data_YTX
#
_chem_comp.id YTX
_chem_comp.name "2-(3-methoxy-4-oxidanyl-phenyl)ethanoic acid"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C9 H10 O4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2016-12-14
_chem_comp.pdbx_modified_date 2017-05-19
_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 182.173
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code YTX
_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 5MOH
_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
YTX C1 C1 C 0 1 Y N N N N N -123.446 -180.381 314.013 -1.583 0.369 -0.056 C1 YTX 1
YTX C2 C2 C 0 1 Y N N N N N -123.347 -181.212 312.906 -0.281 0.657 -0.431 C2 YTX 2
YTX C3 C3 C 0 1 Y N N N N N -123.512 -182.590 313.030 0.628 -0.369 -0.618 C3 YTX 3
YTX O1 O1 O 0 1 N N N N N N -122.550 -185.380 312.977 4.196 0.426 0.083 O1 YTX 4
YTX O2 O2 O 0 1 N N N N N N -122.925 -185.562 310.796 2.397 0.027 1.302 O2 YTX 5
YTX C4 C4 C 0 1 N N N N N N -123.477 -183.473 311.799 2.044 -0.054 -1.026 C4 YTX 6
YTX C5 C5 C 0 1 N N N N N N -122.956 -184.894 311.812 2.891 0.136 0.205 C5 YTX 7
YTX C6 C6 C 0 1 Y N N N N N -123.772 -183.114 314.287 0.240 -1.682 -0.429 C6 YTX 8
YTX C7 C7 C 0 1 Y N N N N N -123.868 -182.296 315.398 -1.058 -1.976 -0.054 C7 YTX 9
YTX C8 C8 C 0 1 Y N N N N N -123.702 -180.927 315.279 -1.973 -0.953 0.134 C8 YTX 10
YTX O3 O3 O 0 1 N N N N N N -123.794 -180.151 316.395 -3.250 -1.240 0.503 O3 YTX 11
YTX O O4 O 0 1 N N N N N N -123.329 -179.018 313.996 -2.476 1.377 0.133 O YTX 12
YTX C C9 C 0 1 N N N N N N -123.214 -178.370 312.728 -2.005 2.709 -0.079 C YTX 13
YTX H1 H1 H 0 1 N N N N N N -123.139 -180.785 311.936 0.025 1.682 -0.580 H1 YTX 14
YTX H2 H2 H 0 1 N N N N N N -122.257 -186.276 312.862 4.699 0.539 0.901 H2 YTX 15
YTX H3 H3 H 0 1 N N N N N N -122.867 -182.935 311.059 2.442 -0.877 -1.619 H3 YTX 16
YTX H4 H4 H 0 1 N N N N N N -124.516 -183.536 311.443 2.056 0.860 -1.620 H4 YTX 17
YTX H5 H5 H 0 1 N N N N N N -123.902 -184.180 314.401 0.953 -2.480 -0.575 H5 YTX 18
YTX H6 H6 H 0 1 N N N N N N -124.074 -182.729 316.366 -1.358 -3.003 0.093 H6 YTX 19
YTX H7 H7 H 0 1 N N N N N N -123.970 -180.700 317.150 -3.853 -1.376 -0.240 H7 YTX 20
YTX H8 H8 H 0 1 N N N N N N -123.128 -177.284 312.877 -1.181 2.917 0.603 H8 YTX 21
YTX H9 H9 H 0 1 N N N N N N -122.319 -178.740 312.207 -1.660 2.813 -1.108 H9 YTX 22
YTX H10 H10 H 0 1 N N N N N N -124.106 -178.588 312.123 -2.816 3.415 0.105 H10 YTX 23
#
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
YTX O2 C5 DOUB N N 1
YTX C4 C5 SING N N 2
YTX C4 C3 SING N N 3
YTX C5 O1 SING N N 4
YTX C O SING N N 5
YTX C2 C3 DOUB Y N 6
YTX C2 C1 SING Y N 7
YTX C3 C6 SING Y N 8
YTX O C1 SING N N 9
YTX C1 C8 DOUB Y N 10
YTX C6 C7 DOUB Y N 11
YTX C8 C7 SING Y N 12
YTX C8 O3 SING N N 13
YTX C2 H1 SING N N 14
YTX O1 H2 SING N N 15
YTX C4 H3 SING N N 16
YTX C4 H4 SING N N 17
YTX C6 H5 SING N N 18
YTX C7 H6 SING N N 19
YTX O3 H7 SING N N 20
YTX C H8 SING N N 21
YTX C H9 SING N N 22
YTX C H10 SING N N 23
#
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
YTX InChI InChI 1.03 InChI=1S/C9H10O4/c1-13-8-4-6(5-9(11)12)2-3-7(8)10/h2-4,10H,5H2,1H3,(H,11,12)
YTX InChIKey InChI 1.03 QRMZSPFSDQBLIX-UHFFFAOYSA-N
YTX SMILES_CANONICAL CACTVS 3.385 COc1cc(CC(O)=O)ccc1O
YTX SMILES CACTVS 3.385 COc1cc(CC(O)=O)ccc1O
YTX SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 COc1cc(ccc1O)CC(=O)O
YTX SMILES "OpenEye OEToolkits" 2.0.6 COc1cc(ccc1O)CC(=O)O
#
_pdbx_chem_comp_identifier.comp_id YTX
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.6
_pdbx_chem_comp_identifier.identifier "2-(3-methoxy-4-oxidanyl-phenyl)ethanoic 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
YTX 'Create component' 2016-12-14 EBI
YTX 'Initial release' 2017-05-24 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
YTX C1 C 6.404 1.965 1
YTX C2 C 7.702 1.215 2
YTX C3 C 7.702 -0.285 3
YTX O1 O 7.702 -3.285 4
YTX O2 O 10.301 -3.285 5
YTX C4 C 9.002 -1.035 6
YTX C5 C 9.002 -2.535 7
YTX C6 C 6.404 -1.035 8
YTX C7 C 5.104 -0.285 9
YTX C8 C 5.104 1.215 10
YTX O3 O 3.805 1.965 11
YTX O O 6.404 3.465 12
YTX C C 7.702 4.215 13
#
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
YTX O2 C5 DOUBLE NONE 1
YTX C4 C5 SINGLE NONE 2
YTX C4 C3 SINGLE NONE 3
YTX C5 O1 SINGLE NONE 4
YTX C O SINGLE NONE 5
YTX C2 C3 SINGLE NONE 6
YTX C2 C1 DOUBLE NONE 7
YTX C3 C6 DOUBLE NONE 8
YTX O C1 SINGLE NONE 9
YTX C1 C8 SINGLE NONE 10
YTX C6 C7 SINGLE NONE 11
YTX C8 C7 DOUBLE NONE 12
YTX C8 O3 SINGLE NONE 13
#
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
YTX MurckoScaffold S1 scaffold c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
YTX phenyl F1 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
YTX C1 S1 1
YTX C2 S1 1
YTX C3 S1 1
YTX C6 S1 1
YTX C7 S1 1
YTX C8 S1 1
YTX C1 F1 1
YTX C2 F1 1
YTX C3 F1 1
YTX C6 F1 1
YTX C7 F1 1
YTX C8 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id YTX
_pdbe_chem_comp_rdkit_properties.exactmw 182.058
_pdbe_chem_comp_rdkit_properties.amw 182.175
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 13
_pdbe_chem_comp_rdkit_properties.NumAtoms 23
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.222
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_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 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 89.613
_pdbe_chem_comp_rdkit_properties.tpsa 66.760
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.048
_pdbe_chem_comp_rdkit_properties.CrippenMR 44.513
_pdbe_chem_comp_rdkit_properties.chi0v 6.133
_pdbe_chem_comp_rdkit_properties.chi1v 3.021
_pdbe_chem_comp_rdkit_properties.chi2v 1.075
_pdbe_chem_comp_rdkit_properties.chi3v 1.075
_pdbe_chem_comp_rdkit_properties.chi4v 0.614
_pdbe_chem_comp_rdkit_properties.chi0n 16.133
_pdbe_chem_comp_rdkit_properties.chi1n 7.837
_pdbe_chem_comp_rdkit_properties.chi2n 1.075
_pdbe_chem_comp_rdkit_properties.chi3n 1.075
_pdbe_chem_comp_rdkit_properties.chi4n 0.614
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.710
_pdbe_chem_comp_rdkit_properties.kappa1 2.637
_pdbe_chem_comp_rdkit_properties.kappa2 3.799
_pdbe_chem_comp_rdkit_properties.kappa3 2.366
_pdbe_chem_comp_rdkit_properties.Phi 0.771
#
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
YTX UniChem ChEMBL CHEMBL1562
YTX UniChem PDBe YTX
YTX UniChem 'KEGG LIGAND' C05582
YTX UniChem ChEBI 545959
YTX UniChem ZINC ZINC000000388262
YTX UniChem fdasrs X77S6GMS36
YTX UniChem HMDB HMDB0000118
YTX UniChem MetaboLights MTBLC545959
YTX UniChem BRENDA 104994
YTX UniChem BRENDA 12554
YTX UniChem BRENDA 196478
YTX UniChem BRENDA 247952
YTX UniChem BRENDA 256594
YTX UniChem BRENDA 48614
YTX UniChem BRENDA 60399
YTX UniChem BRENDA 91496
YTX UniChem MedChemExpress HY-N0384
YTX UniChem 'Probes And Drugs' PD015277
YTX UniChem ChemicalBook CB7198081
YTX UniChem eMolecules 518529
YTX UniChem SureChEMBL SCHEMBL8792
YTX UniChem 'PubChem TPHARMA' 15462669
YTX UniChem PubChem 1738
YTX UniChem Mcule MCULE-8190136486
YTX UniChem NMRShiftDB 20200933
YTX UniChem ACTor 306-08-1
YTX UniChem Nikkaji J61.262F
YTX UniChem 'EPA CompTox Dashboard' DTXSID5059791
#
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
YTX C1 -1.312 0.463 0.403 ETKDGv3 1
YTX C2 -0.434 -0.410 -0.134 ETKDGv3 2
YTX C3 0.760 0.078 -0.867 ETKDGv3 3
YTX O1 2.502 -2.288 0.518 ETKDGv3 4
YTX O2 3.834 -0.603 -0.298 ETKDGv3 5
YTX C4 1.749 -0.909 -1.424 ETKDGv3 6
YTX C5 2.763 -1.261 -0.384 ETKDGv3 7
YTX C6 0.975 1.399 -0.976 ETKDGv3 8
YTX C7 0.015 2.358 -0.396 ETKDGv3 9
YTX C8 -1.071 1.918 0.258 ETKDGv3 10
YTX O3 -1.981 2.819 0.809 ETKDGv3 11
YTX O -2.456 0.048 1.104 ETKDGv3 12
YTX C -2.823 -1.310 1.329 ETKDGv3 13
YTX H1 -0.582 -1.477 -0.040 ETKDGv3 14
YTX H2 3.171 -2.528 1.240 ETKDGv3 15
YTX H3 1.220 -1.831 -1.748 ETKDGv3 16
YTX H4 2.257 -0.492 -2.321 ETKDGv3 17
YTX H5 1.852 1.777 -1.486 ETKDGv3 18
YTX H6 0.199 3.420 -0.502 ETKDGv3 19
YTX H7 -1.852 3.822 0.733 ETKDGv3 20
YTX H8 -2.984 -1.828 0.360 ETKDGv3 21
YTX H9 -3.769 -1.339 1.908 ETKDGv3 22
YTX H10 -2.034 -1.827 1.914 ETKDGv3 23
#