data_YMB # _chem_comp.id YMB _chem_comp.name "7-[(1~{S})-1-[5-[(3-azanylazetidin-1-yl)methyl]-2-oxidanylidene-1,3-oxazolidin-3-yl]ethyl]-3-[3-fluoranyl-4-(methylsulfonylmethyl)phenyl]-1~{H}-indole-2-carboxylic acid" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C26 H29 F 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 2023-06-19 _chem_comp.pdbx_modified_date 2024-07-05 _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 544.595 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YMB _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 8PGJ _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE # 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 YMB C11 C1 C 0 1 Y N N N N N -21.300 -11.944 8.523 2.802 -0.745 0.213 C11 YMB 1 YMB C14 C2 C 0 1 Y N N N N N -20.096 -12.222 6.013 5.458 -0.276 -0.422 C14 YMB 2 YMB C10 C3 C 0 1 Y N N N N N -21.901 -11.791 9.867 1.384 -0.995 0.553 C10 YMB 3 YMB C12 C4 C 0 1 Y N N N N N -20.423 -10.980 8.034 3.804 -1.012 1.146 C12 YMB 4 YMB C13 C5 C 0 1 Y N N N N N -19.855 -11.129 6.805 5.125 -0.777 0.824 C13 YMB 5 YMB C17 C6 C 0 1 N N N N N N -20.738 -9.885 3.756 9.087 1.758 -0.805 C17 YMB 6 YMB C15 C7 C 0 1 N N N N N N -19.461 -12.388 4.653 6.902 -0.022 -0.767 C15 YMB 7 YMB C01 C8 C 0 1 N N N N N N -22.944 -12.499 15.752 -3.991 -3.794 0.539 C01 YMB 8 YMB C02 C9 C 0 1 N N S N N N -23.517 -12.030 14.406 -3.149 -2.558 0.861 C02 YMB 9 YMB C03 C10 C 0 1 Y N N N N N -22.851 -12.820 13.224 -1.810 -2.671 0.179 C03 YMB 10 YMB C04 C11 C 0 1 Y N N N N N -22.571 -12.165 12.001 -0.754 -1.853 0.574 C04 YMB 11 YMB C06 C12 C 0 1 Y N N N N N -22.410 -10.621 10.417 0.638 -0.349 1.523 C06 YMB 12 YMB C07 C13 C 0 1 N N N N N N -22.710 -9.309 9.820 1.126 0.718 2.401 C07 YMB 13 YMB C20 C14 C 0 1 Y N N N N N -20.941 -13.179 6.544 4.469 -0.014 -1.356 C20 YMB 14 YMB C22 C15 C 0 1 Y N N N N N -21.539 -13.064 7.782 3.142 -0.246 -1.045 C22 YMB 15 YMB C23 C16 C 0 1 Y N N N N N -21.977 -12.776 10.888 0.489 -1.974 -0.075 C23 YMB 16 YMB C24 C17 C 0 1 Y N N N N N -21.631 -14.160 10.977 0.651 -2.907 -1.102 C24 YMB 17 YMB C25 C18 C 0 1 Y N N N N N -21.915 -14.814 12.179 -0.398 -3.699 -1.472 C25 YMB 18 YMB C26 C19 C 0 1 Y N N N N N -22.529 -14.178 13.265 -1.627 -3.583 -0.836 C26 YMB 19 YMB C28 C20 C 0 1 N N N N N N -25.753 -13.169 15.067 -4.306 -0.246 1.226 C28 YMB 20 YMB C29 C21 C 0 1 N N N N N N -27.077 -13.005 14.567 -4.953 0.732 0.226 C29 YMB 21 YMB C30 C22 C 0 1 N N N N N N -28.239 -13.913 14.993 -6.438 0.919 0.543 C30 YMB 22 YMB C32 C23 C 0 1 N N N N N N -29.280 -12.929 16.807 -6.948 3.247 0.069 C32 YMB 23 YMB C33 C24 C 0 1 N N N N N N -30.730 -13.329 16.903 -8.389 3.406 -0.447 C33 YMB 24 YMB C35 C25 C 0 1 N N N N N N -30.574 -13.951 15.553 -8.505 1.878 -0.301 C35 YMB 25 YMB C37 C26 C 0 1 N N N N N N -25.841 -11.483 13.472 -4.150 -1.093 -0.893 C37 YMB 26 YMB F21 F1 F 0 1 N N N N N N -21.214 -14.268 5.782 4.801 0.475 -2.571 F21 YMB 27 YMB N05 N1 N 0 1 Y N N N N N -22.774 -10.864 11.665 -0.640 -0.870 1.529 N05 YMB 28 YMB N27 N2 N 0 1 N N N N N N -24.989 -12.186 14.405 -3.840 -1.358 0.383 N27 YMB 29 YMB N31 N3 N 0 1 N N N N N N -29.354 -13.107 15.316 -7.031 1.854 -0.422 N31 YMB 30 YMB N34 N4 N 0 1 N N N N N N -31.588 -12.134 17.003 -8.472 3.875 -1.837 N34 YMB 31 YMB O08 O1 O 0 1 N N N N N N -23.195 -9.296 8.624 2.276 1.103 2.309 O08 YMB 32 YMB O09 O2 O 0 1 N N N N N N -22.598 -8.248 10.490 0.299 1.273 3.312 O09 YMB 33 YMB O18 O3 O 0 1 N N N N N N -21.752 -12.257 3.358 7.268 1.800 1.104 O18 YMB 34 YMB O19 O4 O 0 1 N N N N N N -19.828 -11.630 2.126 6.600 2.573 -1.125 O19 YMB 35 YMB O36 O5 O 0 1 N N N N N N -27.146 -11.987 13.637 -4.785 0.078 -1.065 O36 YMB 36 YMB O38 O6 O 0 1 N N N N N N -25.542 -10.578 12.801 -3.882 -1.842 -1.812 O38 YMB 37 YMB S16 S1 S 0 1 N N N N N N -20.470 -11.605 3.374 7.343 1.677 -0.310 S16 YMB 38 YMB H121 H1 H 0 0 N N N N N N -20.192 -10.110 8.631 3.546 -1.402 2.120 H121 YMB 39 YMB H131 H2 H 0 0 N N N N N N -19.191 -10.359 6.441 5.900 -0.984 1.546 H131 YMB 40 YMB H171 H3 H 0 0 N N N N N N -21.242 -9.799 4.730 9.655 1.006 -0.257 H171 YMB 41 YMB H172 H4 H 0 0 N N N N N N -19.770 -9.363 3.797 9.170 1.568 -1.875 H172 YMB 42 YMB H173 H5 H 0 0 N N N N N N -21.367 -9.430 2.977 9.483 2.748 -0.580 H173 YMB 43 YMB H152 H6 H 0 0 N N N N N N -19.363 -13.461 4.429 7.535 -0.721 -0.220 H152 YMB 44 YMB H151 H7 H 0 0 N N N N N N -18.464 -11.923 4.661 7.050 -0.160 -1.838 H151 YMB 45 YMB H011 H8 H 0 0 N N N N N N -23.420 -11.937 16.569 -4.137 -3.863 -0.539 H011 YMB 46 YMB H013 H9 H 0 0 N N N N N N -23.143 -13.573 15.881 -3.477 -4.687 0.894 H013 YMB 47 YMB H012 H10 H 0 0 N N N N N N -21.858 -12.323 15.770 -4.960 -3.712 1.032 H012 YMB 48 YMB H021 H11 H 0 0 N N N N N N -23.271 -10.965 14.280 -3.003 -2.488 1.939 H021 YMB 49 YMB H221 H12 H 0 0 N N N N N N -22.184 -13.845 8.157 2.371 -0.041 -1.773 H221 YMB 50 YMB H241 H13 H 0 0 N N N N N N -21.169 -14.679 10.150 1.604 -3.002 -1.602 H241 YMB 51 YMB H251 H14 H 0 0 N N N N N N -21.649 -15.856 12.275 -0.272 -4.420 -2.266 H251 YMB 52 YMB H261 H15 H 0 0 N N N N N N -22.758 -14.749 14.152 -2.448 -4.216 -1.140 H261 YMB 53 YMB H281 H16 H 0 0 N N N N N N -25.374 -14.175 14.835 -3.467 0.227 1.735 H281 YMB 54 YMB H1 H17 H 0 1 N N N N N N -25.728 -13.010 16.155 -5.043 -0.597 1.949 H1 YMB 55 YMB H2 H18 H 0 1 N N N N N N -27.312 -12.300 15.378 -4.436 1.691 0.242 H2 YMB 56 YMB H301 H19 H 0 0 N N N N N N -28.500 -14.591 14.167 -6.948 -0.043 0.478 H301 YMB 57 YMB H302 H20 H 0 0 N N N N N N -27.943 -14.504 15.872 -6.547 1.320 1.551 H302 YMB 58 YMB H321 H21 H 0 0 N N N N N N -28.586 -13.618 17.311 -6.220 3.858 -0.466 H321 YMB 59 YMB H322 H22 H 0 0 N N N N N N -29.073 -11.898 17.130 -6.857 3.328 1.152 H322 YMB 60 YMB H331 H23 H 0 0 N N N N N N -30.917 -14.067 17.697 -9.038 3.964 0.229 H331 YMB 61 YMB H351 H24 H 0 0 N N N N N N -31.406 -13.745 14.863 -8.871 1.557 0.675 H351 YMB 62 YMB H352 H25 H 0 0 N N N N N N -30.376 -15.033 15.576 -9.024 1.396 -1.129 H352 YMB 63 YMB H051 H26 H 0 0 N N N N N N -23.152 -10.176 12.284 -1.354 -0.584 2.120 H051 YMB 64 YMB H341 H28 H 0 0 N N N N N N -31.609 -11.817 17.951 -9.433 3.964 -2.132 H341 YMB 65 YMB H342 H29 H 0 0 N N N N N N -31.221 -11.411 16.418 -7.975 4.745 -1.955 H342 YMB 66 YMB H5 H31 H 0 1 N N N N N N -22.915 -7.514 9.977 0.710 1.968 3.844 H5 YMB 67 # 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 YMB O19 S16 DOUB N N 1 YMB O18 S16 DOUB N N 2 YMB S16 C17 SING N N 3 YMB S16 C15 SING N N 4 YMB C15 C14 SING N N 5 YMB F21 C20 SING N N 6 YMB C14 C20 DOUB Y N 7 YMB C14 C13 SING Y N 8 YMB C20 C22 SING Y N 9 YMB C13 C12 DOUB Y N 10 YMB C22 C11 DOUB Y N 11 YMB C12 C11 SING Y N 12 YMB C11 C10 SING N N 13 YMB O08 C07 DOUB N N 14 YMB C07 C06 SING N N 15 YMB C07 O09 SING N N 16 YMB C10 C06 DOUB Y N 17 YMB C10 C23 SING Y N 18 YMB C06 N05 SING Y N 19 YMB C23 C24 DOUB Y N 20 YMB C23 C04 SING Y N 21 YMB C24 C25 SING Y N 22 YMB N05 C04 SING Y N 23 YMB C04 C03 DOUB Y N 24 YMB C25 C26 DOUB Y N 25 YMB O38 C37 DOUB N N 26 YMB C03 C26 SING Y N 27 YMB C03 C02 SING N N 28 YMB C37 O36 SING N N 29 YMB C37 N27 SING N N 30 YMB O36 C29 SING N N 31 YMB N27 C02 SING N N 32 YMB N27 C28 SING N N 33 YMB C02 C01 SING N N 34 YMB C29 C30 SING N N 35 YMB C29 C28 SING N N 36 YMB C30 N31 SING N N 37 YMB N31 C35 SING N N 38 YMB N31 C32 SING N N 39 YMB C35 C33 SING N N 40 YMB C32 C33 SING N N 41 YMB C33 N34 SING N N 42 YMB C12 H121 SING N N 43 YMB C13 H131 SING N N 44 YMB C17 H171 SING N N 45 YMB C17 H172 SING N N 46 YMB C17 H173 SING N N 47 YMB C15 H152 SING N N 48 YMB C15 H151 SING N N 49 YMB C01 H011 SING N N 50 YMB C01 H013 SING N N 51 YMB C01 H012 SING N N 52 YMB C02 H021 SING N N 53 YMB C22 H221 SING N N 54 YMB C24 H241 SING N N 55 YMB C25 H251 SING N N 56 YMB C26 H261 SING N N 57 YMB C28 H281 SING N N 58 YMB C28 H1 SING N N 59 YMB C29 H2 SING N N 60 YMB C30 H301 SING N N 61 YMB C30 H302 SING N N 62 YMB C32 H321 SING N N 63 YMB C32 H322 SING N N 64 YMB C33 H331 SING N N 65 YMB C35 H351 SING N N 66 YMB C35 H352 SING N N 67 YMB N05 H051 SING N N 68 YMB N34 H341 SING N N 69 YMB N34 H342 SING N N 70 YMB O09 H5 SING N N 71 # 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 YMB InChI InChI 1.06 "InChI=1S/C26H29FN4O6S/c1-14(31-12-18(37-26(31)34)11-30-9-17(28)10-30)19-4-3-5-20-22(24(25(32)33)29-23(19)20)15-6-7-16(21(27)8-15)13-38(2,35)36/h3-8,14,17-18,29H,9-13,28H2,1-2H3,(H,32,33)/t14-,18-/m0/s1" YMB InChIKey InChI 1.06 AELVYVNWNWJKTP-KSSFIOAISA-N YMB SMILES_CANONICAL CACTVS 3.385 "C[C@H](N1C[C@H](CN2CC(N)C2)OC1=O)c3cccc4c3[nH]c(C(O)=O)c4c5ccc(C[S](C)(=O)=O)c(F)c5" YMB SMILES CACTVS 3.385 "C[CH](N1C[CH](CN2CC(N)C2)OC1=O)c3cccc4c3[nH]c(C(O)=O)c4c5ccc(C[S](C)(=O)=O)c(F)c5" YMB SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@@H](c1cccc2c1[nH]c(c2c3ccc(c(c3)F)CS(=O)(=O)C)C(=O)O)N4CC(OC4=O)CN5CC(C5)N" YMB SMILES "OpenEye OEToolkits" 2.0.7 "CC(c1cccc2c1[nH]c(c2c3ccc(c(c3)F)CS(=O)(=O)C)C(=O)O)N4CC(OC4=O)CN5CC(C5)N" # _pdbx_chem_comp_identifier.comp_id YMB _pdbx_chem_comp_identifier.type "SYSTEMATIC NAME" _pdbx_chem_comp_identifier.program "OpenEye OEToolkits" _pdbx_chem_comp_identifier.program_version 2.0.7 _pdbx_chem_comp_identifier.identifier "7-[(1~{S})-1-[5-[(3-azanylazetidin-1-yl)methyl]-2-oxidanylidene-1,3-oxazolidin-3-yl]ethyl]-3-[3-fluoranyl-4-(methylsulfonylmethyl)phenyl]-1~{H}-indole-2-carboxylic 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 YMB "Create component" 2023-06-20 PDBE YMB "Initial release" 2024-07-10 RCSB #