data_YM1 # _chem_comp.id YM1 _chem_comp.name "(1S,2S)-1-hydroxy-2-((S)-4-methyl-2-((((perfluorophenyl)methoxy)carbonyl)amino)pentanamido)-3-((R)-2-oxo-2,3-dihydro-1H-pyrrol-3-yl)propane-1-sulfonic acid" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C21 H24 F5 N3 O8 S" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2021-03-12 _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 573.488 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YM1 _chem_comp.pdbx_model_coordinates_details ? _chem_comp.pdbx_model_coordinates_missing_flag Y _chem_comp.pdbx_ideal_coordinates_details Corina _chem_comp.pdbx_ideal_coordinates_missing_flag N _chem_comp.pdbx_model_coordinates_db_code 7M04 _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 YM1 C12 C1 C 0 1 N N N N N N -19.588 -5.979 3.584 -1.556 0.374 0.098 C12 YM1 1 YM1 C13 C2 C 0 1 N N S N N N -21.096 -5.766 3.562 -0.427 0.608 1.069 C13 YM1 2 YM1 C14 C3 C 0 1 N N N N N N -21.762 -7.115 3.924 -0.507 2.037 1.609 C14 YM1 3 YM1 C15 C4 C 0 1 N N N N N N -23.321 -7.009 4.014 -1.834 2.229 2.347 C15 YM1 4 YM1 C16 C5 C 0 1 N N N N N N -23.785 -5.864 4.988 -1.849 1.359 3.605 C16 YM1 5 YM1 C17 C6 C 0 1 N N N N N N -23.942 -8.337 4.432 -1.990 3.699 2.741 C17 YM1 6 YM1 C19 C7 C 0 1 N N N N N N -21.098 -4.062 1.730 1.962 0.132 1.097 C19 YM1 7 YM1 C21 C8 C 0 1 N N N N N N -21.564 -2.409 0.127 4.307 -0.257 1.310 C21 YM1 8 YM1 C01 C9 C 0 1 N N S N N N -17.160 -6.531 6.140 -4.394 1.467 -0.858 C01 YM1 9 YM1 C03 C10 C 0 1 N N S N N N -17.416 -5.712 4.863 -3.924 0.086 -0.397 C03 YM1 10 YM1 C04 C11 C 0 1 N N N N N N -16.635 -4.383 4.884 -5.082 -0.647 0.283 C04 YM1 11 YM1 C05 C12 C 0 1 N N R N N N -16.861 -3.561 3.582 -4.625 -2.047 0.700 C05 YM1 12 YM1 C06 C13 C 0 1 N N N N N N -16.227 -2.086 3.780 -5.714 -2.751 1.485 C06 YM1 13 YM1 C08 C14 C 0 1 N N N N N N -15.086 -3.224 2.049 -5.282 -3.930 -0.392 C08 YM1 14 YM1 C09 C15 C 0 1 N N N N N N -16.258 -4.152 2.525 -4.435 -2.929 -0.517 C09 YM1 15 YM1 C22 C16 C 0 1 Y N N N N N -22.079 -2.212 -1.331 5.547 -0.302 0.453 C22 YM1 16 YM1 C23 C17 C 0 1 Y N N N N N -23.147 -2.977 -1.779 6.291 0.847 0.253 C23 YM1 17 YM1 C25 C18 C 0 1 Y N N N N N -23.620 -2.811 -3.081 7.431 0.806 -0.535 C25 YM1 18 YM1 C27 C19 C 0 1 Y N N N N N -23.034 -1.874 -3.930 7.824 -0.386 -1.122 C27 YM1 19 YM1 C29 C20 C 0 1 Y N N N N N -21.970 -1.102 -3.482 7.078 -1.536 -0.920 C29 YM1 20 YM1 C31 C21 C 0 1 Y N N N N N -21.487 -1.265 -2.180 5.942 -1.495 -0.128 C31 YM1 21 YM1 F24 F1 F 0 1 N N N N N N -23.739 -3.898 -0.967 5.907 2.009 0.825 F24 YM1 22 YM1 F26 F2 F 0 1 N N N N N N -24.661 -3.569 -3.504 8.157 1.928 -0.732 F26 YM1 23 YM1 F28 F3 F 0 1 N N N N N N -23.505 -1.718 -5.202 8.932 -0.426 -1.894 F28 YM1 24 YM1 F30 F4 F 0 1 N N N N N N -21.395 -0.185 -4.314 7.461 -2.699 -1.492 F30 YM1 25 YM1 F32 F5 F 0 1 N N N N N N -20.446 -0.498 -1.757 5.215 -2.616 0.070 F32 YM1 26 YM1 N07 N1 N 0 1 N N N N N N -15.209 -1.905 2.892 -6.034 -3.844 0.765 N07 YM1 27 YM1 N11 N2 N 0 1 N N N N N N -18.848 -5.509 4.784 -2.818 0.237 0.551 N11 YM1 28 YM1 N18 N3 N 0 1 N N N N N N -21.553 -5.346 2.259 0.854 0.415 0.385 N18 YM1 29 YM1 O02 O1 O 0 1 N N N N N N -15.776 -6.630 6.263 -3.282 2.201 -1.373 O02 YM1 30 YM1 O10 O2 O 0 1 N N N N N N -16.582 -1.279 4.579 -6.196 -2.403 2.543 O10 YM1 31 YM1 O20 O3 O 0 1 N N N N N N -21.214 -3.775 0.343 3.157 0.053 0.481 O20 YM1 32 YM1 O33 O4 O 0 1 N N N N N N -20.645 -3.244 2.466 1.884 -0.054 2.295 O33 YM1 33 YM1 O34 O5 O 0 1 N N N N N N -19.019 -6.511 2.679 -1.329 0.313 -1.092 O34 YM1 34 YM1 H1 H1 H 0 1 N N N N N N -21.368 -5.019 4.322 -0.507 -0.098 1.895 H1 YM1 35 YM1 H2 H2 H 0 1 N N N N N N -21.503 -7.855 3.152 0.319 2.212 2.297 H2 YM1 36 YM1 H3 H3 H 0 1 N N N N N N -21.374 -7.450 4.898 -0.447 2.742 0.781 H3 YM1 37 YM1 H4 H4 H 0 1 N N N N N N -23.695 -6.760 3.010 -2.658 1.939 1.695 H4 YM1 38 YM1 H5 H5 H 0 1 N N N N N N -24.884 -5.830 5.017 -1.666 0.320 3.331 H5 YM1 39 YM1 H6 H6 H 0 1 N N N N N N -23.398 -6.063 5.998 -1.070 1.697 4.290 H6 YM1 40 YM1 H7 H7 H 0 1 N N N N N N -23.397 -4.899 4.630 -2.820 1.441 4.093 H7 YM1 41 YM1 H8 H8 H 0 1 N N N N N N -25.035 -8.230 4.486 -1.979 4.319 1.845 H8 YM1 42 YM1 H9 H9 H 0 1 N N N N N N -23.685 -9.110 3.693 -2.935 3.836 3.267 H9 YM1 43 YM1 H10 H10 H 0 1 N N N N N N -23.553 -8.629 5.419 -1.166 3.990 3.394 H10 YM1 44 YM1 H11 H11 H 0 1 N N N N N N -20.679 -1.777 0.289 4.161 -1.225 1.788 H11 YM1 45 YM1 H12 H12 H 0 1 N N N N N N -22.355 -2.120 0.834 4.422 0.512 2.074 H12 YM1 46 YM1 H13 H13 H 0 1 N N N N N N -17.555 -7.538 5.943 -4.825 2.004 -0.013 H13 YM1 47 YM1 S1 S1 S 0 1 N Y N N N N -17.594 -6.060 6.997 -5.648 1.277 -2.155 S1 YM1 48 YM1 H15 H15 H 0 1 N N N N N N -17.077 -6.301 3.998 -3.587 -0.489 -1.260 H15 YM1 49 YM1 H16 H16 H 0 1 N N N N N N -15.562 -4.602 4.985 -5.396 -0.090 1.166 H16 YM1 50 YM1 H17 H17 H 0 1 N N N N N N -16.970 -3.786 5.745 -5.918 -0.729 -0.411 H17 YM1 51 YM1 H18 H18 H 0 1 N N N N N N -17.943 -3.447 3.420 -3.706 -1.991 1.283 H18 YM1 52 YM1 H19 H19 H 0 1 N N N N N N -14.345 -3.447 1.295 -5.378 -4.728 -1.113 H19 YM1 53 YM1 H20 H20 H 0 1 N N N N N N -16.535 -5.099 2.085 -3.741 -2.769 -1.328 H20 YM1 54 YM1 H21 H21 H 0 1 N N N N N N -14.645 -1.085 2.795 -6.708 -4.490 1.026 H21 YM1 55 YM1 H22 H22 H 0 1 N N N N N N -19.335 -5.056 5.531 -2.993 0.240 1.505 H22 YM1 56 YM1 H23 H23 H 0 1 N N N N N N -22.171 -5.924 1.727 0.904 0.493 -0.581 H23 YM1 57 YM1 H24 H24 H 0 1 N N N N N N -15.562 -7.130 7.042 -2.572 2.341 -0.732 H24 YM1 58 YM1 O1 O6 O 0 1 N Y N N N N ? ? ? -6.125 2.548 -2.577 O1 YM1 59 YM1 O2 O7 O 0 1 N Y N N N N ? ? ? -5.243 0.296 -3.100 O2 YM1 60 YM1 O3 O8 O 0 1 N Y N N N N ? ? ? -6.837 0.647 -1.445 O3 YM1 61 YM1 H14 H14 H 0 1 N Y N N N N ? ? ? -7.597 0.483 -2.020 H14 YM1 62 # 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 YM1 F28 C27 SING N N 1 YM1 F30 C29 SING N N 2 YM1 C27 C29 DOUB Y N 3 YM1 C27 C25 SING Y N 4 YM1 F26 C25 SING N N 5 YM1 C29 C31 SING Y N 6 YM1 C25 C23 DOUB Y N 7 YM1 C31 F32 SING N N 8 YM1 C31 C22 DOUB Y N 9 YM1 C23 C22 SING Y N 10 YM1 C23 F24 SING N N 11 YM1 C22 C21 SING N N 12 YM1 C21 O20 SING N N 13 YM1 O20 C19 SING N N 14 YM1 C19 N18 SING N N 15 YM1 C19 O33 DOUB N N 16 YM1 C08 C09 DOUB N N 17 YM1 C08 N07 SING N N 18 YM1 N18 C13 SING N N 19 YM1 C09 C05 SING N N 20 YM1 O34 C12 DOUB N N 21 YM1 N07 C06 SING N N 22 YM1 C13 C12 SING N N 23 YM1 C13 C14 SING N N 24 YM1 C05 C06 SING N N 25 YM1 C05 C04 SING N N 26 YM1 C12 N11 SING N N 27 YM1 C06 O10 DOUB N N 28 YM1 C14 C15 SING N N 29 YM1 C15 C17 SING N N 30 YM1 C15 C16 SING N N 31 YM1 N11 C03 SING N N 32 YM1 C03 C04 SING N N 33 YM1 C03 C01 SING N N 34 YM1 C01 O02 SING N N 35 YM1 C13 H1 SING N N 36 YM1 C14 H2 SING N N 37 YM1 C14 H3 SING N N 38 YM1 C15 H4 SING N N 39 YM1 C16 H5 SING N N 40 YM1 C16 H6 SING N N 41 YM1 C16 H7 SING N N 42 YM1 C17 H8 SING N N 43 YM1 C17 H9 SING N N 44 YM1 C17 H10 SING N N 45 YM1 C21 H11 SING N N 46 YM1 C21 H12 SING N N 47 YM1 C01 H13 SING N N 48 YM1 C01 S1 SING N N 49 YM1 C03 H15 SING N N 50 YM1 C04 H16 SING N N 51 YM1 C04 H17 SING N N 52 YM1 C05 H18 SING N N 53 YM1 C08 H19 SING N N 54 YM1 C09 H20 SING N N 55 YM1 N07 H21 SING N N 56 YM1 N11 H22 SING N N 57 YM1 N18 H23 SING N N 58 YM1 O02 H24 SING N N 59 YM1 S1 O1 DOUB N N 60 YM1 S1 O2 DOUB N N 61 YM1 S1 O3 SING N N 62 YM1 O3 H14 SING N N 63 # 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 YM1 SMILES ACDLabs 12.01 "O=C1NC=CC1CC(NC(=O)C(CC(C)C)NC(=O)OCc1c(F)c(F)c(F)c(F)c1F)C(O)S(=O)(=O)O" YM1 InChI InChI 1.03 "InChI=1S/C21H24F5N3O8S/c1-8(2)5-11(29-21(33)37-7-10-13(22)15(24)17(26)16(25)14(10)23)19(31)28-12(20(32)38(34,35)36)6-9-3-4-27-18(9)30/h3-4,8-9,11-12,20,32H,5-7H2,1-2H3,(H,27,30)(H,28,31)(H,29,33)(H,34,35,36)/t9-,11-,12-,20-/m0/s1" YM1 InChIKey InChI 1.03 VNVWDEQECYLCMA-JJDHJZHUSA-N YM1 SMILES_CANONICAL CACTVS 3.385 "CC(C)C[C@H](NC(=O)OCc1c(F)c(F)c(F)c(F)c1F)C(=O)N[C@@H](C[C@@H]2C=CNC2=O)[C@@H](O)[S](O)(=O)=O" YM1 SMILES CACTVS 3.385 "CC(C)C[CH](NC(=O)OCc1c(F)c(F)c(F)c(F)c1F)C(=O)N[CH](C[CH]2C=CNC2=O)[CH](O)[S](O)(=O)=O" YM1 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1C=CNC1=O)C(O)S(=O)(=O)O)NC(=O)OCc2c(c(c(c(c2F)F)F)F)F" YM1 SMILES "OpenEye OEToolkits" 2.0.7 "CC(C)CC(C(=O)NC(CC1C=CNC1=O)C(O)S(=O)(=O)O)NC(=O)OCc2c(c(c(c(c2F)F)F)F)F" # 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 YM1 "SYSTEMATIC NAME" ACDLabs 12.01 "(1S,2S)-1-hydroxy-3-[(3R)-2-oxo-2,3-dihydro-1H-pyrrol-3-yl]-2-[(N-{[(pentafluorophenyl)methoxy]carbonyl}-L-leucyl)amino]propane-1-sulfonic acid" YM1 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "(2~{S})-2-[[(2~{S})-4-methyl-2-[[2,3,4,5,6-pentakis(fluoranyl)phenyl]methoxycarbonylamino]pentanoyl]amino]-1-oxidanyl-3-[(3~{R})-2-oxidanylidene-1,3-dihydropyrrol-3-yl]propane-1-sulfonic acid" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site YM1 "Create component" 2021-03-12 RCSB YM1 "Initial release" 2021-03-24 RCSB YM1 "Modify PCM" 2024-09-27 PDBE # _pdbx_chem_comp_pcm.pcm_id 1 _pdbx_chem_comp_pcm.comp_id YM1 _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 C01 _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 ? #