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 ?
#