           ACDLabs              12.01 "O=C(N1CCCC(N1)C(=O)OC)C(Cc1cccc(O)c1)NC(=O)C(NC(=O)CCCS)C(C)C"                                                                                                                                                         
YV6 InChI            InChI                1.06  "InChI=1S/C24H36N4O6S/c1-15(2)21(26-20(30)10-6-12-35)22(31)25-19(14-16-7-4-8-17(29)13-16)23(32)28-11-5-9-18(27-28)24(33)34-3/h4,7-8,13,15,18-19,21,27,29,35H,5-6,9-12,14H2,1-3H3,(H,25,31)(H,26,30)/t18-,19-,21-/m0/s1" 
YV6 InChIKey         InChI                1.06  VHGYJBMAJUGDAM-ZJOUEHCJSA-N                                                                                                                                                                                             
YV6 SMILES_CANONICAL CACTVS               3.385 "COC(=O)[C@@H]1CCCN(N1)C(=O)[C@H](Cc2cccc(O)c2)NC(=O)[C@@H](NC(=O)CCCS)C(C)C"                                                                                                                                           
YV6 SMILES           CACTVS               3.385 "COC(=O)[CH]1CCCN(N1)C(=O)[CH](Cc2cccc(O)c2)NC(=O)[CH](NC(=O)CCCS)C(C)C"                                                                                                                                                
YV6 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(C)[C@@H](C(=O)N[C@@H](Cc1cccc(c1)O)C(=O)N2CCC[C@H](N2)C(=O)OC)NC(=O)CCCS"                                                                                                                                           
YV6 SMILES           "OpenEye OEToolkits" 2.0.7 "CC(C)C(C(=O)NC(Cc1cccc(c1)O)C(=O)N2CCCC(N2)C(=O)OC)NC(=O)CCCS"                                                                                                                                                         
# 
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 
YV6 "SYSTEMATIC NAME" ACDLabs              12.01 "methyl (3S)-1-[N-(4-sulfanylbutanoyl)-L-valyl-3-hydroxy-L-phenylalanyl]-1,2-diazinane-3-carboxylate"                                                 
YV6 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "methyl (3~{S})-1-[(2~{S})-3-(3-hydroxyphenyl)-2-[[(2~{S})-3-methyl-2-(4-sulfanylbutanoylamino)butanoyl]amino]propanoyl]-1,2-diazinane-3-carboxylate" 
# 
loop_
_pdbx_chem_comp_audit.comp_id 
_pdbx_chem_comp_audit.action_type 
_pdbx_chem_comp_audit.date 
_pdbx_chem_comp_audit.processing_site 
YV6 "Create component" 2023-02-22 RCSB 
YV6 "Initial release"  2023-08-16 RCSB 
YV6 "Modify PCM"       2024-09-27 PDBE 
# 
_pdbx_chem_comp_pcm.pcm_id                             1 
_pdbx_chem_comp_pcm.comp_id                            YV6 
_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               S1 
_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      ? 
# 
