data_T8M
#
_chem_comp.id T8M
_chem_comp.name '1-{4-[(thiophen-2-yl)methyl]piperazin-1-yl}ethan-1-one'
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula 'C11 H16 N2 O S'
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2020-03-16
_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 224.323
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code T8M
_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 5RFW
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
_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
T8M N1 N1 N 0 1 N N N N N N 8.751 -2.320 22.941 0.000 0.722 -0.231 N1 T8M 1
T8M C4 C1 C 0 1 N N N N N N 10.055 -2.680 23.520 1.204 1.030 -1.015 C4 T8M 2
T8M C5 C2 C 0 1 Y N N N N N 11.025 -1.546 23.560 2.362 0.216 -0.497 C5 T8M 3
T8M C6 C3 C 0 1 Y N N N N N 12.116 -1.303 22.717 2.704 -0.998 -0.930 C6 T8M 4
T8M C7 C4 C 0 1 Y N N N N N 12.806 -0.125 23.098 3.807 -1.551 -0.304 C7 T8M 5
T8M C8 C5 C 0 1 Y N N N N N 12.131 0.595 24.020 4.362 -0.786 0.637 C8 T8M 6
T8M C10 C6 C 0 1 N N N N N N 6.646 -3.236 22.059 -1.562 -1.004 0.529 C10 T8M 7
T8M N N2 N 0 1 N N N N N N 6.909 -2.582 20.785 -2.625 -0.001 0.360 N T8M 8
T8M C C7 C 0 1 N N N N N N 7.173 -2.546 18.336 -4.261 -1.839 0.104 C T8M 9
T8M O O1 O 0 1 N N N N N N 5.882 -4.146 19.549 -4.768 0.465 0.022 O T8M 10
T8M C1 C8 C 0 1 N N N N N N 6.583 -3.138 19.602 -3.904 -0.376 0.159 C1 T8M 11
T8M C2 C9 C 0 1 N N N N N N 7.629 -1.329 20.990 -2.255 1.421 0.417 C2 T8M 12
T8M C3 C10 C 0 1 N N N N N N 8.946 -1.634 21.660 -1.086 1.659 -0.545 C3 T8M 13
T8M C9 C11 C 0 1 N N N N N N 7.962 -3.539 22.734 -0.421 -0.670 -0.437 C9 T8M 14
T8M S S1 S 0 1 Y N N N N N 10.898 -0.317 24.752 3.475 0.727 0.766 S T8M 15
T8M H7 H2 H 0 1 N N N N N N 9.893 -3.035 24.548 1.028 0.785 -2.062 H7 T8M 16
T8M H8 H3 H 0 1 N N N N N N 10.492 -3.490 22.917 1.436 2.091 -0.924 H8 T8M 17
T8M H9 H4 H 0 1 N N N N N N 12.396 -1.932 21.884 2.160 -1.511 -1.709 H9 T8M 18
T8M H10 H5 H 0 1 N N N N N N 13.765 0.165 22.696 4.190 -2.529 -0.558 H10 T8M 19
T8M H11 H6 H 0 1 N N N N N N 12.348 1.625 24.262 5.226 -1.054 1.228 H11 T8M 20
T8M H15 H7 H 0 1 N N N N N N 6.095 -4.172 21.887 -1.194 -0.977 1.554 H15 T8M 21
T8M H14 H8 H 0 1 N N N N N N 6.047 -2.571 22.699 -1.953 -1.997 0.306 H14 T8M 22
T8M H H9 H 0 1 N N N N N N 6.867 -3.151 17.470 -5.332 -1.945 -0.065 H T8M 23
T8M H2 H10 H 0 1 N N N N N N 6.810 -1.515 18.210 -3.715 -2.315 -0.711 H2 T8M 24
T8M H1 H11 H 0 1 N N N N N N 8.270 -2.542 18.410 -3.993 -2.314 1.047 H1 T8M 25
T8M H4 H12 H 0 1 N N N N N N 7.811 -0.843 20.020 -3.106 2.033 0.117 H4 T8M 26
T8M H3 H13 H 0 1 N N N N N N 7.034 -0.660 21.629 -1.957 1.682 1.432 H3 T8M 27
T8M H6 H14 H 0 1 N N N N N N 9.544 -2.277 20.997 -0.727 2.682 -0.435 H6 T8M 28
T8M H5 H15 H 0 1 N N N N N N 9.483 -0.691 21.838 -1.420 1.499 -1.570 H5 T8M 29
T8M H13 H16 H 0 1 N N N N N N 8.536 -4.234 22.103 -0.764 -0.798 -1.464 H13 T8M 30
T8M H12 H17 H 0 1 N N N N N N 7.764 -4.007 23.710 0.421 -1.337 -0.249 H12 T8M 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
T8M C1 C SING N N 1
T8M O C1 DOUB N N 2
T8M C1 N SING N N 3
T8M N C2 SING N N 4
T8M C3 C2 SING N N 5
T8M N1 C3 SING N N 6
T8M N1 C4 SING N N 7
T8M C4 C5 SING N N 8
T8M C5 C6 DOUB Y N 9
T8M C7 C6 SING Y N 10
T8M C8 C7 DOUB Y N 11
T8M S C8 SING Y N 12
T8M C5 S SING Y N 13
T8M C9 N1 SING N N 14
T8M C10 C9 SING N N 15
T8M N C10 SING N N 16
T8M C4 H7 SING N N 17
T8M C4 H8 SING N N 18
T8M C6 H9 SING N N 19
T8M C7 H10 SING N N 20
T8M C8 H11 SING N N 21
T8M C10 H15 SING N N 22
T8M C10 H14 SING N N 23
T8M C H SING N N 24
T8M C H2 SING N N 25
T8M C H1 SING N N 26
T8M C2 H4 SING N N 27
T8M C2 H3 SING N N 28
T8M C3 H6 SING N N 29
T8M C3 H5 SING N N 30
T8M C9 H13 SING N N 31
T8M C9 H12 SING N N 32
#
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
T8M SMILES ACDLabs 12.01 'N1(CCN(CC1)C(C)=O)Cc2cccs2'
T8M InChI InChI 1.03 'InChI=1S/C11H16N2OS/c1-10(14)13-6-4-12(5-7-13)9-11-3-2-8-15-11/h2-3,8H,4-7,9H2,1H3'
T8M InChIKey InChI 1.03 PEHVQKQLQOREKN-UHFFFAOYSA-N
T8M SMILES_CANONICAL CACTVS 3.385 'CC(=O)N1CCN(CC1)Cc2sccc2'
T8M SMILES CACTVS 3.385 'CC(=O)N1CCN(CC1)Cc2sccc2'
T8M SMILES_CANONICAL 'OpenEye OEToolkits' 2.0.7 'CC(=O)N1CCN(CC1)Cc2cccs2'
T8M SMILES 'OpenEye OEToolkits' 2.0.7 'CC(=O)N1CCN(CC1)Cc2cccs2'
#
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
T8M 'SYSTEMATIC NAME' ACDLabs 12.01 '1-{4-[(thiophen-2-yl)methyl]piperazin-1-yl}ethan-1-one'
T8M 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 2.0.7 '1-[4-(thiophen-2-ylmethyl)piperazin-1-yl]ethanone'
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
T8M 'Create component' 2020-03-16 RCSB
T8M 'Initial release' 2020-03-25 RCSB
T8M 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id T8M
_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 C
_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 ?
#
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
T8M N1 N 6.673 -0.598 1
T8M C4 C 6.673 -2.098 2
T8M C5 C 5.374 -2.848 3
T8M C6 C 4.004 -2.238 4
T8M C7 C 3.000 -3.353 5
T8M C8 C 3.750 -4.652 6
T8M C10 C 7.972 1.652 7
T8M N N 6.673 2.402 8
T8M C C 5.374 4.652 9
T8M O O 7.972 4.652 10
T8M C1 C 6.673 3.902 11
T8M C2 C 5.374 1.652 12
T8M C3 C 5.374 0.152 13
T8M C9 C 7.972 0.152 14
T8M S S 5.217 -4.340 15
#
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
T8M C1 C SINGLE NONE 1
T8M O C1 DOUBLE NONE 2
T8M C1 N SINGLE NONE 3
T8M N C2 SINGLE NONE 4
T8M C3 C2 SINGLE NONE 5
T8M N1 C3 SINGLE NONE 6
T8M N1 C4 SINGLE NONE 7
T8M C4 C5 SINGLE NONE 8
T8M C5 C6 DOUBLE NONE 9
T8M C7 C6 SINGLE NONE 10
T8M C8 C7 DOUBLE NONE 11
T8M S C8 SINGLE NONE 12
T8M C5 S SINGLE NONE 13
T8M C9 N1 SINGLE NONE 14
T8M C10 C9 SINGLE NONE 15
T8M N C10 SINGLE 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
T8M MurckoScaffold S1 scaffold c1csc(CN2CCNCC2)c1 InChI=1S/C9H14N2S/c1-2-9(12-7-1)8-11-5-3-10-4-6-11/h1-2,7,10H,3-6,8H2 XTAPGYLDPZMKRN-UHFFFAOYSA-N
T8M amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
T8M piperazine F2 fragment C1CNCCN1 InChI=1S/C4H10N2/c1-2-6-4-3-5-1/h5-6H,1-4H2 GLUUGHFHXGJENI-UHFFFAOYSA-N
T8M thiophen F3 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
T8M N1 S1 1
T8M C4 S1 1
T8M C5 S1 1
T8M C6 S1 1
T8M C7 S1 1
T8M C8 S1 1
T8M C10 S1 1
T8M N S1 1
T8M C2 S1 1
T8M C3 S1 1
T8M C9 S1 1
T8M S S1 1
T8M N F1 1
T8M C1 F1 1
T8M O F1 1
T8M C F1 1
T8M N1 F2 1
T8M C3 F2 1
T8M C2 F2 1
T8M N F2 1
T8M C10 F2 1
T8M C9 F2 1
T8M C5 F3 1
T8M C6 F3 1
T8M C7 F3 1
T8M C8 F3 1
T8M S F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id T8M
_pdbe_chem_comp_rdkit_properties.exactmw 224.098
_pdbe_chem_comp_rdkit_properties.amw 224.329
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 0
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 3
_pdbe_chem_comp_rdkit_properties.NumHBD 0
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 15
_pdbe_chem_comp_rdkit_properties.NumAtoms 31
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.545
_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 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1
_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 116.781
_pdbe_chem_comp_rdkit_properties.tpsa 23.550
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.357
_pdbe_chem_comp_rdkit_properties.CrippenMR 61.584
_pdbe_chem_comp_rdkit_properties.chi0v 8.027
_pdbe_chem_comp_rdkit_properties.chi1v 4.521
_pdbe_chem_comp_rdkit_properties.chi2v 1.945
_pdbe_chem_comp_rdkit_properties.chi3v 1.945
_pdbe_chem_comp_rdkit_properties.chi4v 1.193
_pdbe_chem_comp_rdkit_properties.chi0n 23.211
_pdbe_chem_comp_rdkit_properties.chi1n 11.704
_pdbe_chem_comp_rdkit_properties.chi2n 1.344
_pdbe_chem_comp_rdkit_properties.chi3n 1.344
_pdbe_chem_comp_rdkit_properties.chi4n 0.750
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.870
_pdbe_chem_comp_rdkit_properties.kappa1 2.514
_pdbe_chem_comp_rdkit_properties.kappa2 4.768
_pdbe_chem_comp_rdkit_properties.kappa3 2.793
_pdbe_chem_comp_rdkit_properties.Phi 0.799
#
_pdbe_chem_comp_external_mappings.comp_id T8M
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PubChem
_pdbe_chem_comp_external_mappings.resource_id 60655566
#
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
T8M N1 0.603 -0.026 -0.773 ETKDGv3 1
T8M C4 2.058 -0.156 -0.993 ETKDGv3 2
T8M C5 2.794 -0.087 0.310 ETKDGv3 3
T8M C6 2.830 0.975 1.114 ETKDGv3 4
T8M C7 3.612 0.761 2.351 ETKDGv3 5
T8M C8 4.146 -0.454 2.460 ETKDGv3 6
T8M C10 -1.605 0.172 -1.993 ETKDGv3 7
T8M N -2.120 -0.096 -0.639 ETKDGv3 8
T8M C -4.003 0.125 1.096 ETKDGv3 9
T8M O -4.196 0.873 -1.151 ETKDGv3 10
T8M C1 -3.457 0.325 -0.287 ETKDGv3 11
T8M C2 -1.373 -0.980 0.270 ETKDGv3 12
T8M C3 0.024 -1.279 -0.266 ETKDGv3 13
T8M C9 -0.073 0.387 -2.021 ETKDGv3 14
T8M S 3.718 -1.424 1.031 ETKDGv3 15
T8M H7 2.432 0.678 -1.629 ETKDGv3 16
T8M H8 2.299 -1.109 -1.516 ETKDGv3 17
T8M H9 2.329 1.907 0.886 ETKDGv3 18
T8M H10 3.739 1.525 3.107 ETKDGv3 19
T8M H11 4.746 -0.789 3.295 ETKDGv3 20
T8M H15 -1.867 -0.691 -2.643 ETKDGv3 21
T8M H14 -2.091 1.073 -2.429 ETKDGv3 22
T8M H -5.028 0.546 1.175 ETKDGv3 23
T8M H2 -3.355 0.641 1.834 ETKDGv3 24
T8M H1 -4.049 -0.958 1.332 ETKDGv3 25
T8M H4 -1.927 -1.934 0.411 ETKDGv3 26
T8M H3 -1.263 -0.481 1.257 ETKDGv3 27
T8M H6 -0.029 -2.049 -1.071 ETKDGv3 28
T8M H5 0.632 -1.696 0.567 ETKDGv3 29
T8M H13 0.342 -0.165 -2.897 ETKDGv3 30
T8M H12 0.131 1.468 -2.187 ETKDGv3 31
#