data_Q85
#
_chem_comp.id Q85
_chem_comp.name '~{N}-[(4-methoxyphenyl)methyl]-2-selanyl-benzamide'
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula 'C15 H15 N O2 Se'
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2020-05-26
_chem_comp.pdbx_modified_date 2024-09-27
_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 320.245
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code Q85
_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 6Z4I
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBE
_chem_comp.pdbx_pcm Y
#
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
Q85 O1 O1 O 0 1 N N N N N N 8.053 5.759 22.437 -6.664 -0.476 -0.279 O1 Q85 1
Q85 C1 C1 C 0 1 N N N N N N 8.333 6.882 23.274 -7.319 -0.706 0.970 C1 Q85 2
Q85 O2 O2 O 0 1 N N N N N N 12.451 1.539 19.009 1.367 1.451 0.006 O2 Q85 3
Q85 C2 C2 C 0 1 Y N N N N N 8.960 5.391 21.470 -5.376 -0.045 -0.231 C2 Q85 4
Q85 C3 C3 C 0 1 Y N N N N N 9.066 4.052 21.122 -4.680 0.198 -1.406 C3 Q85 5
Q85 C4 C4 C 0 1 Y N N N N N 9.998 3.653 20.169 -3.371 0.636 -1.354 C4 Q85 6
Q85 C5 C5 C 0 1 Y N N N N N 10.776 4.579 19.488 -2.754 0.832 -0.132 C5 Q85 7
Q85 C6 C6 C 0 1 N N N N N N 11.760 4.156 18.420 -1.324 1.304 -0.079 C6 Q85 8
Q85 C7 C7 C 0 1 N N N N N N 11.725 1.754 18.020 0.907 0.327 -0.032 C7 Q85 9
Q85 C8 C8 C 0 1 Y N N N N N 11.214 0.602 17.206 1.812 -0.842 -0.029 C8 Q85 10
Q85 C9 C9 C 0 1 Y N N N N N 11.152 0.658 15.823 1.288 -2.135 -0.079 C9 Q85 11
Q85 C10 C10 C 0 1 Y N N N N N 10.725 -0.427 15.103 2.138 -3.221 -0.082 C10 Q85 12
Q85 C11 C11 C 0 1 Y N N N N N 10.362 -1.597 15.740 3.508 -3.032 -0.036 C11 Q85 13
Q85 C12 C12 C 0 1 Y N N N N N 10.450 -1.691 17.104 4.034 -1.753 0.013 C12 Q85 14
Q85 C13 C13 C 0 1 Y N N N N N 10.887 -0.604 17.838 3.195 -0.658 0.017 C13 Q85 15
Q85 N1 N1 N 0 1 N N N N N N 11.339 2.984 17.661 -0.427 0.146 -0.076 N1 Q85 16
Q85 SE1 SE1 SE 0 0 N N N N N N 10.991 -0.642 19.742 3.944 1.152 0.078 SE1 Q85 17
Q85 C14 C14 C 0 1 Y N N N N N 10.659 5.917 19.849 -3.446 0.590 1.041 C14 Q85 18
Q85 C15 C15 C 0 1 Y N N N N N 9.750 6.330 20.814 -4.757 0.158 0.994 C15 Q85 19
Q85 H1 H1 H 0 1 N N N N N N 7.504 7.028 23.983 -6.776 -1.468 1.530 H1 Q85 20
Q85 H2 H2 H 0 1 N N N N N N 9.264 6.701 23.831 -7.341 0.220 1.545 H2 Q85 21
Q85 H3 H3 H 0 1 N N N N N N 8.447 7.783 22.653 -8.338 -1.046 0.789 H3 Q85 22
Q85 H4 H4 H 0 1 N N N N N N 8.425 3.320 21.591 -5.161 0.045 -2.361 H4 Q85 23
Q85 H5 H5 H 0 1 N N N N N N 10.119 2.601 19.955 -2.829 0.826 -2.269 H5 Q85 24
Q85 H6 H6 H 0 1 N N N N N N 12.721 3.928 18.905 -1.113 1.925 -0.949 H6 Q85 25
Q85 H7 H7 H 0 1 N N N N N N 11.892 4.994 17.719 -1.168 1.887 0.829 H7 Q85 26
Q85 H8 H8 H 0 1 N N N N N N 11.442 1.563 15.309 0.219 -2.284 -0.114 H8 Q85 27
Q85 H9 H9 H 0 1 N N N N N N 10.672 -0.366 14.026 1.734 -4.222 -0.120 H9 Q85 28
Q85 H10 H10 H 0 1 N N N N N N 10.009 -2.439 15.163 4.169 -3.886 -0.038 H10 Q85 29
Q85 H11 H11 H 0 1 N N N N N N 10.179 -2.610 17.603 5.104 -1.612 0.049 H11 Q85 30
Q85 H12 H12 H 0 1 N N N N N N 10.753 3.101 16.860 -0.794 -0.752 -0.107 H12 Q85 31
Q85 H13 H13 H 0 1 N N N N N N 11.484 0.643 20.229 4.011 1.394 1.618 H13 Q85 32
Q85 H14 H14 H 0 1 N N N N N N 11.289 6.651 19.368 -2.962 0.744 1.994 H14 Q85 33
Q85 H15 H15 H 0 1 N N N N N N 9.656 7.379 21.055 -5.297 -0.031 1.911 H15 Q85 34
#
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
Q85 C10 C11 DOUB Y N 1
Q85 C10 C9 SING Y N 2
Q85 C11 C12 SING Y N 3
Q85 C9 C8 DOUB Y N 4
Q85 C12 C13 DOUB Y N 5
Q85 C8 C13 SING Y N 6
Q85 C8 C7 SING N N 7
Q85 N1 C7 SING N N 8
Q85 N1 C6 SING N N 9
Q85 C13 SE1 SING N N 10
Q85 C7 O2 DOUB N N 11
Q85 C6 C5 SING N N 12
Q85 C5 C14 DOUB Y N 13
Q85 C5 C4 SING Y N 14
Q85 C14 C15 SING Y N 15
Q85 C4 C3 DOUB Y N 16
Q85 C15 C2 DOUB Y N 17
Q85 C3 C2 SING Y N 18
Q85 C2 O1 SING N N 19
Q85 O1 C1 SING N N 20
Q85 C1 H1 SING N N 21
Q85 C1 H2 SING N N 22
Q85 C1 H3 SING N N 23
Q85 C3 H4 SING N N 24
Q85 C4 H5 SING N N 25
Q85 C6 H6 SING N N 26
Q85 C6 H7 SING N N 27
Q85 C9 H8 SING N N 28
Q85 C10 H9 SING N N 29
Q85 C11 H10 SING N N 30
Q85 C12 H11 SING N N 31
Q85 N1 H12 SING N N 32
Q85 SE1 H13 SING N N 33
Q85 C14 H14 SING N N 34
Q85 C15 H15 SING N N 35
#
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
Q85 InChI InChI 1.03 'InChI=1S/C15H15NO2Se/c1-18-12-8-6-11(7-9-12)10-16-15(17)13-4-2-3-5-14(13)19/h2-9,19H,10H2,1H3,(H,16,17)'
Q85 InChIKey InChI 1.03 YYKTWDKCQYEMIR-UHFFFAOYSA-N
Q85 SMILES_CANONICAL CACTVS 3.385 'COc1ccc(CNC(=O)c2ccccc2[SeH])cc1'
Q85 SMILES CACTVS 3.385 'COc1ccc(CNC(=O)c2ccccc2[SeH])cc1'
Q85 SMILES_CANONICAL 'OpenEye OEToolkits' 2.0.7 'COc1ccc(cc1)CNC(=O)c2ccccc2[SeH]'
Q85 SMILES 'OpenEye OEToolkits' 2.0.7 'COc1ccc(cc1)CNC(=O)c2ccccc2[SeH]'
#
_pdbx_chem_comp_identifier.comp_id Q85
_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 '~{N}-[(4-methoxyphenyl)methyl]-2-selanyl-benzamide'
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
Q85 'Create component' 2020-05-26 PDBE
Q85 'Initial release' 2020-09-16 RCSB
Q85 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id Q85
_pdbx_chem_comp_pcm.modified_residue_id CYS
_pdbx_chem_comp_pcm.type None
_pdbx_chem_comp_pcm.category 'Covalent chemical modification'
_pdbx_chem_comp_pcm.position 'Amino-acid side chain'
_pdbx_chem_comp_pcm.polypeptide_position 'Any position'
_pdbx_chem_comp_pcm.comp_id_linking_atom SE1
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom SG
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ?
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
_pdbx_chem_comp_pcm.first_instance_model_db_code 6Z4I
#
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
Q85 O1 O -6.023 -1.873 1
Q85 C1 C -7.320 -1.118 2
Q85 O2 O 1.787 2.599 3
Q85 C2 C -4.721 -1.128 4
Q85 C3 C -4.716 0.372 5
Q85 C4 C -3.414 1.117 6
Q85 C5 C -2.118 0.363 7
Q85 C6 C -0.816 1.108 8
Q85 C7 C 1.782 1.099 9
Q85 C8 C 3.078 0.344 10
Q85 C9 C 3.073 -1.156 11
Q85 C10 C 4.369 -1.910 12
Q85 C11 C 5.671 -1.165 13
Q85 C12 C 5.676 0.335 14
Q85 C13 C 4.380 1.090 15
Q85 N1 N 0.480 0.354 16
Q85 SE1 Se 4.385 2.590 17
Q85 C14 C -2.123 -1.137 18
Q85 C15 C -3.425 -1.883 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
Q85 C10 C11 SINGLE NONE 1
Q85 C10 C9 DOUBLE NONE 2
Q85 C11 C12 DOUBLE NONE 3
Q85 C9 C8 SINGLE NONE 4
Q85 C12 C13 SINGLE NONE 5
Q85 C8 C13 DOUBLE NONE 6
Q85 C8 C7 SINGLE NONE 7
Q85 N1 C7 SINGLE NONE 8
Q85 N1 C6 SINGLE NONE 9
Q85 C13 SE1 SINGLE NONE 10
Q85 C7 O2 DOUBLE NONE 11
Q85 C6 C5 SINGLE NONE 12
Q85 C5 C14 DOUBLE NONE 13
Q85 C5 C4 SINGLE NONE 14
Q85 C14 C15 SINGLE NONE 15
Q85 C4 C3 DOUBLE NONE 16
Q85 C15 C2 DOUBLE NONE 17
Q85 C3 C2 SINGLE NONE 18
Q85 C2 O1 SINGLE NONE 19
Q85 O1 C1 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
Q85 MurckoScaffold S1 scaffold O=C(NCc1ccccc1)c1ccccc1 InChI=1S/C14H13NO/c16-14(13-9-5-2-6-10-13)15-11-12-7-3-1-4-8-12/h1-10H,11H2,(H,15,16) LKQUCICFTHBFAL-UHFFFAOYSA-N
Q85 amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
Q85 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
Q85 O2 S1 1
Q85 C2 S1 1
Q85 C3 S1 1
Q85 C4 S1 1
Q85 C5 S1 1
Q85 C6 S1 1
Q85 C7 S1 1
Q85 C8 S1 1
Q85 C9 S1 1
Q85 C10 S1 1
Q85 C11 S1 1
Q85 C12 S1 1
Q85 C13 S1 1
Q85 N1 S1 1
Q85 C14 S1 1
Q85 C15 S1 1
Q85 N1 F1 1
Q85 C7 F1 1
Q85 O2 F1 1
Q85 C8 F1 1
Q85 C2 F2 1
Q85 C15 F2 1
Q85 C14 F2 1
Q85 C5 F2 1
Q85 C4 F2 1
Q85 C3 F2 1
Q85 C8 F2 2
Q85 C9 F2 2
Q85 C10 F2 2
Q85 C11 F2 2
Q85 C12 F2 2
Q85 C13 F2 2
#
_pdbe_chem_comp_rdkit_properties.comp_id Q85
_pdbe_chem_comp_rdkit_properties.exactmw 321.027
_pdbe_chem_comp_rdkit_properties.amw 320.250
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 6
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 2
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 19
_pdbe_chem_comp_rdkit_properties.NumAtoms 34
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.133
_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 140.949
_pdbe_chem_comp_rdkit_properties.tpsa 38.330
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.579
_pdbe_chem_comp_rdkit_properties.CrippenMR 76.247
_pdbe_chem_comp_rdkit_properties.chi0v 10.885
_pdbe_chem_comp_rdkit_properties.chi1v 5.620
_pdbe_chem_comp_rdkit_properties.chi2v 2.483
_pdbe_chem_comp_rdkit_properties.chi3v 2.483
_pdbe_chem_comp_rdkit_properties.chi4v 1.419
_pdbe_chem_comp_rdkit_properties.chi0n 24.172
_pdbe_chem_comp_rdkit_properties.chi1n 12.119
_pdbe_chem_comp_rdkit_properties.chi2n 1.840
_pdbe_chem_comp_rdkit_properties.chi3n 1.840
_pdbe_chem_comp_rdkit_properties.chi4n 1.022
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.771
_pdbe_chem_comp_rdkit_properties.kappa1 4.110
_pdbe_chem_comp_rdkit_properties.kappa2 6.412
_pdbe_chem_comp_rdkit_properties.kappa3 3.596
_pdbe_chem_comp_rdkit_properties.Phi 1.387
#
_pdbe_chem_comp_external_mappings.comp_id Q85
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PDBe
_pdbe_chem_comp_external_mappings.resource_id Q85
#
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
Q85 O1 4.615 -0.565 1.401 ETKDGv3 1
Q85 C1 5.389 0.584 1.733 ETKDGv3 2
Q85 O2 -1.360 -1.765 -0.159 ETKDGv3 3
Q85 C2 3.555 -0.575 0.480 ETKDGv3 4
Q85 C3 2.847 -1.853 0.247 ETKDGv3 5
Q85 C4 1.830 -1.918 -0.621 ETKDGv3 6
Q85 C5 1.400 -0.708 -1.361 ETKDGv3 7
Q85 C6 0.232 -0.774 -2.306 ETKDGv3 8
Q85 C7 -1.662 -0.632 -0.623 ETKDGv3 9
Q85 C8 -2.794 0.124 -0.042 ETKDGv3 10
Q85 C9 -3.748 0.794 -0.963 ETKDGv3 11
Q85 C10 -4.790 1.481 -0.482 ETKDGv3 12
Q85 C11 -5.001 1.580 0.974 ETKDGv3 13
Q85 C12 -4.149 0.983 1.814 ETKDGv3 14
Q85 C13 -2.990 0.222 1.295 ETKDGv3 15
Q85 N1 -0.925 -0.092 -1.730 ETKDGv3 16
Q85 SE1 -1.772 -0.525 2.592 ETKDGv3 17
Q85 C14 2.038 0.455 -1.147 ETKDGv3 18
Q85 C15 3.163 0.526 -0.191 ETKDGv3 19
Q85 H1 6.154 0.300 2.485 ETKDGv3 20
Q85 H2 4.737 1.371 2.169 ETKDGv3 21
Q85 H3 5.905 0.971 0.830 ETKDGv3 22
Q85 H4 3.154 -2.741 0.784 ETKDGv3 23
Q85 H5 1.321 -2.861 -0.777 ETKDGv3 24
Q85 H6 -0.033 -1.827 -2.544 ETKDGv3 25
Q85 H7 0.510 -0.283 -3.264 ETKDGv3 26
Q85 H8 -3.616 0.718 -2.035 ETKDGv3 27
Q85 H9 -5.484 1.961 -1.159 ETKDGv3 28
Q85 H10 -5.845 2.136 1.359 ETKDGv3 29
Q85 H11 -4.307 1.063 2.883 ETKDGv3 30
Q85 H12 -1.182 0.847 -2.110 ETKDGv3 31
Q85 H13 -2.577 -1.833 2.616 ETKDGv3 32
Q85 H14 1.731 1.355 -1.666 ETKDGv3 33
Q85 H15 3.654 1.479 -0.048 ETKDGv3 34
#