data_RKY
#
_chem_comp.id RKY
_chem_comp.name "4-(3,4-dihydro-2H-1,5-benzodioxepin-7-yl)-4-oxobutanoic acid"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C13 H14 O5"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2020-02-13
_chem_comp.pdbx_modified_date 2020-07-10
_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 250.247
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code RKY
_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 6VSF
_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
RKY C10 C1 C 0 1 Y N N N N N 10.701 6.555 28.661 1.312 1.727 -0.260 C10 RKY 1
RKY C13 C2 C 0 1 N N N N N N 7.581 5.881 27.064 4.509 1.153 0.687 C13 RKY 2
RKY C15 C3 C 0 1 N N N N N N 8.057 7.893 25.717 4.179 -1.351 0.649 C15 RKY 3
RKY C17 C4 C 0 1 Y N N N N N 9.311 8.253 27.695 2.222 -0.503 -0.382 C17 RKY 4
RKY O01 O1 O 0 1 N N N N N N 14.824 12.671 29.517 -6.407 -0.232 0.250 O01 RKY 5
RKY C02 C5 C 0 1 N N N N N N 14.453 11.464 29.587 -5.168 0.277 0.172 C02 RKY 6
RKY O03 O2 O 0 1 N N N N N N 14.403 10.773 28.562 -5.004 1.474 0.185 O03 RKY 7
RKY C04 C6 C 0 1 N N N N N N 14.069 10.826 30.937 -3.980 -0.645 0.069 C04 RKY 8
RKY C05 C7 C 0 1 N N N N N N 13.143 9.569 30.794 -2.696 0.184 -0.006 C05 RKY 9
RKY C06 C8 C 0 1 N N N N N N 11.829 9.946 29.991 -1.508 -0.738 -0.109 C06 RKY 10
RKY O07 O3 O 0 1 N N N N N N 11.484 11.066 29.952 -1.672 -1.940 -0.122 O07 RKY 11
RKY C08 C9 C 0 1 Y N N N N N 11.043 8.849 29.228 -0.152 -0.181 -0.195 C08 RKY 12
RKY C09 C10 C 0 1 Y N N N N N 11.397 7.505 29.350 0.040 1.206 -0.180 C09 RKY 13
RKY C11 C11 C 0 1 Y N N N N N 9.648 6.920 27.833 2.405 0.876 -0.361 C11 RKY 14
RKY O12 O4 O 0 1 N N N N N N 8.986 5.875 27.114 3.665 1.388 -0.442 O12 RKY 15
RKY C14 C12 C 0 1 N N N N N N 7.068 6.833 25.954 5.179 -0.208 0.586 C14 RKY 16
RKY O16 O5 O 0 1 N N N N N N 8.209 8.693 26.840 3.307 -1.325 -0.483 O16 RKY 17
RKY C18 C13 C 0 1 Y N N N N N 10.012 9.222 28.406 0.953 -1.037 -0.301 C18 RKY 18
RKY H1 H1 H 0 1 N N N N N N 10.971 5.514 28.760 1.459 2.797 -0.249 H1 RKY 19
RKY H2 H2 H 0 1 N N N N N N 7.188 6.216 28.035 5.275 1.928 0.729 H2 RKY 20
RKY H3 H3 H 0 1 N N N N N N 7.224 4.861 26.856 3.910 1.191 1.596 H3 RKY 21
RKY H4 H4 H 0 1 N N N N N N 9.025 7.433 25.470 4.718 -2.299 0.664 H4 RKY 22
RKY H5 H5 H 0 1 N N N N N N 7.721 8.516 24.875 3.587 -1.261 1.559 H5 RKY 23
RKY H6 H6 H 0 1 N N N N N N 15.027 12.889 28.615 -7.137 0.398 0.315 H6 RKY 24
RKY H7 H7 H 0 1 N N N N N N 14.991 10.522 31.453 -3.944 -1.292 0.945 H7 RKY 25
RKY H8 H8 H 0 1 N N N N N N 13.542 11.580 31.541 -4.071 -1.256 -0.830 H8 RKY 26
RKY H9 H9 H 0 1 N N N N N N 12.866 9.206 31.795 -2.731 0.830 -0.883 H9 RKY 27
RKY H10 H10 H 0 1 N N N N N N 13.685 8.778 30.254 -2.605 0.794 0.892 H10 RKY 28
RKY H11 H11 H 0 1 N N N N N N 12.220 7.217 29.988 -0.811 1.867 -0.105 H11 RKY 29
RKY H12 H12 H 0 1 N N N N N N 6.116 7.285 26.270 5.722 -0.265 -0.358 H12 RKY 30
RKY H13 H13 H 0 1 N N N N N N 6.913 6.263 25.026 5.889 -0.314 1.406 H13 RKY 31
RKY H14 H14 H 0 1 N N N N N N 9.745 10.264 28.310 0.812 -2.107 -0.317 H14 RKY 32
#
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
RKY C15 C14 SING N N 1
RKY C15 O16 SING N N 2
RKY C14 C13 SING N N 3
RKY O16 C17 SING N N 4
RKY C13 O12 SING N N 5
RKY O12 C11 SING N N 6
RKY C17 C11 DOUB Y N 7
RKY C17 C18 SING Y N 8
RKY C11 C10 SING Y N 9
RKY C18 C08 DOUB Y N 10
RKY O03 C02 DOUB N N 11
RKY C10 C09 DOUB Y N 12
RKY C08 C09 SING Y N 13
RKY C08 C06 SING N N 14
RKY O01 C02 SING N N 15
RKY C02 C04 SING N N 16
RKY O07 C06 DOUB N N 17
RKY C06 C05 SING N N 18
RKY C05 C04 SING N N 19
RKY C10 H1 SING N N 20
RKY C13 H2 SING N N 21
RKY C13 H3 SING N N 22
RKY C15 H4 SING N N 23
RKY C15 H5 SING N N 24
RKY O01 H6 SING N N 25
RKY C04 H7 SING N N 26
RKY C04 H8 SING N N 27
RKY C05 H9 SING N N 28
RKY C05 H10 SING N N 29
RKY C09 H11 SING N N 30
RKY C14 H12 SING N N 31
RKY C14 H13 SING N N 32
RKY C18 H14 SING N N 33
#
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
RKY SMILES ACDLabs 12.01 c1cc(C(CCC(O)=O)=O)cc2c1OCCCO2
RKY InChI InChI 1.03 InChI=1S/C13H14O5/c14-10(3-5-13(15)16)9-2-4-11-12(8-9)18-7-1-6-17-11/h2,4,8H,1,3,5-7H2,(H,15,16)
RKY InChIKey InChI 1.03 RQYNFIARXFWNDM-UHFFFAOYSA-N
RKY SMILES_CANONICAL CACTVS 3.385 OC(=O)CCC(=O)c1ccc2OCCCOc2c1
RKY SMILES CACTVS 3.385 OC(=O)CCC(=O)c1ccc2OCCCOc2c1
RKY SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 c1cc2c(cc1C(=O)CCC(=O)O)OCCCO2
RKY SMILES "OpenEye OEToolkits" 2.0.7 c1cc2c(cc1C(=O)CCC(=O)O)OCCCO2
#
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
RKY "SYSTEMATIC NAME" ACDLabs 12.01 "4-(3,4-dihydro-2H-1,5-benzodioxepin-7-yl)-4-oxobutanoic acid"
RKY "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 "4-(3,4-dihydro-2~{H}-1,5-benzodioxepin-7-yl)-4-oxidanylidene-butanoic 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
RKY 'Create component' 2020-02-13 RCSB
RKY 'Initial release' 2020-07-15 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
RKY C10 C 7.627 -2.228 1
RKY C13 C 3.651 -2.027 2
RKY C15 C 3.651 0.676 3
RKY C17 C 6.286 0.075 4
RKY O01 O 14.188 -1.374 5
RKY C02 C 14.182 0.126 6
RKY O03 O 15.478 0.881 7
RKY C04 C 12.880 0.871 8
RKY C05 C 11.584 0.116 9
RKY C06 C 10.282 0.861 10
RKY O07 O 10.276 2.361 11
RKY C08 C 8.986 0.106 12
RKY C09 C 8.986 -1.457 13
RKY C11 C 6.286 -1.425 14
RKY O12 O 5.113 -2.361 15
RKY C14 C 3.000 -0.675 16
RKY O16 O 5.113 1.010 17
RKY C18 C 7.627 0.876 18
#
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
RKY C15 C14 SINGLE NONE 1
RKY C15 O16 SINGLE NONE 2
RKY C14 C13 SINGLE NONE 3
RKY O16 C17 SINGLE NONE 4
RKY C13 O12 SINGLE NONE 5
RKY O12 C11 SINGLE NONE 6
RKY C17 C11 SINGLE NONE 7
RKY C17 C18 DOUBLE NONE 8
RKY C11 C10 DOUBLE NONE 9
RKY C18 C08 SINGLE NONE 10
RKY O03 C02 DOUBLE NONE 11
RKY C10 C09 SINGLE NONE 12
RKY C08 C09 DOUBLE NONE 13
RKY C08 C06 SINGLE NONE 14
RKY O01 C02 SINGLE NONE 15
RKY C02 C04 SINGLE NONE 16
RKY O07 C06 DOUBLE NONE 17
RKY C06 C05 SINGLE NONE 18
RKY C05 C04 SINGLE NONE 19
#
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
RKY MurckoScaffold S1 scaffold c1ccc2c(c1)OCCCO2 InChI=1S/C9H10O2/c1-2-5-9-8(4-1)10-6-3-7-11-9/h1-2,4-5H,3,6-7H2 CBXMULHQEVXJDI-UHFFFAOYSA-N
RKY 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
RKY C10 S1 1
RKY C13 S1 1
RKY C15 S1 1
RKY C17 S1 1
RKY C08 S1 1
RKY C09 S1 1
RKY C11 S1 1
RKY O12 S1 1
RKY C14 S1 1
RKY O16 S1 1
RKY C18 S1 1
RKY C10 F1 1
RKY C11 F1 1
RKY C17 F1 1
RKY C18 F1 1
RKY C08 F1 1
RKY C09 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id RKY
_pdbe_chem_comp_rdkit_properties.exactmw 250.084
_pdbe_chem_comp_rdkit_properties.amw 250.250
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 18
_pdbe_chem_comp_rdkit_properties.NumAtoms 32
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.385
_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 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 124.081
_pdbe_chem_comp_rdkit_properties.tpsa 72.830
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.916
_pdbe_chem_comp_rdkit_properties.CrippenMR 61.763
_pdbe_chem_comp_rdkit_properties.chi0v 8.541
_pdbe_chem_comp_rdkit_properties.chi1v 4.429
_pdbe_chem_comp_rdkit_properties.chi2v 1.659
_pdbe_chem_comp_rdkit_properties.chi3v 1.659
_pdbe_chem_comp_rdkit_properties.chi4v 0.979
_pdbe_chem_comp_rdkit_properties.chi0n 22.541
_pdbe_chem_comp_rdkit_properties.chi1n 11.337
_pdbe_chem_comp_rdkit_properties.chi2n 1.659
_pdbe_chem_comp_rdkit_properties.chi3n 1.659
_pdbe_chem_comp_rdkit_properties.chi4n 0.979
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.040
_pdbe_chem_comp_rdkit_properties.kappa1 3.726
_pdbe_chem_comp_rdkit_properties.kappa2 5.530
_pdbe_chem_comp_rdkit_properties.kappa3 2.999
_pdbe_chem_comp_rdkit_properties.Phi 1.145
#
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
RKY UniChem ChEMBL CHEMBL1349957
RKY UniChem PDBe RKY
RKY UniChem ZINC ZINC000003888072
RKY UniChem eMolecules 723952
RKY UniChem 'EPA CompTox Dashboard' DTXSID90379636
RKY UniChem SureChEMBL SCHEMBL4259988
RKY UniChem PubChem 2775652
RKY UniChem Mcule MCULE-4410370169
#
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
RKY C10 1.312 -1.449 -0.769 ETKDGv3 1
RKY C13 4.352 0.241 0.253 ETKDGv3 2
RKY C15 3.041 2.413 -0.155 ETKDGv3 3
RKY C17 1.388 0.670 0.444 ETKDGv3 4
RKY O01 -4.901 0.110 -1.675 ETKDGv3 5
RKY C02 -4.767 0.060 -0.291 ETKDGv3 6
RKY O03 -4.822 1.122 0.386 ETKDGv3 7
RKY C04 -4.523 -1.253 0.387 ETKDGv3 8
RKY C05 -3.066 -1.710 0.222 ETKDGv3 9
RKY C06 -2.073 -0.806 0.918 ETKDGv3 10
RKY O07 -2.429 -0.184 1.957 ETKDGv3 11
RKY C08 -0.671 -0.671 0.448 ETKDGv3 12
RKY C09 -0.099 -1.591 -0.353 ETKDGv3 13
RKY C11 2.040 -0.409 -0.348 ETKDGv3 14
RKY O12 3.413 -0.386 -0.618 ETKDGv3 15
RKY C14 4.411 1.758 0.049 ETKDGv3 16
RKY O16 2.048 1.874 0.716 ETKDGv3 17
RKY C18 0.126 0.513 0.865 ETKDGv3 18
RKY H1 1.774 -2.237 -1.350 ETKDGv3 19
RKY H2 4.096 0.009 1.311 ETKDGv3 20
RKY H3 5.358 -0.184 0.057 ETKDGv3 21
RKY H4 3.134 3.502 0.041 ETKDGv3 22
RKY H5 2.716 2.295 -1.213 ETKDGv3 23
RKY H6 -5.053 0.992 -2.150 ETKDGv3 24
RKY H7 -5.190 -2.015 -0.070 ETKDGv3 25
RKY H8 -4.788 -1.187 1.465 ETKDGv3 26
RKY H9 -2.961 -2.733 0.642 ETKDGv3 27
RKY H10 -2.839 -1.762 -0.865 ETKDGv3 28
RKY H11 -0.634 -2.477 -0.667 ETKDGv3 29
RKY H12 4.904 2.214 0.934 ETKDGv3 30
RKY H13 5.043 1.982 -0.838 ETKDGv3 31
RKY H14 -0.341 1.299 1.446 ETKDGv3 32
#