data_YMF # _chem_comp.id YMF _chem_comp.name "7-[(1~{S})-1-[(5~{R})-5-[(2~{R})-3-azanyl-2-methyl-propyl]-2-oxidanylidene-1,3-oxazolidin-3-yl]ethyl]-3-(1~{H}-pyrazol-4-yl)-1~{H}-indole-2-carboxylic acid" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C21 H25 N5 O4" _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 411.454 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YMF _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 8PH1 _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 YMF C10 C1 C 0 1 Y N N N N N -21.367 -13.249 7.632 5.321 0.297 -0.429 C10 YMF 1 YMF C13 C2 C 0 1 Y N N N N N -20.389 -11.207 7.581 4.068 1.983 -1.224 C13 YMF 2 YMF C14 C3 C 0 1 Y N N N N N -22.183 -10.750 10.291 1.985 0.691 1.051 C14 YMF 3 YMF C15 C4 C 0 1 N N N N N N -22.433 -9.363 9.717 2.199 1.959 1.748 C15 YMF 4 YMF C19 C5 C 0 1 Y N N N N N -22.364 -12.236 11.980 1.055 -1.282 0.458 C19 YMF 5 YMF C01 C6 C 0 1 N N N N N N -22.574 -12.432 15.677 -1.370 -4.109 1.073 C01 YMF 6 YMF C02 C7 C 0 1 N N S N N N -23.197 -12.060 14.317 -0.941 -2.643 1.152 C02 YMF 7 YMF C03 C8 C 0 1 Y N N N N N -22.600 -12.887 13.172 0.282 -2.430 0.298 C03 YMF 8 YMF C04 C9 C 0 1 Y N N N N N -22.257 -14.254 13.179 0.639 -3.371 -0.642 C04 YMF 9 YMF C05 C10 C 0 1 Y N N N N N -21.709 -14.820 12.015 1.763 -3.188 -1.436 C05 YMF 10 YMF C06 C11 C 0 1 Y N N N N N -21.464 -14.182 10.859 2.536 -2.070 -1.297 C06 YMF 11 YMF C07 C12 C 0 1 Y N N N N N -21.756 -12.884 10.690 2.193 -1.102 -0.350 C07 YMF 12 YMF C08 C13 C 0 1 Y N N N N N -21.744 -11.787 9.788 2.788 0.179 0.047 C08 YMF 13 YMF C09 C14 C 0 1 Y N N N N N -21.209 -12.040 8.380 4.006 0.802 -0.517 C09 YMF 14 YMF C21 C15 C 0 1 N N N N N N -25.308 -13.442 14.728 -2.734 -0.771 1.462 C21 YMF 15 YMF C22 C16 C 0 1 N N R N N N -26.715 -13.071 14.463 -3.762 -0.184 0.476 C22 YMF 16 YMF C23 C17 C 0 1 N N N N N N -27.742 -12.772 15.746 -3.507 1.309 0.261 C23 YMF 17 YMF C24 C18 C 0 1 N N R N N N -28.697 -13.601 15.077 -4.612 1.893 -0.622 C24 YMF 18 YMF C25 C19 C 0 1 N N N N N N -29.387 -14.638 16.129 -4.292 3.355 -0.939 C25 YMF 19 YMF C27 C20 C 0 1 N N N N N N -27.918 -14.187 14.012 -5.950 1.813 0.116 C27 YMF 20 YMF C29 C21 C 0 1 N N N N N N -25.434 -11.458 13.425 -2.542 -1.806 -0.569 C29 YMF 21 YMF N11 N1 N 0 1 Y N N N N N -20.758 -13.082 6.422 6.117 1.127 -1.047 N11 YMF 22 YMF N12 N2 N 0 1 Y N N N N N -20.139 -11.866 6.375 5.358 2.189 -1.552 N12 YMF 23 YMF N18 N3 N 0 1 Y N N N N N -22.529 -10.865 11.511 0.950 -0.194 1.293 N18 YMF 24 YMF N20 N4 N 0 1 N N N N N N -24.604 -12.281 14.254 -2.028 -1.788 0.669 N20 YMF 25 YMF N26 N5 N 0 1 N N N N N N -30.533 -15.275 15.470 -5.287 3.881 -1.883 N26 YMF 26 YMF O16 O1 O 0 1 N N N N N N -22.765 -9.325 8.523 3.150 2.659 1.457 O16 YMF 27 YMF O17 O2 O 0 1 N N N N N N -22.357 -8.315 10.478 1.342 2.351 2.714 O17 YMF 28 YMF O28 O3 O 0 1 N N N N N N -26.732 -11.985 13.525 -3.530 -0.924 -0.758 O28 YMF 29 YMF O30 O4 O 0 1 N N N N N N -25.130 -10.509 12.770 -2.146 -2.555 -1.440 O30 YMF 30 YMF H101 H1 H 0 0 N N N N N N -21.879 -14.139 7.967 5.617 -0.616 0.067 H101 YMF 31 YMF H131 H2 H 0 0 N N N N N N -20.020 -10.230 7.857 3.235 2.625 -1.469 H131 YMF 32 YMF H011 H3 H 0 0 N N N N N N -23.028 -11.818 16.469 -0.561 -4.745 1.433 H011 YMF 33 YMF H013 H4 H 0 0 N N N N N N -22.759 -13.496 15.886 -2.255 -4.262 1.691 H013 YMF 34 YMF H012 H5 H 0 0 N N N N N N -21.490 -12.248 15.646 -1.601 -4.365 0.038 H012 YMF 35 YMF H021 H6 H 0 0 N N N N N N -22.981 -10.999 14.122 -0.711 -2.387 2.187 H021 YMF 36 YMF H041 H7 H 0 0 N N N N N N -22.412 -14.855 14.062 0.038 -4.260 -0.763 H041 YMF 37 YMF H051 H8 H 0 0 N N N N N N -21.461 -15.870 12.054 2.029 -3.936 -2.169 H051 YMF 38 YMF H061 H9 H 0 0 N N N N N N -21.019 -14.730 10.042 3.409 -1.935 -1.918 H061 YMF 39 YMF H211 H10 H 0 0 N N N N N N -25.132 -13.607 15.801 -2.042 0.001 1.798 H211 YMF 40 YMF H212 H11 H 0 0 N N N N N N -25.019 -14.343 14.167 -3.239 -1.230 2.312 H212 YMF 41 YMF H1 H12 H 0 1 N N N N N N -27.166 -13.934 13.952 -4.777 -0.349 0.837 H1 YMF 42 YMF H232 H13 H 0 0 N N N N N N -27.394 -13.160 16.715 -3.504 1.820 1.224 H232 YMF 43 YMF H231 H14 H 0 0 N N N N N N -28.044 -11.720 15.859 -2.542 1.447 -0.227 H231 YMF 44 YMF H241 H15 H 0 0 N N N N N N -29.500 -12.980 14.652 -4.674 1.325 -1.550 H241 YMF 45 YMF H251 H16 H 0 0 N N N N N N -28.657 -15.405 16.427 -4.317 3.941 -0.020 H251 YMF 46 YMF H252 H17 H 0 0 N N N N N N -29.728 -14.091 17.020 -3.299 3.421 -1.385 H252 YMF 47 YMF H271 H18 H 0 0 N N N N N N -28.556 -14.857 13.417 -5.888 2.382 1.044 H271 YMF 48 YMF H272 H19 H 0 0 N N N N N N -27.521 -13.390 13.367 -6.737 2.230 -0.513 H272 YMF 49 YMF H2 H20 H 0 1 N N N N N N -27.083 -14.761 14.441 -6.178 0.772 0.342 H2 YMF 50 YMF H121 H21 H 0 0 N N N N N N -19.601 -11.510 5.611 5.702 2.944 -2.054 H121 YMF 51 YMF H181 H22 H 0 0 N N N N N N -22.870 -10.113 12.075 0.252 -0.067 1.955 H181 YMF 52 YMF H262 H23 H 0 0 N N N N N N -30.968 -15.915 16.103 -6.222 3.772 -1.520 H262 YMF 53 YMF H3 H24 H 0 1 N N N N N N -31.193 -14.574 15.198 -5.097 4.846 -2.108 H3 YMF 54 YMF H4 H26 H 0 1 N N N N N N -22.592 -7.542 9.978 1.566 3.201 3.116 H4 YMF 55 # 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 YMF C10 C09 SING Y N 1 YMF C10 N11 DOUB Y N 2 YMF C13 C09 DOUB Y N 3 YMF C13 N12 SING Y N 4 YMF C14 C15 SING N N 5 YMF C14 C08 DOUB Y N 6 YMF C14 N18 SING Y N 7 YMF C15 O16 DOUB N N 8 YMF C15 O17 SING N N 9 YMF C19 C03 DOUB Y N 10 YMF C19 C07 SING Y N 11 YMF C19 N18 SING Y N 12 YMF C01 C02 SING N N 13 YMF C02 C03 SING N N 14 YMF C02 N20 SING N N 15 YMF C03 C04 SING Y N 16 YMF C04 C05 DOUB Y N 17 YMF C05 C06 SING Y N 18 YMF C06 C07 DOUB Y N 19 YMF C07 C08 SING Y N 20 YMF C08 C09 SING N N 21 YMF C21 C22 SING N N 22 YMF C21 N20 SING N N 23 YMF C22 C23 SING N N 24 YMF C22 O28 SING N N 25 YMF C23 C24 SING N N 26 YMF C24 C25 SING N N 27 YMF C24 C27 SING N N 28 YMF C25 N26 SING N N 29 YMF C29 N20 SING N N 30 YMF C29 O28 SING N N 31 YMF C29 O30 DOUB N N 32 YMF N11 N12 SING Y N 33 YMF C10 H101 SING N N 34 YMF C13 H131 SING N N 35 YMF C01 H011 SING N N 36 YMF C01 H013 SING N N 37 YMF C01 H012 SING N N 38 YMF C02 H021 SING N N 39 YMF C04 H041 SING N N 40 YMF C05 H051 SING N N 41 YMF C06 H061 SING N N 42 YMF C21 H211 SING N N 43 YMF C21 H212 SING N N 44 YMF C22 H1 SING N N 45 YMF C23 H232 SING N N 46 YMF C23 H231 SING N N 47 YMF C24 H241 SING N N 48 YMF C25 H251 SING N N 49 YMF C25 H252 SING N N 50 YMF C27 H271 SING N N 51 YMF C27 H272 SING N N 52 YMF C27 H2 SING N N 53 YMF N12 H121 SING N N 54 YMF N18 H181 SING N N 55 YMF N26 H262 SING N N 56 YMF N26 H3 SING N N 57 YMF O17 H4 SING N N 58 # 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 YMF InChI InChI 1.06 "InChI=1S/C21H25N5O4/c1-11(7-22)6-14-10-26(21(29)30-14)12(2)15-4-3-5-16-17(13-8-23-24-9-13)19(20(27)28)25-18(15)16/h3-5,8-9,11-12,14,25H,6-7,10,22H2,1-2H3,(H,23,24)(H,27,28)/t11-,12+,14-/m1/s1" YMF InChIKey InChI 1.06 OJYBICGUZCKJGO-MBNYWOFBSA-N YMF SMILES_CANONICAL CACTVS 3.385 "C[C@@H](CN)C[C@@H]1CN([C@@H](C)c2cccc3c2[nH]c(C(O)=O)c3c4c[nH]nc4)C(=O)O1" YMF SMILES CACTVS 3.385 "C[CH](CN)C[CH]1CN([CH](C)c2cccc3c2[nH]c(C(O)=O)c3c4c[nH]nc4)C(=O)O1" YMF SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C[C@H](C[C@@H]1CN(C(=O)O1)[C@@H](C)c2cccc3c2[nH]c(c3c4c[nH]nc4)C(=O)O)CN" YMF SMILES "OpenEye OEToolkits" 2.0.7 "CC(CC1CN(C(=O)O1)C(C)c2cccc3c2[nH]c(c3c4c[nH]nc4)C(=O)O)CN" # _pdbx_chem_comp_identifier.comp_id YMF _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~{R})-5-[(2~{R})-3-azanyl-2-methyl-propyl]-2-oxidanylidene-1,3-oxazolidin-3-yl]ethyl]-3-(1~{H}-pyrazol-4-yl)-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 YMF "Create component" 2023-06-19 PDBE YMF "Initial release" 2024-07-10 RCSB #