data_I6A
#
_chem_comp.id I6A
_chem_comp.name 5-methoxy-6-pyridin-4-yl-1~{H}-indole
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C14 H12 N2 O"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2022-02-12
_chem_comp.pdbx_modified_date 2022-08-22
_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 224.258
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code I6A
_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 7R52
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBE
#
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
I6A C1 C1 C 0 1 Y N N N N N 37.517 32.587 12.171 -0.176 0.177 -0.020 C1 I6A 1
I6A C2 C2 C 0 1 Y N N N N N 36.562 32.719 13.189 0.693 1.257 -0.122 C2 I6A 2
I6A C3 C3 C 0 1 Y N N N N N 38.497 31.580 12.198 0.325 -1.128 0.100 C3 I6A 3
I6A C13 C4 C 0 1 Y N N N N N 37.660 35.892 10.388 -3.833 -0.080 -0.858 C13 I6A 4
I6A C14 C5 C 0 1 Y N N N N N 37.144 34.245 8.787 -3.589 1.553 0.756 C14 I6A 5
I6A C15 C6 C 0 1 Y N N N N N 37.184 33.246 9.765 -2.224 1.363 0.806 C15 I6A 6
I6A C16 C7 C 0 1 Y N N N N N 37.710 34.934 11.401 -2.476 -0.326 -0.879 C16 I6A 7
I6A C17 C8 C 0 1 N N N N N N 40.383 30.447 11.036 0.044 -3.479 0.320 C17 I6A 8
I6A C4 C9 C 0 1 Y N N N N N 36.612 31.804 14.239 2.065 1.044 -0.106 C4 I6A 9
I6A C5 C10 C 0 1 Y N N N N N 37.585 30.823 14.279 2.565 -0.267 0.014 C5 I6A 10
I6A N6 N1 N 0 1 Y N N N N N 35.823 31.705 15.327 3.153 1.888 -0.187 N6 I6A 11
I6A C7 C11 C 0 1 Y N N N N N 38.536 30.672 13.266 1.685 -1.348 0.117 C7 I6A 12
I6A C8 C12 C 0 1 Y N N N N N 36.184 30.693 16.075 4.310 1.161 -0.122 C8 I6A 13
I6A C9 C13 C 0 1 Y N N N N N 37.245 30.067 15.540 4.024 -0.146 -0.000 C9 I6A 14
I6A C10 C14 C 0 1 Y N N N N N 37.489 33.593 11.085 -1.640 0.407 -0.031 C10 I6A 15
I6A N11 N2 N 0 1 Y N N N N N 37.381 35.531 9.121 -4.343 0.835 -0.056 N11 I6A 16
I6A O12 O1 O 0 1 N N N N N N 39.425 31.511 11.152 -0.533 -2.177 0.200 O12 I6A 17
I6A H1 H1 H 0 1 N N N N N N 35.816 33.500 13.161 0.303 2.259 -0.215 H1 I6A 18
I6A H2 H2 H 0 1 N N N N N N 37.846 36.930 10.621 -4.487 -0.642 -1.509 H2 I6A 19
I6A H3 H3 H 0 1 N N N N N N 36.923 33.987 7.762 -4.049 2.292 1.395 H3 I6A 20
I6A H4 H4 H 0 1 N N N N N N 36.982 32.218 9.504 -1.613 1.954 1.473 H4 I6A 21
I6A H5 H5 H 0 1 N N N N N N 37.918 35.227 12.419 -2.065 -1.075 -1.541 H5 I6A 22
I6A H6 H6 H 0 1 N N N N N N 41.001 30.606 10.140 -0.749 -4.223 0.391 H6 I6A 23
I6A H7 H7 H 0 1 N N N N N N 41.026 30.434 11.928 0.659 -3.685 -0.557 H7 I6A 24
I6A H8 H8 H 0 1 N N N N N N 39.855 29.486 10.951 0.664 -3.520 1.216 H8 I6A 25
I6A H9 H9 H 0 1 N N N N N N 35.064 32.322 15.535 3.105 2.852 -0.276 H9 I6A 26
I6A H10 H10 H 0 1 N N N N N N 39.274 29.885 13.304 2.070 -2.353 0.209 H10 I6A 27
I6A H11 H11 H 0 1 N N N N N N 35.697 30.402 16.994 5.306 1.576 -0.163 H11 I6A 28
I6A H12 H12 H 0 1 N N N N N N 37.752 29.198 15.933 4.736 -0.955 0.074 H12 I6A 29
#
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
I6A C14 N11 DOUB Y N 1
I6A C14 C15 SING Y N 2
I6A N11 C13 SING Y N 3
I6A C15 C10 DOUB Y N 4
I6A C13 C16 DOUB Y N 5
I6A C17 O12 SING N N 6
I6A C10 C16 SING Y N 7
I6A C10 C1 SING N N 8
I6A O12 C3 SING N N 9
I6A C1 C3 DOUB Y N 10
I6A C1 C2 SING Y N 11
I6A C3 C7 SING Y N 12
I6A C2 C4 DOUB Y N 13
I6A C7 C5 DOUB Y N 14
I6A C4 C5 SING Y N 15
I6A C4 N6 SING Y N 16
I6A C5 C9 SING Y N 17
I6A N6 C8 SING Y N 18
I6A C9 C8 DOUB Y N 19
I6A C2 H1 SING N N 20
I6A C13 H2 SING N N 21
I6A C14 H3 SING N N 22
I6A C15 H4 SING N N 23
I6A C16 H5 SING N N 24
I6A C17 H6 SING N N 25
I6A C17 H7 SING N N 26
I6A C17 H8 SING N N 27
I6A N6 H9 SING N N 28
I6A C7 H10 SING N N 29
I6A C8 H11 SING N N 30
I6A C9 H12 SING 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
I6A InChI InChI 1.06 InChI=1S/C14H12N2O/c1-17-14-8-11-4-7-16-13(11)9-12(14)10-2-5-15-6-3-10/h2-9,16H,1H3
I6A InChIKey InChI 1.06 CCGSQZWVGGCGET-UHFFFAOYSA-N
I6A SMILES_CANONICAL CACTVS 3.385 COc1cc2cc[nH]c2cc1c3ccncc3
I6A SMILES CACTVS 3.385 COc1cc2cc[nH]c2cc1c3ccncc3
I6A SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 COc1cc2cc[nH]c2cc1c3ccncc3
I6A SMILES "OpenEye OEToolkits" 2.0.7 COc1cc2cc[nH]c2cc1c3ccncc3
#
_pdbx_chem_comp_identifier.comp_id I6A
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.7
_pdbx_chem_comp_identifier.identifier 5-methoxy-6-pyridin-4-yl-1~{H}-indole
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
I6A 'Create component' 2022-02-12 PDBE
I6A 'Initial release' 2022-03-23 RCSB
I6A 'Modify descriptor' 2022-08-22 RCSB
#
loop_
_software.name
_software.version
_software.description
rdkit 2025.03.3 'Core functionality.'
pdbeccdutils 1.0.0 '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
I6A C1 C 6.897 -0.375 1
I6A C2 C 8.196 -1.125 2
I6A C3 C 6.897 1.125 3
I6A C13 C 4.299 -3.375 4
I6A C14 C 3.000 -1.125 5
I6A C15 C 4.299 -0.375 6
I6A C16 C 5.598 -2.625 7
I6A C17 C 5.598 3.375 8
I6A C4 C 9.495 -0.375 9
I6A C5 C 9.495 1.125 10
I6A N6 N 10.915 -0.832 11
I6A C7 C 8.196 1.875 12
I6A C8 C 11.790 0.375 13
I6A C9 C 10.915 1.582 14
I6A C10 C 5.598 -1.125 15
I6A N11 N 3.000 -2.625 16
I6A O12 O 5.598 1.875 17
#
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
I6A C14 N11 SINGLE NONE 1
I6A C14 C15 DOUBLE NONE 2
I6A N11 C13 DOUBLE NONE 3
I6A C15 C10 SINGLE NONE 4
I6A C13 C16 SINGLE NONE 5
I6A C17 O12 SINGLE NONE 6
I6A C10 C16 DOUBLE NONE 7
I6A C10 C1 SINGLE NONE 8
I6A O12 C3 SINGLE NONE 9
I6A C1 C3 SINGLE NONE 10
I6A C1 C2 DOUBLE NONE 11
I6A C3 C7 DOUBLE NONE 12
I6A C2 C4 SINGLE NONE 13
I6A C7 C5 SINGLE NONE 14
I6A C4 C5 DOUBLE NONE 15
I6A C4 N6 SINGLE NONE 16
I6A C5 C9 SINGLE NONE 17
I6A N6 C8 SINGLE NONE 18
I6A C9 C8 DOUBLE 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
I6A MurckoScaffold S1 scaffold 'c1cc(-c2ccc3cc[nH]c3c2)ccn1' InChI=1S/C13H10N2/c1-2-12(10-3-6-14-7-4-10)9-13-11(1)5-8-15-13/h1-9,15H FOCQQVWHCPIMHK-UHFFFAOYSA-N
I6A indole F1 fragment 'c1ccc2[nH]ccc2c1' InChI=1S/C8H7N/c1-2-4-8-7(3-1)5-6-9-8/h1-6,9H SIKJAQJRHWYJAI-UHFFFAOYSA-N
I6A phenyl F2 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
I6A pyridine F3 fragment c1ccncc1 InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H JUJWROOIHBZHMG-UHFFFAOYSA-N
I6A pyrrole F4 fragment 'c1cc[nH]c1' InChI=1S/C4H5N/c1-2-4-5-3-1/h1-5H KAESVJOAVNADME-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
I6A C1 S1 1
I6A C2 S1 1
I6A C3 S1 1
I6A C13 S1 1
I6A C14 S1 1
I6A C15 S1 1
I6A C16 S1 1
I6A C4 S1 1
I6A C5 S1 1
I6A N6 S1 1
I6A C7 S1 1
I6A C8 S1 1
I6A C9 S1 1
I6A C10 S1 1
I6A N11 S1 1
I6A C4 F1 1
I6A C5 F1 1
I6A C9 F1 1
I6A C8 F1 1
I6A N6 F1 1
I6A C7 F1 1
I6A C3 F1 1
I6A C1 F1 1
I6A C2 F1 1
I6A C1 F2 1
I6A C3 F2 1
I6A C7 F2 1
I6A C5 F2 1
I6A C4 F2 1
I6A C2 F2 1
I6A C13 F3 1
I6A C16 F3 1
I6A C10 F3 1
I6A C15 F3 1
I6A C14 F3 1
I6A N11 F3 1
I6A C4 F4 1
I6A C5 F4 1
I6A C9 F4 1
I6A C8 F4 1
I6A N6 F4 1
#
_pdbe_chem_comp_rdkit_properties.comp_id I6A
_pdbe_chem_comp_rdkit_properties.exactmw 224.095
_pdbe_chem_comp_rdkit_properties.amw 224.263
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 3
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 2
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 17
_pdbe_chem_comp_rdkit_properties.NumAtoms 29
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 3
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.071
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 3
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 2
_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 115.995
_pdbe_chem_comp_rdkit_properties.tpsa 37.910
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.968
_pdbe_chem_comp_rdkit_properties.CrippenMR 63.944
_pdbe_chem_comp_rdkit_properties.chi0v 8.303
_pdbe_chem_comp_rdkit_properties.chi1v 4.553
_pdbe_chem_comp_rdkit_properties.chi2v 2.120
_pdbe_chem_comp_rdkit_properties.chi3v 2.120
_pdbe_chem_comp_rdkit_properties.chi4v 1.391
_pdbe_chem_comp_rdkit_properties.chi0n 20.303
_pdbe_chem_comp_rdkit_properties.chi1n 10.500
_pdbe_chem_comp_rdkit_properties.chi2n 2.120
_pdbe_chem_comp_rdkit_properties.chi3n 2.120
_pdbe_chem_comp_rdkit_properties.chi4n 1.391
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.290
_pdbe_chem_comp_rdkit_properties.kappa1 3.354
_pdbe_chem_comp_rdkit_properties.kappa2 3.940
_pdbe_chem_comp_rdkit_properties.kappa3 1.654
_pdbe_chem_comp_rdkit_properties.Phi 0.777
#
_pdbe_chem_comp_external_mappings.comp_id I6A
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PubChem
_pdbe_chem_comp_external_mappings.resource_id 162679117
#
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
I6A C1 0.311 -0.372 -0.069 ETKDGv3 1
I6A C2 -0.451 -1.488 -0.147 ETKDGv3 2
I6A C3 -0.346 0.978 0.055 ETKDGv3 3
I6A C13 3.889 -1.314 -1.016 ETKDGv3 4
I6A C14 3.939 0.123 0.895 ETKDGv3 5
I6A C15 2.605 0.227 0.925 ETKDGv3 6
I6A C16 2.415 -1.229 -1.019 ETKDGv3 7
I6A C17 -0.006 3.460 0.204 ETKDGv3 8
I6A C4 -1.912 -1.348 -0.089 ETKDGv3 9
I6A C5 -2.486 -0.173 0.036 ETKDGv3 10
I6A N6 -2.879 -2.384 -0.145 ETKDGv3 11
I6A C7 -1.698 1.064 0.114 ETKDGv3 12
I6A C8 -4.123 -1.691 -0.040 ETKDGv3 13
I6A C9 -3.929 -0.377 0.069 ETKDGv3 14
I6A C10 1.790 -0.483 -0.091 ETKDGv3 15
I6A N11 4.578 -0.675 -0.116 ETKDGv3 16
I6A O12 0.470 2.122 0.086 ETKDGv3 17
I6A H1 -0.009 -2.473 -0.224 ETKDGv3 18
I6A H2 4.398 -1.907 -1.763 ETKDGv3 19
I6A H3 4.541 0.634 1.635 ETKDGv3 20
I6A H4 2.130 0.814 1.701 ETKDGv3 21
I6A H5 1.857 -1.756 -1.783 ETKDGv3 22
I6A H6 -0.657 3.711 -0.660 ETKDGv3 23
I6A H7 0.860 4.153 0.208 ETKDGv3 24
I6A H8 -0.565 3.584 1.155 ETKDGv3 25
I6A H9 -2.721 -3.411 -0.239 ETKDGv3 26
I6A H10 -2.212 2.011 0.202 ETKDGv3 27
I6A H11 -5.091 -2.175 -0.048 ETKDGv3 28
I6A H12 -4.698 0.377 0.162 ETKDGv3 29
#