data_9CF # _chem_comp.id 9CF _chem_comp.name (3S)-6,8-dihydroxy-3-{[(2R,6R)-6-methyloxan-2-yl]methyl}-3,4-dihydro-1H-2-benzopyran-1-one _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C16 H20 O5" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2018-03-14 _chem_comp.pdbx_modified_date 2018-06-22 _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 292.327 _chem_comp.one_letter_code ? _chem_comp.three_letter_code 9CF _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 5ZH3 _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 9CF C15 C1 C 0 1 N N N N N N 75.340 406.777 29.796 4.047 1.850 -0.024 C15 9CF 1 9CF C14 C2 C 0 1 N N N N N N 74.259 406.647 28.760 5.272 1.106 -0.566 C14 9CF 2 9CF C13 C3 C 0 1 N N N N N N 74.639 405.647 27.691 5.318 -0.295 0.052 C13 9CF 3 9CF C12 C4 C 0 1 N N R N N N 74.839 404.311 28.340 4.009 -1.025 -0.260 C12 9CF 4 9CF C16 C5 C 0 1 N N N N N N 75.318 403.333 27.276 4.023 -2.404 0.404 C16 9CF 5 9CF O5 O1 O 0 1 N N N N N N 75.876 404.417 29.318 2.909 -0.265 0.244 O5 9CF 6 9CF C11 C6 C 0 1 N N R N N N 75.754 405.420 30.328 2.788 1.037 -0.333 C11 9CF 7 9CF C10 C7 C 0 1 N N N N N N 77.200 405.570 30.783 1.566 1.744 0.258 C10 9CF 8 9CF C7 C8 C 0 1 N N S N N N 77.496 404.832 32.088 0.296 0.999 -0.156 C7 9CF 9 9CF C6 C9 C 0 1 N N N N N N 78.536 403.763 31.765 -0.931 1.771 0.333 C6 9CF 10 9CF O3 O2 O 0 1 N N N N N N 76.274 404.288 32.619 0.296 -0.331 0.439 O3 9CF 11 9CF C8 C10 C 0 1 N N N N N N 76.417 403.437 33.669 -0.765 -1.104 0.089 C8 9CF 12 9CF O4 O3 O 0 1 N N N N N N 75.720 403.506 34.683 -0.629 -2.282 -0.177 O4 9CF 13 9CF C9 C11 C 0 1 Y N N N N N 77.417 402.468 33.521 -2.088 -0.453 0.046 C9 9CF 14 9CF C5 C12 C 0 1 Y N N N N N 78.451 402.647 32.592 -2.174 0.939 0.160 C5 9CF 15 9CF C4 C13 C 0 1 Y N N N N N 79.441 401.682 32.458 -3.398 1.547 0.114 C4 9CF 16 9CF C3 C14 C 0 1 Y N N N N N 79.414 400.543 33.239 -4.555 0.790 -0.042 C3 9CF 17 9CF O2 O4 O 0 1 N N N N N N 80.388 399.635 33.080 -5.763 1.407 -0.086 O2 9CF 18 9CF C2 C15 C 0 1 Y N N N N N 78.401 400.340 34.163 -4.483 -0.590 -0.154 C2 9CF 19 9CF C1 C16 C 0 1 Y N N N N N 77.409 401.308 34.291 -3.250 -1.221 -0.110 C1 9CF 20 9CF O1 O5 O 0 1 N N N N N N 76.394 401.181 35.179 -3.168 -2.571 -0.216 O1 9CF 21 9CF H1 H1 H 0 1 N N N N N N 76.214 407.267 29.343 4.145 1.975 1.054 H1 9CF 22 9CF H2 H2 H 0 1 N N N N N N 74.967 407.391 30.629 3.975 2.829 -0.499 H2 9CF 23 9CF H3 H3 H 0 1 N N N N N N 74.093 407.628 28.290 5.198 1.024 -1.650 H3 9CF 24 9CF H4 H4 H 0 1 N N N N N N 73.332 406.313 29.249 6.177 1.653 -0.302 H4 9CF 25 9CF H5 H5 H 0 1 N N N N N N 75.571 405.964 27.200 6.155 -0.851 -0.370 H5 9CF 26 9CF H6 H6 H 0 1 N N N N N N 73.835 405.580 26.943 5.442 -0.213 1.132 H6 9CF 27 9CF H7 H7 H 0 1 N N N N N N 73.899 403.955 28.786 3.907 -1.143 -1.339 H7 9CF 28 9CF H8 H8 H 0 1 N N N N N N 75.472 402.343 27.730 4.126 -2.286 1.483 H8 9CF 29 9CF H9 H9 H 0 1 N N N N N N 74.562 403.258 26.480 3.092 -2.924 0.183 H9 9CF 30 9CF H10 H10 H 0 1 N N N N N N 76.266 403.692 26.849 4.863 -2.983 0.021 H10 9CF 31 9CF H11 H11 H 0 1 N N N N N N 75.108 405.105 31.160 2.669 0.947 -1.413 H11 9CF 32 9CF H12 H12 H 0 1 N N N N N N 77.858 405.170 29.997 1.643 1.755 1.345 H12 9CF 33 9CF H13 H13 H 0 1 N N N N N N 77.412 406.639 30.929 1.524 2.768 -0.114 H13 9CF 34 9CF H14 H14 H 0 1 N N N N N N 77.932 405.544 32.805 0.262 0.912 -1.242 H14 9CF 35 9CF H15 H15 H 0 1 N N N N N N 78.392 403.438 30.724 -0.805 2.017 1.387 H15 9CF 36 9CF H16 H16 H 0 1 N N N N N N 79.537 404.205 31.876 -1.030 2.692 -0.242 H16 9CF 37 9CF H17 H17 H 0 1 N N N N N N 80.235 401.823 31.740 -3.467 2.621 0.201 H17 9CF 38 9CF H18 H18 H 0 1 N N N N N N 80.245 398.909 33.676 -6.043 1.661 -0.976 H18 9CF 39 9CF H19 H19 H 0 1 N N N N N N 78.382 399.448 34.772 -5.385 -1.172 -0.274 H19 9CF 40 9CF H20 H20 H 0 1 N N N N N N 75.902 401.993 35.216 -3.213 -3.035 0.631 H20 9CF 41 # 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 9CF C16 C12 SING N N 1 9CF C13 C12 SING N N 2 9CF C13 C14 SING N N 3 9CF C12 O5 SING N N 4 9CF C14 C15 SING N N 5 9CF O5 C11 SING N N 6 9CF C15 C11 SING N N 7 9CF C11 C10 SING N N 8 9CF C10 C7 SING N N 9 9CF C6 C7 SING N N 10 9CF C6 C5 SING N N 11 9CF C7 O3 SING N N 12 9CF C4 C5 DOUB Y N 13 9CF C4 C3 SING Y N 14 9CF C5 C9 SING Y N 15 9CF O3 C8 SING N N 16 9CF O2 C3 SING N N 17 9CF C3 C2 DOUB Y N 18 9CF C9 C8 SING N N 19 9CF C9 C1 DOUB Y N 20 9CF C8 O4 DOUB N N 21 9CF C2 C1 SING Y N 22 9CF C1 O1 SING N N 23 9CF C15 H1 SING N N 24 9CF C15 H2 SING N N 25 9CF C14 H3 SING N N 26 9CF C14 H4 SING N N 27 9CF C13 H5 SING N N 28 9CF C13 H6 SING N N 29 9CF C12 H7 SING N N 30 9CF C16 H8 SING N N 31 9CF C16 H9 SING N N 32 9CF C16 H10 SING N N 33 9CF C11 H11 SING N N 34 9CF C10 H12 SING N N 35 9CF C10 H13 SING N N 36 9CF C7 H14 SING N N 37 9CF C6 H15 SING N N 38 9CF C6 H16 SING N N 39 9CF C4 H17 SING N N 40 9CF O2 H18 SING N N 41 9CF C2 H19 SING N N 42 9CF O1 H20 SING N N 43 # 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 9CF SMILES ACDLabs 12.01 C1C(OC(CC1)C)CC2OC(=O)c3c(cc(cc3C2)O)O 9CF InChI InChI 1.03 InChI=1S/C16H20O5/c1-9-3-2-4-12(20-9)8-13-6-10-5-11(17)7-14(18)15(10)16(19)21-13/h5,7,9,12-13,17-18H,2-4,6,8H2,1H3/t9-,12-,13+/m1/s1 9CF InChIKey InChI 1.03 WOMKDMUZNBFXKG-WQAKAFBOSA-N 9CF SMILES_CANONICAL CACTVS 3.385 C[C@@H]1CCC[C@H](C[C@@H]2Cc3cc(O)cc(O)c3C(=O)O2)O1 9CF SMILES CACTVS 3.385 C[CH]1CCC[CH](C[CH]2Cc3cc(O)cc(O)c3C(=O)O2)O1 9CF SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 C[C@@H]1CCC[C@@H](O1)C[C@@H]2Cc3cc(cc(c3C(=O)O2)O)O 9CF SMILES "OpenEye OEToolkits" 2.0.6 CC1CCCC(O1)CC2Cc3cc(cc(c3C(=O)O2)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 9CF "SYSTEMATIC NAME" ACDLabs 12.01 (3S)-6,8-dihydroxy-3-{[(2R,6R)-6-methyloxan-2-yl]methyl}-3,4-dihydro-1H-2-benzopyran-1-one 9CF "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 (3~{S})-3-[[(2~{R},6~{R})-6-methyloxan-2-yl]methyl]-6,8-bis(oxidanyl)-3,4-dihydroisochromen-1-one # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site 9CF 'Create component' 2018-03-14 RCSB 9CF 'Initial release' 2018-06-27 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 9CF C15 C 12.999 0.237 1 9CF C14 C 14.298 -0.513 2 9CF C13 C 15.598 0.237 3 9CF C12 C 15.598 1.737 4 9CF C16 C 16.897 2.487 5 9CF O5 O 14.298 2.487 6 9CF C11 C 12.999 1.737 7 9CF C10 C 11.700 2.487 8 9CF C7 C 10.402 1.737 9 9CF C6 C 9.102 2.487 10 9CF O3 O 10.402 0.237 11 9CF C8 C 9.102 -0.513 12 9CF O4 O 9.102 -2.013 13 9CF C9 C 7.803 0.237 14 9CF C5 C 7.803 1.737 15 9CF C4 C 6.463 2.539 16 9CF C3 C 5.103 1.768 17 9CF O2 O 3.807 2.523 18 9CF C2 C 5.103 0.206 19 9CF C1 C 6.463 -0.565 20 9CF O1 O 6.480 -2.065 21 # 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 9CF C12 C16 SINGLE BEGINDASH 1 9CF C13 C12 SINGLE NONE 2 9CF C13 C14 SINGLE NONE 3 9CF C12 O5 SINGLE NONE 4 9CF C14 C15 SINGLE NONE 5 9CF O5 C11 SINGLE NONE 6 9CF C15 C11 SINGLE NONE 7 9CF C11 C10 SINGLE BEGINDASH 8 9CF C7 C10 SINGLE BEGINWEDGE 9 9CF C6 C7 SINGLE NONE 10 9CF C6 C5 SINGLE NONE 11 9CF C7 O3 SINGLE NONE 12 9CF C4 C5 DOUBLE NONE 13 9CF C4 C3 SINGLE NONE 14 9CF C5 C9 SINGLE NONE 15 9CF O3 C8 SINGLE NONE 16 9CF O2 C3 SINGLE NONE 17 9CF C3 C2 DOUBLE NONE 18 9CF C9 C8 SINGLE NONE 19 9CF C9 C1 DOUBLE NONE 20 9CF C8 O4 DOUBLE NONE 21 9CF C2 C1 SINGLE NONE 22 9CF C1 O1 SINGLE NONE 23 # 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 9CF MurckoScaffold S1 scaffold 'O=C1O[C@H](C[C@H]2CCCCO2)Cc2ccccc21' InChI=1S/C15H18O3/c16-15-14-7-2-1-5-11(14)9-13(18-15)10-12-6-3-4-8-17-12/h1-2,5,7,12-13H,3-4,6,8-10H2/t12-,13+/m1/s1 DNDDTJZAZCEBSE-OLZOCXBDSA-N 9CF 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 9CF C15 S1 1 9CF C14 S1 1 9CF C13 S1 1 9CF C12 S1 1 9CF O5 S1 1 9CF C11 S1 1 9CF C10 S1 1 9CF C7 S1 1 9CF C6 S1 1 9CF O3 S1 1 9CF C8 S1 1 9CF O4 S1 1 9CF C9 S1 1 9CF C5 S1 1 9CF C4 S1 1 9CF C3 S1 1 9CF C2 S1 1 9CF C1 S1 1 9CF C9 F1 1 9CF C5 F1 1 9CF C4 F1 1 9CF C3 F1 1 9CF C2 F1 1 9CF C1 F1 1 # _pdbe_chem_comp_rdkit_properties.comp_id 9CF _pdbe_chem_comp_rdkit_properties.exactmw 292.131 _pdbe_chem_comp_rdkit_properties.amw 292.331 _pdbe_chem_comp_rdkit_properties.lipinskiHBA 5 _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 5 _pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 21 _pdbe_chem_comp_rdkit_properties.NumAtoms 41 _pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5 _pdbe_chem_comp_rdkit_properties.NumAmideBonds 0 _pdbe_chem_comp_rdkit_properties.FractionCSP3 0.562 _pdbe_chem_comp_rdkit_properties.NumRings 3 _pdbe_chem_comp_rdkit_properties.NumAromaticRings 1 _pdbe_chem_comp_rdkit_properties.NumAliphaticRings 2 _pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1 _pdbe_chem_comp_rdkit_properties.NumHeterocycles 2 _pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0 _pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1 _pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 2 _pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0 _pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 0 _pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 3 _pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0 _pdbe_chem_comp_rdkit_properties.labuteASA 151.319 _pdbe_chem_comp_rdkit_properties.tpsa 75.990 _pdbe_chem_comp_rdkit_properties.CrippenClogP 1.493 _pdbe_chem_comp_rdkit_properties.CrippenMR 73.730 _pdbe_chem_comp_rdkit_properties.chi0v 10.041 _pdbe_chem_comp_rdkit_properties.chi1v 5.429 _pdbe_chem_comp_rdkit_properties.chi2v 2.363 _pdbe_chem_comp_rdkit_properties.chi3v 2.363 _pdbe_chem_comp_rdkit_properties.chi4v 1.572 _pdbe_chem_comp_rdkit_properties.chi0n 30.041 _pdbe_chem_comp_rdkit_properties.chi1n 15.245 _pdbe_chem_comp_rdkit_properties.chi2n 2.363 _pdbe_chem_comp_rdkit_properties.chi3n 2.363 _pdbe_chem_comp_rdkit_properties.chi4n 1.572 _pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.750 _pdbe_chem_comp_rdkit_properties.kappa1 3.768 _pdbe_chem_comp_rdkit_properties.kappa2 5.561 _pdbe_chem_comp_rdkit_properties.kappa3 2.975 _pdbe_chem_comp_rdkit_properties.Phi 0.998 # 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 9CF UniChem ChEMBL CHEMBL4215398 9CF UniChem PDBe 9CF 9CF UniChem PubChem 92276885 9CF UniChem Nikkaji J3.558.445E 9CF UniChem BindingDb 50457626 # 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 9CF C15 -1.879 1.945 -0.296 ETKDGv3 1 9CF C14 -3.377 2.103 0.008 ETKDGv3 2 9CF C13 -3.852 1.035 0.995 ETKDGv3 3 9CF C12 -3.495 -0.391 0.482 ETKDGv3 4 9CF C16 -4.740 -1.103 -0.048 ETKDGv3 5 9CF O5 -2.518 -0.380 -0.552 ETKDGv3 6 9CF C11 -1.435 0.465 -0.208 ETKDGv3 7 9CF C10 -0.247 0.196 -1.150 ETKDGv3 8 9CF C7 0.256 -1.267 -1.120 ETKDGv3 9 9CF C6 0.971 -1.640 0.198 ETKDGv3 10 9CF O3 1.135 -1.484 -2.229 ETKDGv3 11 9CF C8 2.479 -1.094 -2.207 ETKDGv3 12 9CF O4 3.146 -1.126 -3.275 ETKDGv3 13 9CF C9 3.097 -0.694 -0.921 ETKDGv3 14 9CF C5 2.300 -0.936 0.311 ETKDGv3 15 9CF C4 2.804 -0.605 1.511 ETKDGv3 16 9CF C3 4.133 0.028 1.612 ETKDGv3 17 9CF O2 4.629 0.379 2.867 ETKDGv3 18 9CF C2 4.851 0.256 0.502 ETKDGv3 19 9CF C1 4.317 -0.120 -0.828 ETKDGv3 20 9CF O1 5.080 0.132 -1.967 ETKDGv3 21 9CF H1 -1.287 2.543 0.432 ETKDGv3 22 9CF H2 -1.685 2.364 -1.308 ETKDGv3 23 9CF H3 -3.574 3.115 0.422 ETKDGv3 24 9CF H4 -3.958 2.001 -0.936 ETKDGv3 25 9CF H5 -4.943 1.151 1.172 ETKDGv3 26 9CF H6 -3.345 1.207 1.970 ETKDGv3 27 9CF H7 -3.113 -0.997 1.336 ETKDGv3 28 9CF H8 -5.499 -1.204 0.757 ETKDGv3 29 9CF H9 -5.179 -0.533 -0.895 ETKDGv3 30 9CF H10 -4.470 -2.120 -0.403 ETKDGv3 31 9CF H11 -1.099 0.270 0.836 ETKDGv3 32 9CF H12 0.587 0.888 -0.901 ETKDGv3 33 9CF H13 -0.565 0.427 -2.191 ETKDGv3 34 9CF H14 -0.615 -1.945 -1.248 ETKDGv3 35 9CF H15 1.163 -2.734 0.198 ETKDGv3 36 9CF H16 0.324 -1.427 1.073 ETKDGv3 37 9CF H17 2.244 -0.803 2.417 ETKDGv3 38 9CF H18 5.537 0.814 2.980 ETKDGv3 39 9CF H19 5.827 0.719 0.572 ETKDGv3 40 9CF H20 5.994 0.564 -1.903 ETKDGv3 41 #