data_2K6
#
_chem_comp.id 2K6
_chem_comp.name (3R)-3-(4-methoxyphenyl)-5-oxohexanenitrile
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C13 H15 N O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2014-04-08
_chem_comp.pdbx_modified_date 2015-03-27
_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 217.264
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 2K6
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag Y
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 4PA8
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
#
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
2K6 C1 C11 C 0 1 N N N N N N 5.664 -17.247 11.664 4.916 -0.918 0.879 C11 2K6 1
2K6 O1 O1 O 0 1 N N N N N N 5.155 -17.992 10.591 4.304 -0.439 -0.319 O1 2K6 2
2K6 C2 C10 C 0 1 Y N N N N N 5.309 -18.165 9.246 2.952 -0.294 -0.306 C10 2K6 3
2K6 C3 C9 C 0 1 Y N N N N N 6.020 -17.323 8.434 2.292 0.167 -1.436 C9 2K6 4
2K6 C4 C7 C 0 1 Y N N N N N 6.170 -17.517 7.069 0.919 0.313 -1.421 C7 2K6 5
2K6 C5 C8 C 0 1 Y N N N N N 4.727 -19.257 8.612 2.230 -0.613 0.835 C8 2K6 6
2K6 C6 C6 C 0 1 Y N N N N N 4.842 -19.484 7.239 0.857 -0.465 0.845 C6 2K6 7
2K6 C7 C5 C 0 1 Y N N N N N 5.582 -18.600 6.434 0.202 0.000 -0.280 C5 2K6 8
2K6 C8 C4 C 0 1 N N R N N N 5.723 -18.782 4.955 -1.296 0.161 -0.266 C4 2K6 9
2K6 C9 C3 C 0 1 N N N N N N 4.880 -17.780 4.150 -1.952 -1.192 0.018 C3 2K6 10
2K6 C10 C2 C 0 1 N N N N N N 3.360 -18.127 4.227 -3.449 -1.057 -0.089 C2 2K6 11
2K6 C11 C1 C 0 1 N N N N N N 2.453 -17.191 5.010 -4.332 -2.255 0.147 C1 2K6 12
2K6 C12 C12 C 0 1 N N N N N N 7.132 -19.195 4.424 -1.692 1.158 0.826 C12 2K6 13
2K6 C13 C13 C 0 1 N N N N N N 8.038 -18.005 4.402 -1.160 2.489 0.490 C13 2K6 14
2K6 N1 N14 N 0 1 N N N N N N 8.779 -17.097 4.312 -0.750 3.516 0.231 N14 2K6 15
2K6 H1 H1 H 0 1 N N N N N N 5.140 -17.530 12.589 4.518 -1.904 1.122 H1 2K6 16
2K6 H2 H2 H 0 1 N N N N N N 6.739 -17.451 11.775 5.994 -0.987 0.734 H2 2K6 17
2K6 H3 H3 H 0 1 N N N N N N 5.513 -16.175 11.470 4.703 -0.229 1.697 H3 2K6 18
2K6 H4 H4 H 0 1 N N N N N N 6.490 -16.460 8.881 2.851 0.411 -2.327 H4 2K6 19
2K6 H5 H5 H 0 1 N N N N N N 6.753 -16.814 6.492 0.404 0.672 -2.300 H5 2K6 20
2K6 H6 H6 H 0 1 N N N N N N 4.162 -19.959 9.207 2.742 -0.976 1.714 H6 2K6 21
2K6 H7 H7 H 0 1 N N N N N N 4.361 -20.342 6.794 0.294 -0.713 1.733 H7 2K6 22
2K6 H8 H8 H 0 1 N N N N N N 5.158 -19.712 4.795 -1.632 0.531 -1.235 H8 2K6 23
2K6 H9 H9 H 0 1 N N N N N N 5.201 -17.806 3.098 -1.601 -1.925 -0.708 H9 2K6 24
2K6 H10 H10 H 0 1 N N N N N N 5.038 -16.770 4.557 -1.688 -1.520 1.023 H10 2K6 25
2K6 H13 H13 H 0 1 N N N N N N 2.449 -16.200 4.533 -4.173 -2.630 1.158 H13 2K6 26
2K6 H14 H14 H 0 1 N N N N N N 1.430 -17.596 5.022 -5.377 -1.966 0.027 H14 2K6 27
2K6 H15 H15 H 0 1 N N N N N N 2.823 -17.100 6.042 -4.087 -3.035 -0.573 H15 2K6 28
2K6 H16 H16 H 0 1 N N N N N N 7.034 -19.597 3.405 -2.778 1.208 0.896 H16 2K6 29
2K6 H17 H17 H 0 1 N N N N N N 7.558 -19.966 5.083 -1.280 0.833 1.781 H17 2K6 30
2K6 O2 O2 O 0 1 N Y N N N N ? ? ? -3.941 0.011 -0.363 O2 2K6 31
#
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
2K6 C9 C10 SING N N 1
2K6 C9 C8 SING N N 2
2K6 C10 C11 SING N N 3
2K6 N1 C13 TRIP N N 4
2K6 C13 C12 SING N N 5
2K6 C12 C8 SING N N 6
2K6 C8 C7 SING N N 7
2K6 C7 C4 DOUB Y N 8
2K6 C7 C6 SING Y N 9
2K6 C4 C3 SING Y N 10
2K6 C6 C5 DOUB Y N 11
2K6 C3 C2 DOUB Y N 12
2K6 C5 C2 SING Y N 13
2K6 C2 O1 SING N N 14
2K6 O1 C1 SING N N 15
2K6 C1 H1 SING N N 16
2K6 C1 H2 SING N N 17
2K6 C1 H3 SING N N 18
2K6 C3 H4 SING N N 19
2K6 C4 H5 SING N N 20
2K6 C5 H6 SING N N 21
2K6 C6 H7 SING N N 22
2K6 C8 H8 SING N N 23
2K6 C9 H9 SING N N 24
2K6 C9 H10 SING N N 25
2K6 C11 H13 SING N N 26
2K6 C11 H14 SING N N 27
2K6 C11 H15 SING N N 28
2K6 C12 H16 SING N N 29
2K6 C12 H17 SING N N 30
2K6 C10 O2 DOUB 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
2K6 SMILES ACDLabs 12.01 "O=C(C)CC(c1ccc(OC)cc1)CC#N"
2K6 InChI InChI 1.03 InChI=1S/C13H15NO2/c1-10(15)9-12(7-8-14)11-3-5-13(16-2)6-4-11/h3-6,12H,7,9H2,1-2H3/t12-/m1/s1
2K6 InChIKey InChI 1.03 UZVHUQSCXULJKG-GFCCVEGCSA-N
2K6 SMILES_CANONICAL CACTVS 3.385 "COc1ccc(cc1)[C@H](CC#N)CC(C)=O"
2K6 SMILES CACTVS 3.385 "COc1ccc(cc1)[CH](CC#N)CC(C)=O"
2K6 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 "CC(=O)C[C@@H](CC#N)c1ccc(cc1)OC"
2K6 SMILES "OpenEye OEToolkits" 1.7.6 "CC(=O)CC(CC#N)c1ccc(cc1)OC"
#
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
2K6 "SYSTEMATIC NAME" ACDLabs 12.01 (3R)-3-(4-methoxyphenyl)-5-oxohexanenitrile
2K6 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 (3R)-3-(4-methoxyphenyl)-5-oxidanylidene-hexanenitrile
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
2K6 'Create component' 2014-04-08 EBI
2K6 'Other modification' 2014-04-08 EBI
2K6 'Initial release' 2015-04-01 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
2K6 C1 C 3.000 -5.250 1
2K6 O1 O 4.299 -4.500 2
2K6 C2 C 4.299 -3.000 3
2K6 C3 C 5.598 -2.250 4
2K6 C4 C 5.598 -0.750 5
2K6 C5 C 3.000 -2.250 6
2K6 C6 C 3.000 -0.750 7
2K6 C7 C 4.299 0.000 8
2K6 C8 C 4.299 1.500 9
2K6 C9 C 5.598 2.250 10
2K6 C10 C 5.598 3.750 11
2K6 C11 C 4.299 4.500 12
2K6 C12 C 3.000 2.250 13
2K6 C13 C 3.000 3.750 14
2K6 N1 N 3.000 5.250 15
2K6 O2 O 6.897 4.500 16
#
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
2K6 C9 C10 SINGLE NONE 1
2K6 C8 C9 SINGLE BEGINDASH 2
2K6 C10 C11 SINGLE NONE 3
2K6 N1 C13 TRIPLE NONE 4
2K6 C13 C12 SINGLE NONE 5
2K6 C12 C8 SINGLE NONE 6
2K6 C8 C7 SINGLE NONE 7
2K6 C7 C4 DOUBLE NONE 8
2K6 C7 C6 SINGLE NONE 9
2K6 C4 C3 SINGLE NONE 10
2K6 C6 C5 DOUBLE NONE 11
2K6 C3 C2 DOUBLE NONE 12
2K6 C5 C2 SINGLE NONE 13
2K6 C2 O1 SINGLE NONE 14
2K6 O1 C1 SINGLE NONE 15
2K6 C10 O2 DOUBLE NONE 16
#
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
2K6 MurckoScaffold S1 scaffold c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
2K6 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
2K6 C2 S1 1
2K6 C3 S1 1
2K6 C4 S1 1
2K6 C5 S1 1
2K6 C6 S1 1
2K6 C7 S1 1
2K6 C2 F1 1
2K6 C3 F1 1
2K6 C4 F1 1
2K6 C7 F1 1
2K6 C6 F1 1
2K6 C5 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 2K6
_pdbe_chem_comp_rdkit_properties.exactmw 217.110
_pdbe_chem_comp_rdkit_properties.amw 217.268
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 0
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 7
_pdbe_chem_comp_rdkit_properties.NumHBD 0
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 16
_pdbe_chem_comp_rdkit_properties.NumAtoms 31
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 3
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.385
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_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 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 116.728
_pdbe_chem_comp_rdkit_properties.tpsa 50.090
_pdbe_chem_comp_rdkit_properties.CrippenClogP 2.154
_pdbe_chem_comp_rdkit_properties.CrippenMR 60.387
_pdbe_chem_comp_rdkit_properties.chi0v 7.764
_pdbe_chem_comp_rdkit_properties.chi1v 3.836
_pdbe_chem_comp_rdkit_properties.chi2v 1.374
_pdbe_chem_comp_rdkit_properties.chi3v 1.374
_pdbe_chem_comp_rdkit_properties.chi4v 0.803
_pdbe_chem_comp_rdkit_properties.chi0n 22.764
_pdbe_chem_comp_rdkit_properties.chi1n 11.336
_pdbe_chem_comp_rdkit_properties.chi2n 1.374
_pdbe_chem_comp_rdkit_properties.chi3n 1.374
_pdbe_chem_comp_rdkit_properties.chi4n 0.803
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.820
_pdbe_chem_comp_rdkit_properties.kappa1 2.893
_pdbe_chem_comp_rdkit_properties.kappa2 5.916
_pdbe_chem_comp_rdkit_properties.kappa3 3.394
_pdbe_chem_comp_rdkit_properties.Phi 1.070
#
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
2K6 UniChem PDBe 2K6
2K6 UniChem ZINC ZINC000263621113
2K6 UniChem PubChem 137348056
#
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
2K6 C1 5.216 -0.865 -0.967 ETKDGv3 1
2K6 O1 4.381 -0.187 -0.033 ETKDGv3 2
2K6 C2 2.983 -0.106 -0.122 ETKDGv3 3
2K6 C3 2.283 -0.673 -1.124 ETKDGv3 4
2K6 C4 0.811 -0.554 -1.166 ETKDGv3 5
2K6 C5 2.259 0.637 0.930 ETKDGv3 6
2K6 C6 0.926 0.742 0.897 ETKDGv3 7
2K6 C7 0.145 0.106 -0.199 ETKDGv3 8
2K6 C8 -1.368 0.248 -0.274 ETKDGv3 9
2K6 C9 -2.038 -0.019 1.097 ETKDGv3 10
2K6 C10 -3.523 -0.241 0.969 ETKDGv3 11
2K6 C11 -4.089 -1.628 1.029 ETKDGv3 12
2K6 C12 -1.763 1.602 -0.908 ETKDGv3 13
2K6 C13 -1.432 2.756 -0.058 ETKDGv3 14
2K6 N1 -1.173 3.664 0.611 ETKDGv3 15
2K6 H1 4.953 -1.944 -1.001 ETKDGv3 16
2K6 H2 6.273 -0.767 -0.647 ETKDGv3 17
2K6 H3 5.106 -0.413 -1.976 ETKDGv3 18
2K6 H4 2.775 -1.221 -1.915 ETKDGv3 19
2K6 H5 0.280 -1.008 -1.994 ETKDGv3 20
2K6 H6 2.815 1.104 1.733 ETKDGv3 21
2K6 H7 0.426 1.300 1.676 ETKDGv3 22
2K6 H8 -1.751 -0.541 -0.962 ETKDGv3 23
2K6 H9 -1.859 0.816 1.806 ETKDGv3 24
2K6 H10 -1.581 -0.928 1.545 ETKDGv3 25
2K6 H13 -3.900 -2.064 2.032 ETKDGv3 26
2K6 H14 -5.185 -1.612 0.844 ETKDGv3 27
2K6 H15 -3.605 -2.262 0.257 ETKDGv3 28
2K6 H16 -1.240 1.722 -1.881 ETKDGv3 29
2K6 H17 -2.851 1.620 -1.122 ETKDGv3 30
2K6 O2 -4.274 0.715 0.853 ETKDGv3 31
#