data_5VK
#
_chem_comp.id 5VK
_chem_comp.name "ethyl 3-[4-(2-hydroxyphenyl)-3-oxidanyl-phenyl]propanoate"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C17 H18 O4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2015-12-09
_chem_comp.pdbx_modified_date 2016-04-22
_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 286.322
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 5VK
_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 5F6U
_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
5VK CAA C1 C 0 1 N N N N N N -12.095 11.000 -25.889 7.758 1.317 -0.853 CAA 5VK 1
5VK CAL C2 C 0 1 N N N N N N -13.596 11.007 -25.871 6.842 0.286 -0.190 CAL 5VK 2
5VK OAO O1 O 0 1 N N N N N N -14.039 11.467 -24.580 5.456 0.677 -0.380 OAO 5VK 3
5VK CAP C3 C 0 1 N N N N N N -14.173 10.468 -23.599 4.519 -0.128 0.144 CAP 5VK 4
5VK OAB O2 O 0 1 N N N N N N -13.923 9.312 -23.859 4.845 -1.126 0.743 OAB 5VK 5
5VK CAM C4 C 0 1 N N N N N N -14.293 10.912 -22.095 3.059 0.213 -0.013 CAM 5VK 6
5VK CAN C5 C 0 1 N N N N N N -12.957 10.740 -21.373 2.208 -0.859 0.672 CAN 5VK 7
5VK CAQ C6 C 0 1 Y N N N N N -11.810 11.666 -21.968 0.749 -0.518 0.515 CAQ 5VK 8
5VK CAK C7 C 0 1 Y N N N N N -11.977 13.033 -22.026 0.047 -0.988 -0.580 CAK 5VK 9
5VK CAS C8 C 0 1 Y N N N N N -10.953 13.857 -22.548 -1.295 -0.677 -0.729 CAS 5VK 10
5VK OAD O3 O 0 1 N N N N N N -11.154 15.256 -22.596 -1.986 -1.138 -1.804 OAD 5VK 11
5VK CAI C9 C 0 1 Y N N N N N -10.610 11.093 -22.446 0.117 0.258 1.469 CAI 5VK 12
5VK CAJ C10 C 0 1 Y N N N N N -9.620 11.889 -22.960 -1.220 0.575 1.333 CAJ 5VK 13
5VK CAU C11 C 0 1 Y N N N N N -9.774 13.286 -23.034 -1.936 0.112 0.232 CAU 5VK 14
5VK CAT C12 C 0 1 Y N N N N N -8.615 14.072 -23.577 -3.372 0.449 0.081 CAT 5VK 15
5VK CAH C13 C 0 1 Y N N N N N -7.393 13.507 -23.388 -3.763 1.773 -0.109 CAH 5VK 16
5VK CAF C14 C 0 1 Y N N N N N -6.226 14.162 -23.842 -5.101 2.082 -0.250 CAF 5VK 17
5VK CAE C15 C 0 1 Y N N N N N -6.300 15.393 -24.475 -6.056 1.082 -0.203 CAE 5VK 18
5VK CAG C16 C 0 1 Y N N N N N -7.509 15.967 -24.667 -5.679 -0.234 -0.014 CAG 5VK 19
5VK CAR C17 C 0 1 Y N N N N N -8.686 15.318 -24.217 -4.339 -0.560 0.123 CAR 5VK 20
5VK OAC O4 O 0 1 N N N N N N -9.905 15.973 -24.443 -3.967 -1.853 0.308 OAC 5VK 21
5VK H1 H1 H 0 1 N N N N N N -11.741 10.650 -26.870 7.537 1.367 -1.919 H1 5VK 22
5VK H2 H2 H 0 1 N N N N N N -11.721 12.018 -25.706 7.590 2.295 -0.401 H2 5VK 23
5VK H3 H3 H 0 1 N N N N N N -11.722 10.326 -25.104 8.798 1.024 -0.710 H3 5VK 24
5VK H4 H4 H 0 1 N N N N N N -13.973 11.682 -26.654 7.009 -0.692 -0.642 H4 5VK 25
5VK H5 H5 H 0 1 N N N N N N -13.973 9.990 -26.051 7.062 0.236 0.876 H5 5VK 26
5VK H6 H6 H 0 1 N N N N N N -14.592 11.970 -22.053 2.861 1.181 0.445 H6 5VK 27
5VK H7 H7 H 0 1 N N N N N N -15.055 10.295 -21.596 2.808 0.254 -1.073 H7 5VK 28
5VK H8 H8 H 0 1 N N N N N N -13.097 10.992 -20.311 2.407 -1.828 0.213 H8 5VK 29
5VK H9 H9 H 0 1 N N N N N N -12.642 9.690 -21.462 2.460 -0.900 1.732 H9 5VK 30
5VK H10 H10 H 0 1 N N N N N N -12.895 13.477 -21.671 0.545 -1.596 -1.320 H10 5VK 31
5VK H11 H11 H 0 1 N N N N N N -12.003 15.467 -22.226 -2.404 -1.999 -1.663 H11 5VK 32
5VK H12 H12 H 0 1 N N N N N N -10.472 10.023 -22.406 0.671 0.618 2.324 H12 5VK 33
5VK H13 H13 H 0 1 N N N N N N -8.706 11.436 -23.314 -1.711 1.181 2.080 H13 5VK 34
5VK H14 H14 H 0 1 N N N N N N -7.314 12.553 -22.888 -3.020 2.556 -0.146 H14 5VK 35
5VK H15 H15 H 0 1 N N N N N N -5.263 13.697 -23.694 -5.403 3.108 -0.397 H15 5VK 36
5VK H16 H16 H 0 1 N N N N N N -5.401 15.888 -24.811 -7.101 1.331 -0.313 H16 5VK 37
5VK H17 H17 H 0 1 N N N N N N -7.578 16.923 -25.165 -6.429 -1.011 0.023 H17 5VK 38
5VK H18 H18 H 0 1 N N N N N N -10.617 15.445 -24.100 -3.795 -2.335 -0.513 H18 5VK 39
#
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
5VK CAA CAL SING N N 1
5VK CAL OAO SING N N 2
5VK CAG CAE DOUB Y N 3
5VK CAG CAR SING Y N 4
5VK OAO CAP SING N N 5
5VK CAE CAF SING Y N 6
5VK OAC CAR SING N N 7
5VK CAR CAT DOUB Y N 8
5VK OAB CAP DOUB N N 9
5VK CAF CAH DOUB Y N 10
5VK CAP CAM SING N N 11
5VK CAT CAH SING Y N 12
5VK CAT CAU SING N N 13
5VK CAU CAJ DOUB Y N 14
5VK CAU CAS SING Y N 15
5VK CAJ CAI SING Y N 16
5VK OAD CAS SING N N 17
5VK CAS CAK DOUB Y N 18
5VK CAI CAQ DOUB Y N 19
5VK CAM CAN SING N N 20
5VK CAK CAQ SING Y N 21
5VK CAQ CAN SING N N 22
5VK CAA H1 SING N N 23
5VK CAA H2 SING N N 24
5VK CAA H3 SING N N 25
5VK CAL H4 SING N N 26
5VK CAL H5 SING N N 27
5VK CAM H6 SING N N 28
5VK CAM H7 SING N N 29
5VK CAN H8 SING N N 30
5VK CAN H9 SING N N 31
5VK CAK H10 SING N N 32
5VK OAD H11 SING N N 33
5VK CAI H12 SING N N 34
5VK CAJ H13 SING N N 35
5VK CAH H14 SING N N 36
5VK CAF H15 SING N N 37
5VK CAE H16 SING N N 38
5VK CAG H17 SING N N 39
5VK OAC H18 SING N N 40
#
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
5VK InChI InChI 1.03 InChI=1S/C17H18O4/c1-2-21-17(20)10-8-12-7-9-14(16(19)11-12)13-5-3-4-6-15(13)18/h3-7,9,11,18-19H,2,8,10H2,1H3
5VK InChIKey InChI 1.03 NLRSDRXKCXNRRG-UHFFFAOYSA-N
5VK SMILES_CANONICAL CACTVS 3.385 CCOC(=O)CCc1ccc(c(O)c1)c2ccccc2O
5VK SMILES CACTVS 3.385 CCOC(=O)CCc1ccc(c(O)c1)c2ccccc2O
5VK SMILES_CANONICAL "OpenEye OEToolkits" 2.0.4 CCOC(=O)CCc1ccc(c(c1)O)c2ccccc2O
5VK SMILES "OpenEye OEToolkits" 2.0.4 CCOC(=O)CCc1ccc(c(c1)O)c2ccccc2O
#
_pdbx_chem_comp_identifier.comp_id 5VK
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.4
_pdbx_chem_comp_identifier.identifier "ethyl 3-[4-(2-hydroxyphenyl)-3-oxidanyl-phenyl]propanoate"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
5VK 'Create component' 2015-12-09 RCSB
5VK 'Initial release' 2016-04-27 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
5VK CAA C 10.301 -7.125 1
5VK CAL C 9.002 -6.375 2
5VK OAO O 9.002 -4.875 3
5VK CAP C 7.702 -4.125 4
5VK OAB O 6.404 -4.875 5
5VK CAM C 7.702 -2.625 6
5VK CAN C 6.404 -1.875 7
5VK CAQ C 6.404 -0.375 8
5VK CAK C 5.104 0.375 9
5VK CAS C 5.104 1.875 10
5VK OAD O 3.805 2.625 11
5VK CAI C 7.702 0.375 12
5VK CAJ C 7.702 1.875 13
5VK CAU C 6.404 2.625 14
5VK CAT C 6.404 4.125 15
5VK CAH C 5.104 4.875 16
5VK CAF C 5.104 6.375 17
5VK CAE C 6.404 7.125 18
5VK CAG C 7.702 6.375 19
5VK CAR C 7.702 4.875 20
5VK OAC O 9.002 4.125 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
5VK CAA CAL SINGLE NONE 1
5VK CAL OAO SINGLE NONE 2
5VK CAG CAE DOUBLE NONE 3
5VK CAG CAR SINGLE NONE 4
5VK OAO CAP SINGLE NONE 5
5VK CAE CAF SINGLE NONE 6
5VK OAC CAR SINGLE NONE 7
5VK CAR CAT DOUBLE NONE 8
5VK OAB CAP DOUBLE NONE 9
5VK CAF CAH DOUBLE NONE 10
5VK CAP CAM SINGLE NONE 11
5VK CAT CAH SINGLE NONE 12
5VK CAT CAU SINGLE NONE 13
5VK CAU CAJ DOUBLE NONE 14
5VK CAU CAS SINGLE NONE 15
5VK CAJ CAI SINGLE NONE 16
5VK OAD CAS SINGLE NONE 17
5VK CAS CAK DOUBLE NONE 18
5VK CAI CAQ DOUBLE NONE 19
5VK CAM CAN SINGLE NONE 20
5VK CAK CAQ SINGLE NONE 21
5VK CAQ CAN SINGLE NONE 22
#
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
5VK MurckoScaffold S1 scaffold c1ccc(-c2ccccc2)cc1 InChI=1S/C12H10/c1-3-7-11(8-4-1)12-9-5-2-6-10-12/h1-10H ZUOUZKKEUPVFJK-UHFFFAOYSA-N
5VK 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
5VK CAQ S1 1
5VK CAK S1 1
5VK CAS S1 1
5VK CAI S1 1
5VK CAJ S1 1
5VK CAU S1 1
5VK CAT S1 1
5VK CAH S1 1
5VK CAF S1 1
5VK CAE S1 1
5VK CAG S1 1
5VK CAR S1 1
5VK CAQ F1 1
5VK CAI F1 1
5VK CAJ F1 1
5VK CAU F1 1
5VK CAS F1 1
5VK CAK F1 1
5VK CAT F1 2
5VK CAR F1 2
5VK CAG F1 2
5VK CAE F1 2
5VK CAF F1 2
5VK CAH F1 2
#
_pdbe_chem_comp_rdkit_properties.comp_id 5VK
_pdbe_chem_comp_rdkit_properties.exactmw 286.121
_pdbe_chem_comp_rdkit_properties.amw 286.327
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 8
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 21
_pdbe_chem_comp_rdkit_properties.NumAtoms 39
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.235
_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 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 148.640
_pdbe_chem_comp_rdkit_properties.tpsa 66.760
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.901
_pdbe_chem_comp_rdkit_properties.CrippenMR 77.354
_pdbe_chem_comp_rdkit_properties.chi0v 10.133
_pdbe_chem_comp_rdkit_properties.chi1v 5.271
_pdbe_chem_comp_rdkit_properties.chi2v 2.114
_pdbe_chem_comp_rdkit_properties.chi3v 2.114
_pdbe_chem_comp_rdkit_properties.chi4v 1.290
_pdbe_chem_comp_rdkit_properties.chi0n 28.133
_pdbe_chem_comp_rdkit_properties.chi1n 14.087
_pdbe_chem_comp_rdkit_properties.chi2n 2.114
_pdbe_chem_comp_rdkit_properties.chi3n 2.114
_pdbe_chem_comp_rdkit_properties.chi4n 1.290
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.490
_pdbe_chem_comp_rdkit_properties.kappa1 4.034
_pdbe_chem_comp_rdkit_properties.kappa2 6.791
_pdbe_chem_comp_rdkit_properties.kappa3 3.751
_pdbe_chem_comp_rdkit_properties.Phi 1.304
#
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
5VK UniChem ChEMBL CHEMBL5199188
5VK UniChem PDBe 5VK
5VK UniChem ZINC ZINC000584905285
5VK UniChem PubChem 118987242
5VK UniChem BRENDA 250928
#
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
5VK CAA 6.583 2.199 1.126 ETKDGv3 1
5VK CAL 6.223 0.919 0.389 ETKDGv3 2
5VK OAO 4.828 0.667 0.524 ETKDGv3 3
5VK CAP 4.204 -0.443 -0.050 ETKDGv3 4
5VK OAB 4.865 -1.270 -0.736 ETKDGv3 5
5VK CAM 2.728 -0.622 0.111 ETKDGv3 6
5VK CAN 1.975 0.151 -0.973 ETKDGv3 7
5VK CAQ 0.488 -0.011 -0.801 ETKDGv3 8
5VK CAK -0.258 0.921 0.077 ETKDGv3 9
5VK CAS -1.577 0.765 0.274 ETKDGv3 10
5VK OAD -2.270 1.635 1.116 ETKDGv3 11
5VK CAI -0.163 -1.030 -1.386 ETKDGv3 12
5VK CAJ -1.616 -1.199 -1.185 ETKDGv3 13
5VK CAU -2.300 -0.351 -0.395 ETKDGv3 14
5VK CAT -3.764 -0.505 -0.218 ETKDGv3 15
5VK CAH -4.652 0.647 -0.517 ETKDGv3 16
5VK CAF -5.977 0.538 -0.369 ETKDGv3 17
5VK CAE -6.568 -0.732 0.094 ETKDGv3 18
5VK CAG -5.778 -1.776 0.369 ETKDGv3 19
5VK CAR -4.308 -1.664 0.214 ETKDGv3 20
5VK OAC -3.499 -2.755 0.532 ETKDGv3 21
5VK H1 6.017 3.054 0.699 ETKDGv3 22
5VK H2 6.336 2.099 2.204 ETKDGv3 23
5VK H3 7.670 2.398 1.022 ETKDGv3 24
5VK H4 6.801 0.072 0.820 ETKDGv3 25
5VK H5 6.482 1.029 -0.686 ETKDGv3 26
5VK H6 2.476 -1.704 0.049 ETKDGv3 27
5VK H7 2.428 -0.253 1.116 ETKDGv3 28
5VK H8 2.285 -0.210 -1.979 ETKDGv3 29
5VK H9 2.237 1.230 -0.914 ETKDGv3 30
5VK H10 0.271 1.728 0.569 ETKDGv3 31
5VK H11 -1.808 2.402 1.590 ETKDGv3 32
5VK H12 0.366 -1.737 -2.013 ETKDGv3 33
5VK H13 -2.122 -2.008 -1.698 ETKDGv3 34
5VK H14 -4.230 1.581 -0.868 ETKDGv3 35
5VK H15 -6.620 1.380 -0.592 ETKDGv3 36
5VK H16 -7.640 -0.815 0.210 ETKDGv3 37
5VK H17 -6.217 -2.705 0.710 ETKDGv3 38
5VK H18 -3.896 -3.627 0.860 ETKDGv3 39
#