data_YWO # _chem_comp.id YWO _chem_comp.name O-(5-methyl-2-nitrophenyl)-D-tyrosinamide _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C16 H17 N3 O4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2014-08-20 _chem_comp.pdbx_modified_date 2014-10-03 _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 315.324 _chem_comp.one_letter_code ? _chem_comp.three_letter_code YWO _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 4ux6 _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site EBI # 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 YWO C1 C1 C 0 1 Y N N N N N 19.108 69.817 21.108 -4.934 0.619 -0.024 C1 YWO 1 YWO N1 N1 N 1 1 N N N N N N 20.180 67.717 22.068 -4.326 -1.780 0.116 N1 YWO 2 YWO O1 O1 O 0 1 N N N N N N 21.098 69.364 24.153 -1.646 -0.936 0.067 O1 YWO 3 YWO C2 C2 C 0 1 Y N N N N N 19.873 69.213 22.115 -3.952 -0.351 0.033 C2 YWO 4 YWO N2 N2 N 0 1 N N N N N N 22.209 70.724 30.355 4.482 -1.278 -1.130 N2 YWO 5 YWO O2 O2 O 0 1 N N N N N N 19.820 67.122 21.014 -5.501 -2.102 0.135 O2 YWO 6 YWO C3 C3 C 0 1 Y N N N N N 20.370 70.002 23.196 -2.614 0.016 0.011 C3 YWO 7 YWO N3 N3 N 0 1 N N N N N N 24.700 73.410 30.672 6.571 0.380 1.387 N3 YWO 8 YWO O3 O3 O -1 1 N N N N N N 20.782 67.147 23.045 -3.460 -2.635 0.166 O3 YWO 9 YWO C4 C4 C 0 1 Y N N N N N 20.093 71.424 23.252 -2.266 1.357 -0.068 C4 YWO 10 YWO O4 O4 O 0 1 N N N N N N 24.752 71.228 31.315 6.790 -0.007 -0.786 O4 YWO 11 YWO C5 C5 C 0 1 Y N N N N N 19.339 72.013 22.245 -3.252 2.323 -0.124 C5 YWO 12 YWO C6 C6 C 0 1 Y N N N N N 18.843 71.236 21.184 -4.584 1.955 -0.102 C6 YWO 13 YWO C7 C7 C 0 1 Y N N N N N 21.801 69.944 25.188 -0.349 -0.529 0.054 C7 YWO 14 YWO C8 C8 C 0 1 Y N N N N N 21.302 69.669 26.430 0.306 -0.258 1.247 C8 YWO 15 YWO C9 C9 C 0 1 Y N N N N N 21.986 70.171 27.602 1.624 0.155 1.232 C9 YWO 16 YWO C10 C10 C 0 1 Y N N N N N 23.184 70.954 27.428 2.290 0.299 0.030 C10 YWO 17 YWO C11 C11 C 0 1 Y N N N N N 23.687 71.254 26.113 1.640 0.031 -1.161 C11 YWO 18 YWO C12 C12 C 0 1 Y N N N N N 22.994 70.754 24.975 0.324 -0.388 -1.151 C12 YWO 19 YWO C13 C13 C 0 1 N N N N N N 19.057 73.426 22.286 -2.875 3.780 -0.210 C13 YWO 20 YWO C14 C14 C 0 1 N N N N N N 23.950 71.447 28.660 3.728 0.751 0.016 C14 YWO 21 YWO C15 C15 C 0 1 N N R N N N 23.103 71.841 29.897 4.647 -0.471 0.086 C15 YWO 22 YWO C16 C16 C 0 1 N N N N N N 24.045 72.238 31.019 6.080 -0.016 0.197 C16 YWO 23 YWO H1 H1 H 0 1 N N N N N N 18.722 69.231 20.287 -5.975 0.333 -0.011 H1 YWO 24 YWO HN2 HN2 H 0 1 N N N N N N 21.684 71.022 31.152 3.545 -1.649 -1.193 HN2 YWO 25 YWO HN2A HN2A H 0 0 N N N N N N 21.582 70.475 29.617 4.716 -0.744 -1.953 HN2A YWO 26 YWO HN3 HN3 H 0 1 N N N N N N 25.699 73.440 30.661 7.493 0.672 1.459 HN3 YWO 27 YWO HN3A HN3A H 0 0 N N N N N N 24.173 74.225 30.433 6.003 0.372 2.174 HN3A YWO 28 YWO H4 H4 H 0 1 N N N N N N 20.470 72.020 24.070 -1.225 1.646 -0.085 H4 YWO 29 YWO H6 H6 H 0 1 N N N N N N 18.253 71.708 20.412 -5.354 2.711 -0.146 H6 YWO 30 YWO H8 H8 H 0 1 N N N N N N 20.403 69.081 26.536 -0.215 -0.370 2.187 H8 YWO 31 YWO H9 H9 H 0 1 N N N N N N 21.605 69.963 28.591 2.134 0.366 2.161 H9 YWO 32 YWO H11 H11 H 0 1 N N N N N N 24.579 71.851 25.992 2.163 0.144 -2.099 H11 YWO 33 YWO H12 H12 H 0 1 N N N N N N 23.344 70.970 23.976 -0.182 -0.602 -2.081 H12 YWO 34 YWO H13 H13 H 0 1 N N N N N N 19.850 73.974 21.756 -2.785 4.071 -1.257 H13 YWO 35 YWO H13A H13A H 0 0 N N N N N N 18.090 73.621 21.800 -3.646 4.383 0.269 H13A YWO 36 YWO H13B H13B H 0 0 N N N N N N 19.016 73.761 23.333 -1.923 3.939 0.295 H13B YWO 37 YWO H14 H14 H 0 1 N N N N N N 24.636 70.645 28.968 3.927 1.303 -0.902 H14 YWO 38 YWO H14A H14A H 0 0 N N N N N N 24.531 72.331 28.359 3.915 1.395 0.875 H14A YWO 39 YWO H15 H15 H 0 1 N N N N N N 22.483 72.710 29.631 4.388 -1.071 0.959 H15 YWO 40 # 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 YWO C1 C2 DOUB Y N 1 YWO C1 C6 SING Y N 2 YWO N1 C2 SING N N 3 YWO N1 O2 DOUB N N 4 YWO N1 O3 SING N N 5 YWO O1 C3 SING N N 6 YWO O1 C7 SING N N 7 YWO C2 C3 SING Y N 8 YWO N2 C15 SING N N 9 YWO C3 C4 DOUB Y N 10 YWO N3 C16 SING N N 11 YWO C4 C5 SING Y N 12 YWO O4 C16 DOUB N N 13 YWO C5 C6 DOUB Y N 14 YWO C5 C13 SING N N 15 YWO C7 C8 DOUB Y N 16 YWO C7 C12 SING Y N 17 YWO C8 C9 SING Y N 18 YWO C9 C10 DOUB Y N 19 YWO C10 C11 SING Y N 20 YWO C10 C14 SING N N 21 YWO C11 C12 DOUB Y N 22 YWO C14 C15 SING N N 23 YWO C15 C16 SING N N 24 YWO C1 H1 SING N N 25 YWO N2 HN2 SING N N 26 YWO N2 HN2A SING N N 27 YWO N3 HN3 SING N N 28 YWO N3 HN3A SING N N 29 YWO C4 H4 SING N N 30 YWO C6 H6 SING N N 31 YWO C8 H8 SING N N 32 YWO C9 H9 SING N N 33 YWO C11 H11 SING N N 34 YWO C12 H12 SING N N 35 YWO C13 H13 SING N N 36 YWO C13 H13A SING N N 37 YWO C13 H13B SING N N 38 YWO C14 H14 SING N N 39 YWO C14 H14A SING N N 40 YWO C15 H15 SING N N 41 # 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 YWO SMILES ACDLabs 12.01 O=C(N)C(N)Cc2ccc(Oc1cc(ccc1[N+]([O-])=O)C)cc2 YWO InChI InChI 1.03 InChI=1S/C16H17N3O4/c1-10-2-7-14(19(21)22)15(8-10)23-12-5-3-11(4-6-12)9-13(17)16(18)20/h2-8,13H,9,17H2,1H3,(H2,18,20)/t13-/m1/s1 YWO InChIKey InChI 1.03 YQBKHPZUMXXXFB-CYBMUJFWSA-N YWO SMILES_CANONICAL CACTVS 3.385 Cc1ccc(c(Oc2ccc(C[C@@H](N)C(N)=O)cc2)c1)[N+]([O-])=O YWO SMILES CACTVS 3.385 Cc1ccc(c(Oc2ccc(C[CH](N)C(N)=O)cc2)c1)[N+]([O-])=O YWO SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 Cc1ccc(c(c1)Oc2ccc(cc2)C[C@H](C(=O)N)N)[N+](=O)[O-] YWO SMILES "OpenEye OEToolkits" 1.7.6 Cc1ccc(c(c1)Oc2ccc(cc2)CC(C(=O)N)N)[N+](=O)[O-] # 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 YWO "SYSTEMATIC NAME" ACDLabs 12.01 O-(5-methyl-2-nitrophenyl)-D-tyrosinamide YWO "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 (2R)-2-azanyl-3-[4-(5-methyl-2-nitro-phenoxy)phenyl]propanamide # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site YWO 'Create component' 2014-08-20 EBI YWO 'Initial release' 2014-10-08 RCSB # loop_ _software.name _software.version _software.description rdkit 2023.03.3 'Core functionality.' pdbeccdutils 0.8.4 'Wrapper to provide 2D templates and molecular fragments.' # loop_ _pdbe_chem_comp_atom_depiction.comp_id _pdbe_chem_comp_atom_depiction.atom_id _pdbe_chem_comp_atom_depiction.element _pdbe_chem_comp_atom_depiction.model_Cartn_x _pdbe_chem_comp_atom_depiction.model_Cartn_y _pdbe_chem_comp_atom_depiction.pdbx_ordinal YWO C1 C 5.598 -5.107 1 YWO N1 N 4.299 -2.857 2 YWO O1 O 6.897 -1.357 3 YWO C2 C 5.598 -3.607 4 YWO N2 N 10.794 3.893 5 YWO O2 O 3.000 -3.607 6 YWO C3 C 6.897 -2.857 7 YWO N3 N 14.691 3.143 8 YWO O3 O 4.299 -1.357 9 YWO C4 C 8.196 -3.607 10 YWO O4 O 13.392 5.393 11 YWO C5 C 8.196 -5.107 12 YWO C6 C 6.897 -5.857 13 YWO C7 C 8.196 -0.608 14 YWO C8 C 8.196 0.892 15 YWO C9 C 9.495 1.643 16 YWO C10 C 10.794 0.892 17 YWO C11 C 10.794 -0.608 18 YWO C12 C 9.495 -1.357 19 YWO C13 C 9.495 -5.857 20 YWO C14 C 12.093 1.643 21 YWO C15 C 12.093 3.143 22 YWO C16 C 13.392 3.893 23 # loop_ _pdbe_chem_comp_bond_depiction.comp_id _pdbe_chem_comp_bond_depiction.atom_id_1 _pdbe_chem_comp_bond_depiction.atom_id_2 _pdbe_chem_comp_bond_depiction.value_order _pdbe_chem_comp_bond_depiction.bond_dir _pdbe_chem_comp_bond_depiction.pdbx_ordinal YWO C1 C2 DOUBLE NONE 1 YWO C1 C6 SINGLE NONE 2 YWO N1 C2 SINGLE NONE 3 YWO N1 O2 DOUBLE NONE 4 YWO N1 O3 SINGLE NONE 5 YWO O1 C3 SINGLE NONE 6 YWO O1 C7 SINGLE NONE 7 YWO C2 C3 SINGLE NONE 8 YWO C15 N2 SINGLE BEGINWEDGE 9 YWO C3 C4 DOUBLE NONE 10 YWO N3 C16 SINGLE NONE 11 YWO C4 C5 SINGLE NONE 12 YWO O4 C16 DOUBLE NONE 13 YWO C5 C6 DOUBLE NONE 14 YWO C5 C13 SINGLE NONE 15 YWO C7 C8 DOUBLE NONE 16 YWO C7 C12 SINGLE NONE 17 YWO C8 C9 SINGLE NONE 18 YWO C9 C10 DOUBLE NONE 19 YWO C10 C11 SINGLE NONE 20 YWO C10 C14 SINGLE NONE 21 YWO C11 C12 DOUBLE NONE 22 YWO C14 C15 SINGLE NONE 23 YWO C15 C16 SINGLE NONE 24 # loop_ _pdbe_chem_comp_substructure.comp_id _pdbe_chem_comp_substructure.substructure_name _pdbe_chem_comp_substructure.id _pdbe_chem_comp_substructure.substructure_type _pdbe_chem_comp_substructure.substructure_smiles _pdbe_chem_comp_substructure.substructure_inchis _pdbe_chem_comp_substructure.substructure_inchikeys YWO MurckoScaffold S1 scaffold c1ccc(Oc2ccccc2)cc1 InChI=1S/C12H10O/c1-3-7-11(8-4-1)13-12-9-5-2-6-10-12/h1-10H USIUVYZYUHIAEV-UHFFFAOYSA-N YWO amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N YWO peptide F2 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N YWO phenyl F3 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N # loop_ _pdbe_chem_comp_substructure_mapping.comp_id _pdbe_chem_comp_substructure_mapping.atom_id _pdbe_chem_comp_substructure_mapping.substructure_id _pdbe_chem_comp_substructure_mapping.substructure_ordinal YWO C1 S1 1 YWO O1 S1 1 YWO C2 S1 1 YWO C3 S1 1 YWO C4 S1 1 YWO C5 S1 1 YWO C6 S1 1 YWO C7 S1 1 YWO C8 S1 1 YWO C9 S1 1 YWO C10 S1 1 YWO C11 S1 1 YWO C12 S1 1 YWO N3 F1 1 YWO C16 F1 1 YWO O4 F1 1 YWO C15 F1 1 YWO O4 F2 1 YWO C16 F2 1 YWO C15 F2 1 YWO N2 F2 1 YWO C1 F3 1 YWO C2 F3 1 YWO C3 F3 1 YWO C4 F3 1 YWO C5 F3 1 YWO C6 F3 1 YWO C7 F3 2 YWO C8 F3 2 YWO C9 F3 2 YWO C10 F3 2 YWO C11 F3 2 YWO C12 F3 2 # _pdbe_chem_comp_rdkit_properties.comp_id YWO _pdbe_chem_comp_rdkit_properties.exactmw 315.122 _pdbe_chem_comp_rdkit_properties.amw 315.329 _pdbe_chem_comp_rdkit_properties.lipinskiHBA 7 _pdbe_chem_comp_rdkit_properties.lipinskiHBD 4 _pdbe_chem_comp_rdkit_properties.NumRotatableBonds 8 _pdbe_chem_comp_rdkit_properties.NumHBD 2 _pdbe_chem_comp_rdkit_properties.NumHBA 5 _pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 23 _pdbe_chem_comp_rdkit_properties.NumAtoms 40 _pdbe_chem_comp_rdkit_properties.NumHeteroatoms 7 _pdbe_chem_comp_rdkit_properties.NumAmideBonds 1 _pdbe_chem_comp_rdkit_properties.FractionCSP3 0.188 _pdbe_chem_comp_rdkit_properties.NumRings 2 _pdbe_chem_comp_rdkit_properties.NumAromaticRings 2 _pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0 _pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0 _pdbe_chem_comp_rdkit_properties.NumHeterocycles 0 _pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0 _pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0 _pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 0 _pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0 _pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0 _pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 1 _pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0 _pdbe_chem_comp_rdkit_properties.labuteASA 156.673 _pdbe_chem_comp_rdkit_properties.tpsa 121.480 _pdbe_chem_comp_rdkit_properties.CrippenClogP 0.636 _pdbe_chem_comp_rdkit_properties.CrippenMR 82.647 _pdbe_chem_comp_rdkit_properties.chi0v 10.975 _pdbe_chem_comp_rdkit_properties.chi1v 5.648 _pdbe_chem_comp_rdkit_properties.chi2v 2.194 _pdbe_chem_comp_rdkit_properties.chi3v 2.194 _pdbe_chem_comp_rdkit_properties.chi4v 1.273 _pdbe_chem_comp_rdkit_properties.chi0n 27.975 _pdbe_chem_comp_rdkit_properties.chi1n 13.937 _pdbe_chem_comp_rdkit_properties.chi2n 2.194 _pdbe_chem_comp_rdkit_properties.chi3n 2.194 _pdbe_chem_comp_rdkit_properties.chi4n 1.273 _pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.930 _pdbe_chem_comp_rdkit_properties.kappa1 5.036 _pdbe_chem_comp_rdkit_properties.kappa2 6.887 _pdbe_chem_comp_rdkit_properties.kappa3 4.271 _pdbe_chem_comp_rdkit_properties.Phi 1.508 # loop_ _pdbe_chem_comp_external_mappings.comp_id _pdbe_chem_comp_external_mappings.source _pdbe_chem_comp_external_mappings.resource _pdbe_chem_comp_external_mappings.resource_id YWO UniChem PDBe YWO YWO UniChem ZINC ZINC000213030897 YWO UniChem PubChem 78350473 # loop_ _pdbe_chem_comp_rdkit_conformer.comp_id _pdbe_chem_comp_rdkit_conformer.atom_id _pdbe_chem_comp_rdkit_conformer.Cartn_x_rdkit _pdbe_chem_comp_rdkit_conformer.Cartn_y_rdkit _pdbe_chem_comp_rdkit_conformer.Cartn_z_rdkit _pdbe_chem_comp_rdkit_conformer.rdkit_method _pdbe_chem_comp_rdkit_conformer.rdkit_ordinal YWO C1 -4.878 0.647 -1.884 ETKDGv3 1 YWO N1 -3.153 0.652 -3.583 ETKDGv3 2 YWO O1 -1.399 -0.637 -1.618 ETKDGv3 3 YWO C2 -3.613 0.354 -2.247 ETKDGv3 4 YWO N2 5.355 0.942 2.133 ETKDGv3 5 YWO O2 -3.951 1.053 -4.457 ETKDGv3 6 YWO C3 -2.701 -0.274 -1.242 ETKDGv3 7 YWO N3 5.576 -0.530 -0.519 ETKDGv3 8 YWO O3 -1.825 0.527 -3.917 ETKDGv3 9 YWO C4 -3.159 -0.542 -0.004 ETKDGv3 10 YWO O4 4.417 1.402 -1.089 ETKDGv3 11 YWO C5 -4.541 -0.187 0.387 ETKDGv3 12 YWO C6 -5.361 0.362 -0.520 ETKDGv3 13 YWO C7 -0.266 -0.569 -0.794 ETKDGv3 14 YWO C8 0.775 -1.369 -1.058 ETKDGv3 15 YWO C9 1.990 -1.321 -0.219 ETKDGv3 16 YWO C10 2.066 -0.469 0.818 ETKDGv3 17 YWO C11 0.928 0.441 1.093 ETKDGv3 18 YWO C12 -0.172 0.398 0.332 ETKDGv3 19 YWO C13 -5.040 -0.517 1.762 ETKDGv3 20 YWO C14 3.312 -0.385 1.662 ETKDGv3 21 YWO C15 4.225 0.778 1.215 ETKDGv3 22 YWO C16 4.738 0.580 -0.189 ETKDGv3 23 YWO H1 -5.567 1.104 -2.583 ETKDGv3 24 YWO HN2 4.986 1.242 3.065 ETKDGv3 25 YWO HN2A 5.832 0.022 2.274 ETKDGv3 26 YWO HN3 5.851 -1.232 0.202 ETKDGv3 27 YWO HN3A 5.918 -0.655 -1.498 ETKDGv3 28 YWO H4 -2.524 -1.046 0.714 ETKDGv3 29 YWO H6 -6.386 0.602 -0.264 ETKDGv3 30 YWO H8 0.730 -2.064 -1.887 ETKDGv3 31 YWO H9 2.817 -1.979 -0.456 ETKDGv3 32 YWO H11 0.990 1.155 1.905 ETKDGv3 33 YWO H12 -0.980 1.089 0.530 ETKDGv3 34 YWO H13 -5.571 -1.492 1.740 ETKDGv3 35 YWO H13A -4.194 -0.585 2.478 ETKDGv3 36 YWO H13B -5.735 0.269 2.126 ETKDGv3 37 YWO H14 3.011 -0.225 2.720 ETKDGv3 38 YWO H14A 3.868 -1.348 1.635 ETKDGv3 39 YWO H15 3.627 1.717 1.241 ETKDGv3 40 #