data_LX6
#
_chem_comp.id LX6
_chem_comp.name 2-amino-4,5,6,7-tetrahydro-1-benzothiophene-3-carbonitrile
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C9 H10 N2 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2022-03-09
_chem_comp.pdbx_modified_date 2022-11-04
_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 178.254
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code LX6
_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 7U8H
_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
LX6 C01 C1 C 0 1 Y N N N N N 42.918 59.220 9.735 1.057 0.481 0.011 C01 LX6 1
LX6 C02 C2 C 0 1 Y N N N N N 42.873 58.855 8.264 1.615 -0.767 -0.009 C02 LX6 2
LX6 C03 C3 C 0 1 Y N N N N N 41.584 59.992 10.092 -0.395 0.462 0.008 C03 LX6 3
LX6 S04 S1 S 0 1 Y N N N N N 41.486 59.406 7.650 0.407 -1.966 -0.032 S04 LX6 4
LX6 C05 C4 C 0 1 Y N N N N N 40.716 60.096 8.790 -0.889 -0.781 -0.019 C05 LX6 5
LX6 C06 C5 C 0 1 N N N N N N 44.016 58.914 10.696 1.828 1.688 0.039 C06 LX6 6
LX6 N07 N1 N 0 1 N N N N N N 44.850 58.685 11.442 2.439 2.645 0.061 N07 LX6 7
LX6 N08 N2 N 0 1 N N N N N N 43.882 58.155 7.535 2.975 -1.020 -0.011 N08 LX6 8
LX6 C09 C6 C 0 1 N N N N N N 41.021 60.621 11.373 -1.264 1.710 0.033 C09 LX6 9
LX6 C10 C7 C 0 1 N N N N N N 39.363 60.814 8.901 -2.368 -1.113 -0.030 C10 LX6 10
LX6 C11 C8 C 0 1 N N N N N N 39.929 61.501 11.196 -2.681 1.332 -0.405 C11 LX6 11
LX6 C12 C9 C 0 1 N N N N N N 38.920 61.110 10.213 -3.155 0.128 0.400 C12 LX6 12
LX6 H1 H1 H 0 1 N N N N N N 43.598 58.057 6.581 3.606 -0.283 0.003 H1 LX6 13
LX6 H2 H2 H 0 1 N N N N N N 44.739 58.668 7.576 3.298 -1.935 -0.026 H2 LX6 14
LX6 H3 H3 H 0 1 N N N N N N 40.694 59.805 12.034 -1.290 2.117 1.044 H3 LX6 15
LX6 H4 H4 H 0 1 N N N N N N 39.440 61.763 8.350 -2.670 -1.406 -1.036 H4 LX6 16
LX6 H5 H5 H 0 1 N N N N N N 40.334 62.476 10.887 -3.352 2.174 -0.233 H5 LX6 17
LX6 H6 H6 H 0 1 N N N N N N 38.197 61.935 10.138 -4.218 -0.036 0.226 H6 LX6 18
LX6 H7 H7 H 0 1 N N N N N N 41.833 61.183 11.858 -0.854 2.454 -0.650 H7 LX6 19
LX6 H8 H8 H 0 1 N N N N N N 38.604 60.175 8.426 -2.565 -1.930 0.665 H8 LX6 20
LX6 H9 H9 H 0 1 N N N N N N 39.424 61.605 12.168 -2.679 1.079 -1.465 H9 LX6 21
LX6 H10 H10 H 0 1 N N N N N N 38.414 60.213 10.600 -2.983 0.319 1.460 H10 LX6 22
#
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
LX6 N08 C02 SING N N 1
LX6 S04 C02 SING Y N 2
LX6 S04 C05 SING Y N 3
LX6 C02 C01 DOUB Y N 4
LX6 C05 C10 SING N N 5
LX6 C05 C03 DOUB Y N 6
LX6 C10 C12 SING N N 7
LX6 C01 C03 SING Y N 8
LX6 C01 C06 SING N N 9
LX6 C03 C09 SING N N 10
LX6 C12 C11 SING N N 11
LX6 C06 N07 TRIP N N 12
LX6 C11 C09 SING N N 13
LX6 N08 H1 SING N N 14
LX6 N08 H2 SING N N 15
LX6 C09 H3 SING N N 16
LX6 C10 H4 SING N N 17
LX6 C11 H5 SING N N 18
LX6 C12 H6 SING N N 19
LX6 C09 H7 SING N N 20
LX6 C10 H8 SING N N 21
LX6 C11 H9 SING N N 22
LX6 C12 H10 SING N N 23
#
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
LX6 SMILES ACDLabs 12.01 "N#Cc1c2CCCCc2sc1N"
LX6 InChI InChI 1.03 InChI=1S/C9H10N2S/c10-5-7-6-3-1-2-4-8(6)12-9(7)11/h1-4,11H2
LX6 InChIKey InChI 1.03 ADHVMGAFAKSNOM-UHFFFAOYSA-N
LX6 SMILES_CANONICAL CACTVS 3.385 "Nc1sc2CCCCc2c1C#N"
LX6 SMILES CACTVS 3.385 "Nc1sc2CCCCc2c1C#N"
LX6 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "C1CCc2c(c(c(s2)N)C#N)C1"
LX6 SMILES "OpenEye OEToolkits" 2.0.7 "C1CCc2c(c(c(s2)N)C#N)C1"
#
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
LX6 "SYSTEMATIC NAME" ACDLabs 12.01 2-amino-4,5,6,7-tetrahydro-1-benzothiophene-3-carbonitrile
LX6 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 2-azanyl-4,5,6,7-tetrahydro-1-benzothiophene-3-carbonitrile
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
LX6 'Create component' 2022-03-09 RCSB
LX6 'Initial release' 2022-11-09 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
LX6 C01 C 7.018 -0.072 1
LX6 C02 C 7.893 -1.279 2
LX6 C03 C 5.598 -0.529 3
LX6 S04 S 7.018 -2.486 4
LX6 C05 C 5.598 -2.029 5
LX6 C06 C 7.483 1.354 6
LX6 N07 N 7.949 2.779 7
LX6 N08 N 9.393 -1.279 8
LX6 C09 C 4.299 0.221 9
LX6 C10 C 4.299 -2.779 10
LX6 C11 C 3.000 -0.529 11
LX6 C12 C 3.000 -2.029 12
#
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
LX6 N08 C02 SINGLE NONE 1
LX6 S04 C02 SINGLE NONE 2
LX6 S04 C05 SINGLE NONE 3
LX6 C02 C01 DOUBLE NONE 4
LX6 C05 C10 SINGLE NONE 5
LX6 C05 C03 DOUBLE NONE 6
LX6 C10 C12 SINGLE NONE 7
LX6 C01 C03 SINGLE NONE 8
LX6 C01 C06 SINGLE NONE 9
LX6 C03 C09 SINGLE NONE 10
LX6 C12 C11 SINGLE NONE 11
LX6 C06 N07 TRIPLE NONE 12
LX6 C11 C09 SINGLE NONE 13
#
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
LX6 MurckoScaffold S1 scaffold c1cc2c(s1)CCCC2 InChI=1S/C8H10S/c1-2-4-8-7(3-1)5-6-9-8/h5-6H,1-4H2 CBKDCOKSXCTDAA-UHFFFAOYSA-N
LX6 thiophen F1 fragment c1ccsc1 InChI=1S/C4H4S/c1-2-4-5-3-1/h1-4H YTPLMLYBLZKORZ-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
LX6 C01 S1 1
LX6 C02 S1 1
LX6 C03 S1 1
LX6 S04 S1 1
LX6 C05 S1 1
LX6 C09 S1 1
LX6 C10 S1 1
LX6 C11 S1 1
LX6 C12 S1 1
LX6 C02 F1 1
LX6 C01 F1 1
LX6 C03 F1 1
LX6 C05 F1 1
LX6 S04 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id LX6
_pdbe_chem_comp_rdkit_properties.exactmw 178.056
_pdbe_chem_comp_rdkit_properties.amw 178.260
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 2
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 1
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 12
_pdbe_chem_comp_rdkit_properties.NumAtoms 22
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 3
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.444
_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 1
_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 89.789
_pdbe_chem_comp_rdkit_properties.tpsa 49.810
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.536
_pdbe_chem_comp_rdkit_properties.CrippenMR 48.466
_pdbe_chem_comp_rdkit_properties.chi0v 6.619
_pdbe_chem_comp_rdkit_properties.chi1v 3.922
_pdbe_chem_comp_rdkit_properties.chi2v 2.335
_pdbe_chem_comp_rdkit_properties.chi3v 2.335
_pdbe_chem_comp_rdkit_properties.chi4v 1.712
_pdbe_chem_comp_rdkit_properties.chi0n 15.803
_pdbe_chem_comp_rdkit_properties.chi1n 8.000
_pdbe_chem_comp_rdkit_properties.chi2n 1.427
_pdbe_chem_comp_rdkit_properties.chi3n 1.427
_pdbe_chem_comp_rdkit_properties.chi4n 0.912
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.010
_pdbe_chem_comp_rdkit_properties.kappa1 2.268
_pdbe_chem_comp_rdkit_properties.kappa2 2.797
_pdbe_chem_comp_rdkit_properties.kappa3 0.997
_pdbe_chem_comp_rdkit_properties.Phi 0.529
#
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
LX6 UniChem ChEMBL CHEMBL1632047
LX6 UniChem PDBe LX6
LX6 UniChem ZINC ZINC000000126979
LX6 UniChem eMolecules 440455
LX6 UniChem ACTor 4651-91-6
LX6 UniChem ChemicalBook CB3323681
LX6 UniChem 'EPA CompTox Dashboard' DTXSID30196864
LX6 UniChem SureChEMBL SCHEMBL620749
LX6 UniChem 'PubChem TPHARMA' 16069384
LX6 UniChem PubChem 78382
LX6 UniChem Mcule MCULE-3255541087
LX6 UniChem Nikkaji J284.261K
#
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
LX6 C01 0.248 0.134 -1.681 ETKDGv3 1
LX6 C02 0.757 -1.031 -2.096 ETKDGv3 2
LX6 C03 -0.031 0.170 -0.223 ETKDGv3 3
LX6 S04 0.946 -2.157 -0.731 ETKDGv3 4
LX6 C05 0.319 -0.952 0.419 ETKDGv3 5
LX6 C06 -0.008 1.248 -2.558 ETKDGv3 6
LX6 N07 -0.214 2.144 -3.262 ETKDGv3 7
LX6 N08 1.115 -1.345 -3.443 ETKDGv3 8
LX6 C09 -0.552 1.386 0.502 ETKDGv3 9
LX6 C10 0.083 -1.203 1.880 ETKDGv3 10
LX6 C11 -1.094 1.033 1.897 ETKDGv3 11
LX6 C12 -0.122 0.112 2.646 ETKDGv3 12
LX6 H1 0.990 -0.653 -4.216 ETKDGv3 13
LX6 H2 1.510 -2.284 -3.669 ETKDGv3 14
LX6 H3 0.279 2.117 0.605 ETKDGv3 15
LX6 H4 -0.822 -1.838 1.987 ETKDGv3 16
LX6 H5 -1.246 1.967 2.480 ETKDGv3 17
LX6 H6 -0.524 -0.110 3.658 ETKDGv3 18
LX6 H7 -1.361 1.860 -0.092 ETKDGv3 19
LX6 H8 0.949 -1.752 2.307 ETKDGv3 20
LX6 H9 -2.080 0.527 1.796 ETKDGv3 21
LX6 H10 0.856 0.627 2.770 ETKDGv3 22
#