data_HDI
#
_chem_comp.id HDI
_chem_comp.name "3-(4-HYDROXYPHENYL)-4,5-DIHYDRO-5-ISOXAZOLE-ACETIC ACID METHYL ESTER"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C12 H13 N O4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2002-04-25
_chem_comp.pdbx_modified_date 2011-06-04
_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 235.236
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code HDI
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 1LJT
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
#
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
HDI C12 C12 C 0 1 N N N N N N -44.265 43.120 11.882 -0.068 -0.123 6.484 C12 HDI 1
HDI C11 C11 C 0 1 N N N N N N -42.859 42.623 9.960 0.206 0.049 4.085 C11 HDI 2
HDI O3 O3 O 0 1 N N N N N N -42.397 43.739 9.698 -0.761 0.772 4.054 O3 HDI 3
HDI O4 O4 O 0 1 N N N N N N -44.019 42.362 10.677 0.632 -0.451 5.256 O4 HDI 4
HDI C10 C10 C 0 1 N N N N N N -42.179 41.340 9.508 0.934 -0.290 2.810 C10 HDI 5
HDI N1 N1 N 0 1 N N N N N N -40.610 41.718 6.431 -1.276 -0.167 0.001 N1 HDI 6
HDI O2 O2 O 0 1 N N N N N N -41.080 42.313 7.495 -1.062 -0.150 1.398 O2 HDI 7
HDI C9 C9 C 0 1 N N R N N N -40.880 41.574 8.711 0.249 0.402 1.631 C9 HDI 8
HDI C8 C8 C 0 1 N N N N N N -40.168 40.304 8.230 0.969 0.076 0.302 C8 HDI 9
HDI C7 C7 C 0 1 N N N N N N -40.089 40.605 6.755 -0.182 -0.049 -0.675 C7 HDI 10
HDI O1 O1 O 0 1 N N N N N N -37.593 37.054 3.054 0.231 -0.007 -6.264 O1 HDI 11
HDI C5 C5 C 0 1 Y N N N N N -39.637 39.823 4.358 -1.220 -0.163 -2.935 C5 HDI 12
HDI C6 C6 C 0 1 Y N N N N N -39.439 39.663 5.745 -0.073 -0.038 -2.146 C6 HDI 13
HDI C1 C1 C 0 1 Y N N N N N -38.616 38.621 6.203 1.175 0.103 -2.755 C1 HDI 14
HDI C2 C2 C 0 1 Y N N N N N -38.008 37.760 5.310 1.273 0.107 -4.129 C2 HDI 15
HDI C3 C3 C 0 1 Y N N N N N -38.204 37.917 3.935 0.131 -0.017 -4.910 C3 HDI 16
HDI C4 C4 C 0 1 Y N N N N N -39.027 38.958 3.462 -1.113 -0.152 -4.308 C4 HDI 17
HDI H121 1H12 H 0 0 N N N N N N -44.223 44.208 11.642 0.419 -0.618 7.324 H121 HDI 18
HDI H122 2H12 H 0 0 N N N N N N -45.196 42.910 12.458 -0.049 0.955 6.637 H122 HDI 19
HDI H123 3H12 H 0 0 N N N N N N -43.387 43.017 12.562 -1.102 -0.462 6.414 H123 HDI 20
HDI H101 1H10 H 0 0 N N N N N N -42.887 40.703 8.928 1.967 0.048 2.881 H101 HDI 21
HDI H102 2H10 H 0 0 N N N N N N -41.991 40.667 10.377 0.915 -1.370 2.658 H102 HDI 22
HDI HC9 HC9 H 0 1 N N N N N N -40.271 42.122 9.468 0.195 1.479 1.792 HC9 HDI 23
HDI HC81 1HC8 H 0 0 N N N N N N -40.651 39.338 8.507 1.635 0.890 0.013 HC81 HDI 24
HDI HC82 2HC8 H 0 0 N N N N N N -39.202 40.064 8.733 1.516 -0.863 0.378 HC82 HDI 25
HDI HO1 HO1 H 0 1 N N N N N N -37.726 37.161 2.120 0.152 0.915 -6.543 HO1 HDI 26
HDI HC5 HC5 H 0 1 N N N N N N -40.276 40.634 3.970 -2.188 -0.268 -2.468 HC5 HDI 27
HDI HC1 HC1 H 0 1 N N N N N N -38.444 38.476 7.283 2.064 0.201 -2.149 HC1 HDI 28
HDI HC2 HC2 H 0 1 N N N N N N -37.367 36.949 5.694 2.239 0.212 -4.601 HC2 HDI 29
HDI HC4 HC4 H 0 1 N N N N N N -39.195 39.097 2.381 -1.999 -0.249 -4.919 HC4 HDI 30
#
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
HDI C12 O4 SING N N 1
HDI C12 H121 SING N N 2
HDI C12 H122 SING N N 3
HDI C12 H123 SING N N 4
HDI C11 O3 DOUB N N 5
HDI C11 O4 SING N N 6
HDI C11 C10 SING N N 7
HDI C10 C9 SING N N 8
HDI C10 H101 SING N N 9
HDI C10 H102 SING N N 10
HDI N1 O2 SING N N 11
HDI N1 C7 DOUB N N 12
HDI O2 C9 SING N N 13
HDI C9 C8 SING N N 14
HDI C9 HC9 SING N N 15
HDI C8 C7 SING N N 16
HDI C8 HC81 SING N N 17
HDI C8 HC82 SING N N 18
HDI C7 C6 SING N N 19
HDI O1 C3 SING N N 20
HDI O1 HO1 SING N N 21
HDI C5 C6 DOUB Y N 22
HDI C5 C4 SING Y N 23
HDI C5 HC5 SING N N 24
HDI C6 C1 SING Y N 25
HDI C1 C2 DOUB Y N 26
HDI C1 HC1 SING N N 27
HDI C2 C3 SING Y N 28
HDI C2 HC2 SING N N 29
HDI C3 C4 DOUB Y N 30
HDI C4 HC4 SING N N 31
#
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
HDI SMILES ACDLabs 10.04 O=C(OC)CC2ON=C(c1ccc(O)cc1)C2
HDI SMILES_CANONICAL CACTVS 3.341 COC(=O)C[C@H]1CC(=NO1)c2ccc(O)cc2
HDI SMILES CACTVS 3.341 COC(=O)C[CH]1CC(=NO1)c2ccc(O)cc2
HDI SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 COC(=O)C[C@H]1CC(=NO1)c2ccc(cc2)O
HDI SMILES "OpenEye OEToolkits" 1.5.0 COC(=O)CC1CC(=NO1)c2ccc(cc2)O
HDI InChI InChI 1.03 InChI=1S/C12H13NO4/c1-16-12(15)7-10-6-11(13-17-10)8-2-4-9(14)5-3-8/h2-5,10,14H,6-7H2,1H3/t10-/m1/s1
HDI InChIKey InChI 1.03 AIXMJTYHQHQJLU-SNVBAGLBSA-N
#
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
HDI "SYSTEMATIC NAME" ACDLabs 10.04 "methyl [(5R)-3-(4-hydroxyphenyl)-4,5-dihydroisoxazol-5-yl]acetate"
HDI "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "methyl 2-[(5R)-3-(4-hydroxyphenyl)-4,5-dihydro-1,2-oxazol-5-yl]ethanoate"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
HDI 'Create component' 2002-04-25 RCSB
HDI 'Modify descriptor' 2011-06-04 RCSB
#
_pdbe_chem_comp_drugbank_details.comp_id HDI
_pdbe_chem_comp_drugbank_details.drugbank_id DB07888
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name '3-(4-HYDROXYPHENYL)-4,5-DIHYDRO-5-ISOXAZOLE-ACETIC ACID METHYL ESTER'
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number ?
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
_pdbe_chem_comp_drugbank_classification.comp_id HDI
_pdbe_chem_comp_drugbank_classification.drugbank_id DB07888
_pdbe_chem_comp_drugbank_classification.parent '1-hydroxy-2-unsubstituted benzenoids'
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class Phenols
_pdbe_chem_comp_drugbank_classification.superclass Benzenoids
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as 1-hydroxy-2-unsubstituted benzenoids. These are phenols that a unsubstituted at the 2-position.'
#
_pdbe_chem_comp_drugbank_targets.comp_id HDI
_pdbe_chem_comp_drugbank_targets.drugbank_id DB07888
_pdbe_chem_comp_drugbank_targets.name 'Macrophage migration inhibitory factor'
_pdbe_chem_comp_drugbank_targets.organism Humans
_pdbe_chem_comp_drugbank_targets.uniprot_id P14174
_pdbe_chem_comp_drugbank_targets.pharmacologically_active unknown
_pdbe_chem_comp_drugbank_targets.ordinal 1
#
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
HDI C12 C 3.610 6.971 1
HDI C11 C 3.882 4.387 2
HDI O3 O 5.373 4.543 3
HDI O4 O 3.000 5.600 4
HDI C10 C 3.272 3.016 5
HDI N1 N 6.117 0.376 6
HDI O2 O 5.653 1.803 7
HDI C9 C 4.153 1.803 8
HDI C8 C 3.690 0.376 9
HDI C7 C 4.903 -0.505 10
HDI O1 O 4.903 -6.505 11
HDI C5 C 3.604 -2.756 12
HDI C6 C 4.903 -2.006 13
HDI C1 C 6.202 -2.756 14
HDI C2 C 6.202 -4.255 15
HDI C3 C 4.903 -5.005 16
HDI C4 C 3.604 -4.255 17
#
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
HDI C12 O4 SINGLE NONE 1
HDI C11 O3 DOUBLE NONE 2
HDI C11 O4 SINGLE NONE 3
HDI C11 C10 SINGLE NONE 4
HDI C9 C10 SINGLE BEGINDASH 5
HDI N1 O2 SINGLE NONE 6
HDI N1 C7 DOUBLE NONE 7
HDI O2 C9 SINGLE NONE 8
HDI C9 C8 SINGLE NONE 9
HDI C8 C7 SINGLE NONE 10
HDI C7 C6 SINGLE NONE 11
HDI O1 C3 SINGLE NONE 12
HDI C5 C6 DOUBLE NONE 13
HDI C5 C4 SINGLE NONE 14
HDI C6 C1 SINGLE NONE 15
HDI C1 C2 DOUBLE NONE 16
HDI C2 C3 SINGLE NONE 17
HDI C3 C4 DOUBLE NONE 18
#
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
HDI MurckoScaffold S1 scaffold c1ccc(C2=NOCC2)cc1 InChI=1S/C9H9NO/c1-2-4-8(5-3-1)9-6-7-11-10-9/h1-5H,6-7H2 UKFPAGCSDWQXFT-UHFFFAOYSA-N
HDI 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
HDI N1 S1 1
HDI O2 S1 1
HDI C9 S1 1
HDI C8 S1 1
HDI C7 S1 1
HDI C5 S1 1
HDI C6 S1 1
HDI C1 S1 1
HDI C2 S1 1
HDI C3 S1 1
HDI C4 S1 1
HDI C5 F1 1
HDI C6 F1 1
HDI C1 F1 1
HDI C2 F1 1
HDI C3 F1 1
HDI C4 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id HDI
_pdbe_chem_comp_rdkit_properties.exactmw 235.084
_pdbe_chem_comp_rdkit_properties.amw 235.239
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 17
_pdbe_chem_comp_rdkit_properties.NumAtoms 30
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.333
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1
_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 116.999
_pdbe_chem_comp_rdkit_properties.tpsa 68.120
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.931
_pdbe_chem_comp_rdkit_properties.CrippenMR 59.891
_pdbe_chem_comp_rdkit_properties.chi0v 8.080
_pdbe_chem_comp_rdkit_properties.chi1v 4.177
_pdbe_chem_comp_rdkit_properties.chi2v 1.607
_pdbe_chem_comp_rdkit_properties.chi3v 1.607
_pdbe_chem_comp_rdkit_properties.chi4v 0.944
_pdbe_chem_comp_rdkit_properties.chi0n 21.080
_pdbe_chem_comp_rdkit_properties.chi1n 10.585
_pdbe_chem_comp_rdkit_properties.chi2n 1.607
_pdbe_chem_comp_rdkit_properties.chi3n 1.607
_pdbe_chem_comp_rdkit_properties.chi4n 0.944
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.040
_pdbe_chem_comp_rdkit_properties.kappa1 3.476
_pdbe_chem_comp_rdkit_properties.kappa2 4.862
_pdbe_chem_comp_rdkit_properties.kappa3 2.747
_pdbe_chem_comp_rdkit_properties.Phi 0.994
#
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
HDI UniChem ChEMBL CHEMBL211769
HDI UniChem DrugBank DB07888
HDI UniChem PDBe HDI
HDI UniChem ZINC ZINC000100036051
HDI UniChem SureChEMBL SCHEMBL667764
HDI UniChem PubChem 5288525
HDI UniChem Nikkaji J1.787.546I
HDI UniChem BRENDA 78620
HDI UniChem 'Probes And Drugs' PD004919
HDI UniChem BindingDb 50186434
#
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
HDI C12 -3.291 1.528 0.728 ETKDGv3 1
HDI C11 -2.843 -0.833 1.310 ETKDGv3 2
HDI O3 -2.806 -0.560 2.541 ETKDGv3 3
HDI O4 -3.095 0.167 0.367 ETKDGv3 4
HDI C10 -2.575 -2.236 0.850 ETKDGv3 5
HDI N1 0.602 -1.229 1.638 ETKDGv3 6
HDI O2 -0.362 -2.175 1.866 ETKDGv3 7
HDI C9 -1.073 -2.526 0.689 ETKDGv3 8
HDI C8 -0.391 -1.679 -0.404 ETKDGv3 9
HDI C7 0.620 -0.912 0.389 ETKDGv3 10
HDI O1 4.177 2.975 -1.821 ETKDGv3 11
HDI C5 2.420 0.755 0.617 ETKDGv3 12
HDI C6 1.550 0.096 -0.174 ETKDGv3 13
HDI C1 1.532 0.400 -1.630 ETKDGv3 14
HDI C2 2.367 1.312 -2.143 ETKDGv3 15
HDI C3 3.316 2.029 -1.268 ETKDGv3 16
HDI C4 3.340 1.762 0.046 ETKDGv3 17
HDI H121 -2.385 1.919 1.239 ETKDGv3 18
HDI H122 -4.171 1.622 1.399 ETKDGv3 19
HDI H123 -3.472 2.126 -0.189 ETKDGv3 20
HDI H101 -3.092 -2.413 -0.118 ETKDGv3 21
HDI H102 -3.002 -2.947 1.590 ETKDGv3 22
HDI HC9 -0.925 -3.608 0.479 ETKDGv3 23
HDI HC81 0.121 -2.330 -1.144 ETKDGv3 24
HDI HC82 -1.091 -0.988 -0.921 ETKDGv3 25
HDI HO1 4.842 3.488 -1.254 ETKDGv3 26
HDI HC5 2.463 0.565 1.682 ETKDGv3 27
HDI HC1 0.846 -0.114 -2.291 ETKDGv3 28
HDI HC2 2.347 1.526 -3.204 ETKDGv3 29
HDI HC4 4.030 2.279 0.700 ETKDGv3 30
#