data_A8V
#
_chem_comp.id A8V
_chem_comp.name (1S)-1-[3-(cyclohexylmethoxy)phenyl]propane-1,3-diol
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C16 H24 O3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2015-04-27
_chem_comp.pdbx_modified_date 2015-05-22
_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 264.360
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code A8V
_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 4ZHK
_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
A8V O1 O1 O 0 1 N N N N N N -49.821 111.277 -41.559 -4.631 1.037 1.052 O1 A8V 1
A8V C2 C1 C 0 1 N N S N N N -50.520 112.329 -40.910 -3.672 0.026 0.735 C2 A8V 2
A8V C1 C2 C 0 1 N N N N N N -49.508 113.429 -40.637 -4.232 -0.884 -0.360 C1 A8V 3
A8V C C3 C 0 1 N N N N N N -48.199 112.889 -40.094 -5.451 -1.636 0.176 C A8V 4
A8V O O2 O 0 1 N N N N N N -48.289 112.243 -38.860 -5.974 -2.486 -0.846 O A8V 5
A8V C3 C4 C 0 1 Y N N N N N -51.636 112.872 -41.786 -2.401 0.674 0.249 C3 A8V 6
A8V C15 C5 C 0 1 Y N N N N N -52.827 113.314 -41.215 -1.178 0.108 0.553 C15 A8V 7
A8V C7 C6 C 0 1 Y N N N N N -53.899 113.704 -42.026 -0.008 0.705 0.105 C7 A8V 8
A8V C6 C7 C 0 1 Y N N N N N -53.757 113.716 -43.398 -0.070 1.869 -0.647 C6 A8V 9
A8V C5 C8 C 0 1 Y N N N N N -52.551 113.336 -43.960 -1.296 2.431 -0.948 C5 A8V 10
A8V C4 C9 C 0 1 Y N N N N N -51.498 112.924 -43.162 -2.460 1.831 -0.505 C4 A8V 11
A8V O2 O3 O 0 1 N N N N N N -55.104 114.075 -41.479 1.196 0.150 0.403 O2 A8V 12
A8V C8 C10 C 0 1 N N N N N N -55.303 114.072 -40.054 2.358 0.819 -0.091 C8 A8V 13
A8V C9 C11 C 0 1 N N N N N N -56.785 114.270 -39.789 3.610 0.053 0.341 C9 A8V 14
A8V C14 C12 C 0 1 N N N N N N -57.660 113.182 -40.424 3.621 -1.324 -0.326 C14 A8V 15
A8V C13 C13 C 0 1 N N N N N N -59.154 113.424 -40.200 4.873 -2.090 0.107 C13 A8V 16
A8V C12 C14 C 0 1 N N N N N N -59.494 113.564 -38.721 6.120 -1.309 -0.315 C12 A8V 17
A8V C11 C15 C 0 1 N N N N N N -58.589 114.595 -38.034 6.109 0.068 0.352 C11 A8V 18
A8V C10 C16 C 0 1 N N N N N N -57.098 114.331 -38.296 4.857 0.834 -0.080 C10 A8V 19
A8V H1 H1 H 0 1 N N N N N N -49.131 110.957 -40.990 -4.867 1.603 0.304 H1 A8V 20
A8V H2 H2 H 0 1 N N N N N N -50.944 111.982 -39.956 -3.460 -0.565 1.626 H2 A8V 21
A8V H3 H3 H 0 1 N N N N N N -49.307 113.965 -41.576 -4.526 -0.280 -1.218 H3 A8V 22
A8V H4 H4 H 0 1 N N N N N N -49.935 114.127 -39.901 -3.468 -1.599 -0.663 H4 A8V 23
A8V H5 H5 H 0 1 N N N N N N -47.797 112.172 -40.825 -5.157 -2.240 1.035 H5 A8V 24
A8V H6 H6 H 0 1 N N N N N N -47.501 113.733 -39.986 -6.215 -0.920 0.480 H6 A8V 25
A8V H7 H7 H 0 1 N N N N N N -47.428 111.939 -38.598 -6.751 -2.995 -0.576 H7 A8V 26
A8V H8 H8 H 0 1 N N N N N N -52.924 113.356 -40.140 -1.132 -0.798 1.139 H8 A8V 27
A8V H9 H9 H 0 1 N N N N N N -54.580 114.019 -44.028 0.839 2.336 -0.997 H9 A8V 28
A8V H10 H10 H 0 1 N N N N N N -52.430 113.361 -45.033 -1.344 3.338 -1.533 H10 A8V 29
A8V H11 H11 H 0 1 N N N N N N -50.560 112.641 -43.617 -3.417 2.272 -0.742 H11 A8V 30
A8V H12 H12 H 0 1 N N N N N N -54.973 113.111 -39.633 2.317 0.863 -1.180 H12 A8V 31
A8V H13 H13 H 0 1 N N N N N N -54.729 114.890 -39.595 2.394 1.831 0.312 H13 A8V 32
A8V H14 H14 H 0 1 N N N N N N -57.079 115.233 -40.231 3.606 -0.068 1.424 H14 A8V 33
A8V H15 H15 H 0 1 N N N N N N -57.390 112.211 -39.983 2.733 -1.880 -0.026 H15 A8V 34
A8V H16 H16 H 0 1 N N N N N N -57.465 113.160 -41.506 3.626 -1.203 -1.409 H16 A8V 35
A8V H17 H17 H 0 1 N N N N N N -59.446 114.348 -40.721 4.869 -2.211 1.190 H17 A8V 36
A8V H18 H18 H 0 1 N N N N N N -59.717 112.575 -40.615 4.881 -3.071 -0.368 H18 A8V 37
A8V H19 H19 H 0 1 N N N N N N -60.541 113.886 -38.623 7.012 -1.855 -0.006 H19 A8V 38
A8V H20 H20 H 0 1 N N N N N N -59.363 112.589 -38.230 6.124 -1.188 -1.398 H20 A8V 39
A8V H21 H21 H 0 1 N N N N N N -58.843 115.596 -38.413 6.104 -0.053 1.436 H21 A8V 40
A8V H22 H22 H 0 1 N N N N N N -58.769 114.557 -36.950 6.997 0.624 0.052 H22 A8V 41
A8V H23 H23 H 0 1 N N N N N N -56.820 113.372 -37.835 4.861 0.955 -1.163 H23 A8V 42
A8V H24 H24 H 0 1 N N N N N N -56.508 115.141 -37.842 4.849 1.815 0.395 H24 A8V 43
#
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
A8V C5 C6 DOUB Y N 1
A8V C5 C4 SING Y N 2
A8V C6 C7 SING Y N 3
A8V C4 C3 DOUB Y N 4
A8V C7 O2 SING N N 5
A8V C7 C15 DOUB Y N 6
A8V C3 C15 SING Y N 7
A8V C3 C2 SING N N 8
A8V O1 C2 SING N N 9
A8V O2 C8 SING N N 10
A8V C2 C1 SING N N 11
A8V C1 C SING N N 12
A8V C14 C13 SING N N 13
A8V C14 C9 SING N N 14
A8V C13 C12 SING N N 15
A8V C O SING N N 16
A8V C8 C9 SING N N 17
A8V C9 C10 SING N N 18
A8V C12 C11 SING N N 19
A8V C10 C11 SING N N 20
A8V O1 H1 SING N N 21
A8V C2 H2 SING N N 22
A8V C1 H3 SING N N 23
A8V C1 H4 SING N N 24
A8V C H5 SING N N 25
A8V C H6 SING N N 26
A8V O H7 SING N N 27
A8V C15 H8 SING N N 28
A8V C6 H9 SING N N 29
A8V C5 H10 SING N N 30
A8V C4 H11 SING N N 31
A8V C8 H12 SING N N 32
A8V C8 H13 SING N N 33
A8V C9 H14 SING N N 34
A8V C14 H15 SING N N 35
A8V C14 H16 SING N N 36
A8V C13 H17 SING N N 37
A8V C13 H18 SING N N 38
A8V C12 H19 SING N N 39
A8V C12 H20 SING N N 40
A8V C11 H21 SING N N 41
A8V C11 H22 SING N N 42
A8V C10 H23 SING N N 43
A8V C10 H24 SING N N 44
#
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
A8V SMILES ACDLabs 12.01 OC(CCO)c2cc(OCC1CCCCC1)ccc2
A8V InChI InChI 1.03 InChI=1S/C16H24O3/c17-10-9-16(18)14-7-4-8-15(11-14)19-12-13-5-2-1-3-6-13/h4,7-8,11,13,16-18H,1-3,5-6,9-10,12H2/t16-/m0/s1
A8V InChIKey InChI 1.03 JEPZJYPEDPLQFU-INIZCTEOSA-N
A8V SMILES_CANONICAL CACTVS 3.385 OCC[C@H](O)c1cccc(OCC2CCCCC2)c1
A8V SMILES CACTVS 3.385 OCC[CH](O)c1cccc(OCC2CCCCC2)c1
A8V SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 c1cc(cc(c1)OCC2CCCCC2)[C@H](CCO)O
A8V SMILES "OpenEye OEToolkits" 1.9.2 c1cc(cc(c1)OCC2CCCCC2)C(CCO)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
A8V "SYSTEMATIC NAME" ACDLabs 12.01 (1S)-1-[3-(cyclohexylmethoxy)phenyl]propane-1,3-diol
A8V "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 (1S)-1-[3-(cyclohexylmethoxy)phenyl]propane-1,3-diol
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
A8V 'Create component' 2015-04-27 RCSB
A8V 'Initial release' 2015-05-27 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
A8V O1 O 8.196 3.285 1
A8V C2 C 9.495 2.535 2
A8V C1 C 10.794 3.285 3
A8V C C 10.794 4.785 4
A8V O O 12.093 5.535 5
A8V C3 C 9.495 1.035 6
A8V C15 C 8.196 0.285 7
A8V C7 C 8.196 -1.215 8
A8V C6 C 9.495 -1.965 9
A8V C5 C 10.794 -1.215 10
A8V C4 C 10.794 0.285 11
A8V O2 O 6.897 -1.965 12
A8V C8 C 6.897 -3.465 13
A8V C9 C 5.598 -4.215 14
A8V C14 C 4.299 -3.465 15
A8V C13 C 3.000 -4.215 16
A8V C12 C 3.000 -5.715 17
A8V C11 C 4.299 -6.465 18
A8V C10 C 5.598 -5.715 19
#
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
A8V C5 C6 DOUBLE NONE 1
A8V C5 C4 SINGLE NONE 2
A8V C6 C7 SINGLE NONE 3
A8V C4 C3 DOUBLE NONE 4
A8V C7 O2 SINGLE NONE 5
A8V C7 C15 DOUBLE NONE 6
A8V C3 C15 SINGLE NONE 7
A8V C3 C2 SINGLE NONE 8
A8V C2 O1 SINGLE BEGINWEDGE 9
A8V O2 C8 SINGLE NONE 10
A8V C2 C1 SINGLE NONE 11
A8V C1 C SINGLE NONE 12
A8V C14 C13 SINGLE NONE 13
A8V C14 C9 SINGLE NONE 14
A8V C13 C12 SINGLE NONE 15
A8V C O SINGLE NONE 16
A8V C8 C9 SINGLE NONE 17
A8V C9 C10 SINGLE NONE 18
A8V C12 C11 SINGLE NONE 19
A8V C10 C11 SINGLE NONE 20
#
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
A8V MurckoScaffold S1 scaffold c1ccc(OCC2CCCCC2)cc1 InChI=1S/C13H18O/c1-3-7-12(8-4-1)11-14-13-9-5-2-6-10-13/h2,5-6,9-10,12H,1,3-4,7-8,11H2 ZETPYKRXIXPMQA-UHFFFAOYSA-N
A8V cyclohexane F1 fragment C1CCCCC1 InChI=1S/C6H12/c1-2-4-6-5-3-1/h1-6H2 XDTMQSROBMDMFD-UHFFFAOYSA-N
A8V phenyl F2 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
A8V C3 S1 1
A8V C15 S1 1
A8V C7 S1 1
A8V C6 S1 1
A8V C5 S1 1
A8V C4 S1 1
A8V O2 S1 1
A8V C8 S1 1
A8V C9 S1 1
A8V C14 S1 1
A8V C13 S1 1
A8V C12 S1 1
A8V C11 S1 1
A8V C10 S1 1
A8V C9 F1 1
A8V C14 F1 1
A8V C13 F1 1
A8V C12 F1 1
A8V C11 F1 1
A8V C10 F1 1
A8V C3 F2 1
A8V C4 F2 1
A8V C5 F2 1
A8V C6 F2 1
A8V C7 F2 1
A8V C15 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id A8V
_pdbe_chem_comp_rdkit_properties.exactmw 264.173
_pdbe_chem_comp_rdkit_properties.amw 264.365
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_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 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 19
_pdbe_chem_comp_rdkit_properties.NumAtoms 43
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 3
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.625
_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 1
_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 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 148.670
_pdbe_chem_comp_rdkit_properties.tpsa 49.690
_pdbe_chem_comp_rdkit_properties.CrippenClogP 2.544
_pdbe_chem_comp_rdkit_properties.CrippenMR 74.299
_pdbe_chem_comp_rdkit_properties.chi0v 9.225
_pdbe_chem_comp_rdkit_properties.chi1v 4.816
_pdbe_chem_comp_rdkit_properties.chi2v 1.749
_pdbe_chem_comp_rdkit_properties.chi3v 1.749
_pdbe_chem_comp_rdkit_properties.chi4v 1.003
_pdbe_chem_comp_rdkit_properties.chi0n 33.225
_pdbe_chem_comp_rdkit_properties.chi1n 16.633
_pdbe_chem_comp_rdkit_properties.chi2n 1.749
_pdbe_chem_comp_rdkit_properties.chi3n 1.749
_pdbe_chem_comp_rdkit_properties.chi4n 1.003
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.060
_pdbe_chem_comp_rdkit_properties.kappa1 2.792
_pdbe_chem_comp_rdkit_properties.kappa2 7.510
_pdbe_chem_comp_rdkit_properties.kappa3 4.515
_pdbe_chem_comp_rdkit_properties.Phi 1.104
#
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
A8V UniChem PDBe A8V
A8V UniChem ZINC ZINC000230507470
A8V UniChem PubChem 91758404
#
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
A8V O1 4.047 -2.817 0.739 ETKDGv3 1
A8V C2 3.919 -1.432 0.949 ETKDGv3 2
A8V C1 5.269 -0.711 0.731 ETKDGv3 3
A8V C 5.254 0.747 1.206 ETKDGv3 4
A8V O 4.492 1.536 0.334 ETKDGv3 5
A8V C3 2.806 -0.868 0.086 ETKDGv3 6
A8V C15 1.656 -0.180 0.729 ETKDGv3 7
A8V C7 0.664 0.342 -0.007 ETKDGv3 8
A8V C6 0.727 0.232 -1.490 ETKDGv3 9
A8V C5 1.759 -0.385 -2.075 ETKDGv3 10
A8V C4 2.844 -0.958 -1.257 ETKDGv3 11
A8V O2 -0.393 0.981 0.659 ETKDGv3 12
A8V C8 -1.572 1.488 0.033 ETKDGv3 13
A8V C9 -2.532 0.346 -0.357 ETKDGv3 14
A8V C14 -3.684 0.898 -1.235 ETKDGv3 15
A8V C13 -4.911 -0.017 -1.190 ETKDGv3 16
A8V C12 -5.487 -0.123 0.237 ETKDGv3 17
A8V C11 -4.430 0.072 1.342 ETKDGv3 18
A8V C10 -3.048 -0.418 0.895 ETKDGv3 19
A8V H1 4.471 -2.958 -0.147 ETKDGv3 20
A8V H2 3.644 -1.302 2.018 ETKDGv3 21
A8V H3 5.570 -0.751 -0.338 ETKDGv3 22
A8V H4 6.048 -1.251 1.312 ETKDGv3 23
A8V H5 4.843 0.808 2.239 ETKDGv3 24
A8V H6 6.300 1.127 1.222 ETKDGv3 25
A8V H7 4.501 2.453 0.714 ETKDGv3 26
A8V H8 1.617 -0.096 1.808 ETKDGv3 27
A8V H9 -0.052 0.647 -2.113 ETKDGv3 28
A8V H10 1.802 -0.463 -3.154 ETKDGv3 29
A8V H11 3.671 -1.442 -1.760 ETKDGv3 30
A8V H12 -1.299 2.104 -0.852 ETKDGv3 31
A8V H13 -2.083 2.165 0.750 ETKDGv3 32
A8V H14 -1.967 -0.384 -0.975 ETKDGv3 33
A8V H15 -3.334 0.995 -2.286 ETKDGv3 34
A8V H16 -3.990 1.912 -0.890 ETKDGv3 35
A8V H17 -5.692 0.372 -1.878 ETKDGv3 36
A8V H18 -4.620 -1.029 -1.550 ETKDGv3 37
A8V H19 -5.963 -1.121 0.355 ETKDGv3 38
A8V H20 -6.284 0.640 0.371 ETKDGv3 39
A8V H21 -4.743 -0.478 2.256 ETKDGv3 40
A8V H22 -4.363 1.150 1.607 ETKDGv3 41
A8V H23 -2.336 -0.331 1.744 ETKDGv3 42
A8V H24 -3.123 -1.502 0.655 ETKDGv3 43
#