data_T9O
#
_chem_comp.id T9O
_chem_comp.name "(5R)-2-butanimidoyl-5-[(2R)-2-ethylsulfanylpropyl]-3-oxidanyl-cyclohex-2-en-1-one"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C15 H25 N O2 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2023-04-20
_chem_comp.pdbx_modified_date 2023-12-15
_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 283.430
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code T9O
_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 8HZU
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBJ
#
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
T9O C10 C1 C 0 1 N N N N N N 1.077 -2.245 86.137 2.199 1.743 -0.305 C10 T9O 1
T9O C15 C2 C 0 1 N N N N N N -3.233 0.678 85.417 5.385 -2.446 1.038 C15 T9O 2
T9O C17 C3 C 0 1 N N N N N N 5.345 -6.657 83.632 -5.553 -0.733 0.156 C17 T9O 3
T9O C1 C4 C 0 1 N N N N N N 4.040 -3.893 83.476 -1.768 0.038 -0.002 C1 T9O 4
T9O C2 C5 C 0 1 N N N N N N 3.016 -3.235 82.985 -0.941 -0.333 -1.033 C2 T9O 5
T9O C3 C6 C 0 1 N N N N N N 1.827 -2.942 83.891 0.396 0.308 -1.266 C3 T9O 6
T9O C4 C7 C 0 1 N N R N N N 2.232 -2.166 85.142 0.922 0.961 0.010 C4 T9O 7
T9O C5 C8 C 0 1 N N N N N N 3.429 -2.811 85.850 -0.141 1.919 0.564 C5 T9O 8
T9O C6 C9 C 0 1 N N N N N N 4.286 -3.754 84.993 -1.354 1.090 0.932 C6 T9O 9
T9O C9 C10 C 0 1 N N N N N N 5.072 -4.509 82.513 -3.076 -0.616 0.162 C9 T9O 10
T9O C11 C11 C 0 1 N N R N N N 0.219 -0.984 86.292 3.303 0.769 -0.722 C11 T9O 11
T9O C12 C12 C 0 1 N N N N N N 0.752 0.204 85.491 4.540 1.557 -1.158 C12 T9O 12
T9O C14 C13 C 0 1 N N N N N N -2.645 -0.223 86.503 4.921 -1.462 -0.038 C14 T9O 13
T9O C18 C14 C 0 1 N N N N N N 6.115 -5.511 82.997 -4.337 0.110 -0.231 C18 T9O 14
T9O C19 C15 C 0 1 N N N N N N 5.029 -7.623 82.512 -6.833 0.004 -0.243 C19 T9O 15
T9O N16 N1 N 0 1 N N N N N N 5.090 -4.215 81.291 -3.144 -1.817 0.644 N16 T9O 16
T9O O7 O1 O 0 1 N N N N N N 5.139 -4.358 85.559 -1.961 1.289 1.963 O7 T9O 17
T9O O8 O2 O 0 1 N N N N N N 3.132 -2.531 81.779 -1.344 -1.306 -1.864 O8 T9O 18
T9O S13 S1 S 0 1 N N N N N N -1.472 -1.394 85.755 3.730 -0.298 0.682 S13 T9O 19
T9O H1 H1 H 0 1 N N N N N N 0.415 -3.062 85.816 2.006 2.442 -1.118 H1 T9O 20
T9O H2 H2 H 0 1 N N N N N N 1.502 -2.483 87.123 2.516 2.294 0.580 H2 T9O 21
T9O H3 H3 H 0 1 N N N N N N -3.942 1.386 85.871 5.860 -1.898 1.851 H3 T9O 22
T9O H4 H4 H 0 1 N N N N N N -2.423 1.236 84.925 4.526 -2.996 1.422 H4 T9O 23
T9O H5 H5 H 0 1 N N N N N N -3.757 0.061 84.673 6.101 -3.146 0.605 H5 T9O 24
T9O H6 H6 H 0 1 N N N N N N 4.416 -6.286 84.089 -5.510 -1.692 -0.361 H6 T9O 25
T9O H7 H7 H 0 1 N N N N N N 5.959 -7.150 84.400 -5.551 -0.901 1.233 H7 T9O 26
T9O H10 H10 H 0 1 N N N N N N 1.091 -2.348 83.329 1.103 -0.452 -1.597 H10 T9O 27
T9O H11 H11 H 0 1 N N N N N N 1.372 -3.895 84.197 0.298 1.067 -2.042 H11 T9O 28
T9O H12 H12 H 0 1 N N N N N N 2.453 -1.118 84.891 1.140 0.191 0.751 H12 T9O 29
T9O H13 H13 H 0 1 N N N N N N 3.045 -3.388 86.704 0.242 2.427 1.449 H13 T9O 30
T9O H14 H14 H 0 1 N N N N N N 4.080 -2.003 86.216 -0.410 2.653 -0.196 H14 T9O 31
T9O H15 H15 H 0 1 N N N N N N 0.150 -0.713 87.356 2.952 0.155 -1.551 H15 T9O 32
T9O H16 H16 H 0 1 N N N N N N 1.773 0.443 85.823 5.327 0.863 -1.455 H16 T9O 33
T9O H17 H17 H 0 1 N N N N N N 0.765 -0.052 84.421 4.284 2.198 -2.002 H17 T9O 34
T9O H18 H18 H 0 1 N N N N N N 0.101 1.076 85.652 4.891 2.171 -0.329 H18 T9O 35
T9O H19 H19 H 0 1 N N N N N N -2.121 0.395 87.247 5.780 -0.912 -0.423 H19 T9O 36
T9O H20 H20 H 0 1 N N N N N N -3.456 -0.781 86.995 4.446 -2.010 -0.852 H20 T9O 37
T9O H21 H21 H 0 1 N N N N N N 6.713 -5.878 82.149 -4.339 0.278 -1.308 H21 T9O 38
T9O H22 H22 H 0 1 N N N N N N 6.779 -5.042 83.738 -4.380 1.069 0.286 H22 T9O 39
T9O H23 H23 H 0 1 N N N N N N 4.468 -8.480 82.913 -6.876 0.963 0.274 H23 T9O 40
T9O H24 H24 H 0 1 N N N N N N 4.423 -7.113 81.748 -6.835 0.171 -1.320 H24 T9O 41
T9O H25 H25 H 0 1 N N N N N N 5.966 -7.978 82.059 -7.699 -0.597 0.033 H25 T9O 42
T9O H26 H26 H 0 1 N N N N N N 4.374 -3.559 81.053 -2.341 -2.256 0.965 H26 T9O 43
T9O H27 H27 H 0 1 N N N N N N 2.303 -2.116 81.573 -2.174 -1.753 -1.648 H27 T9O 44
#
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
T9O N16 C9 DOUB N N 1
T9O O8 C2 SING N N 2
T9O C19 C17 SING N N 3
T9O C9 C18 SING N N 4
T9O C9 C1 SING N N 5
T9O C2 C1 DOUB N N 6
T9O C2 C3 SING N N 7
T9O C18 C17 SING N N 8
T9O C1 C6 SING N N 9
T9O C3 C4 SING N N 10
T9O C6 O7 DOUB N N 11
T9O C6 C5 SING N N 12
T9O C4 C5 SING N N 13
T9O C4 C10 SING N N 14
T9O C15 C14 SING N N 15
T9O C12 C11 SING N N 16
T9O S13 C11 SING N N 17
T9O S13 C14 SING N N 18
T9O C10 C11 SING N N 19
T9O C10 H1 SING N N 20
T9O C10 H2 SING N N 21
T9O C15 H3 SING N N 22
T9O C15 H4 SING N N 23
T9O C15 H5 SING N N 24
T9O C17 H6 SING N N 25
T9O C17 H7 SING N N 26
T9O C3 H10 SING N N 27
T9O C3 H11 SING N N 28
T9O C4 H12 SING N N 29
T9O C5 H13 SING N N 30
T9O C5 H14 SING N N 31
T9O C11 H15 SING N N 32
T9O C12 H16 SING N N 33
T9O C12 H17 SING N N 34
T9O C12 H18 SING N N 35
T9O C14 H19 SING N N 36
T9O C14 H20 SING N N 37
T9O C18 H21 SING N N 38
T9O C18 H22 SING N N 39
T9O C19 H23 SING N N 40
T9O C19 H24 SING N N 41
T9O C19 H25 SING N N 42
T9O N16 H26 SING N N 43
T9O O8 H27 SING N N 44
#
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
T9O InChI InChI 1.06 "InChI=1S/C15H25NO2S/c1-4-6-12(16)15-13(17)8-11(9-14(15)18)7-10(3)19-5-2/h10-11,16-17H,4-9H2,1-3H3/b16-12+/t10-,11-/m1/s1"
T9O InChIKey InChI 1.06 HITMLPXCKXYULH-XLMABRIASA-N
T9O SMILES_CANONICAL CACTVS 3.385 "CCCC(=N)C1=C(O)C[C@@H](C[C@@H](C)SCC)CC1=O"
T9O SMILES CACTVS 3.385 "CCCC(=N)C1=C(O)C[CH](C[CH](C)SCC)CC1=O"
T9O SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 "[H]/N=C(\CCC)/C1=C(C[C@H](CC1=O)C[C@@H](C)SCC)O"
T9O SMILES "OpenEye OEToolkits" 2.0.7 "CCCC(=N)C1=C(CC(CC1=O)CC(C)SCC)O"
#
_pdbx_chem_comp_identifier.comp_id T9O
_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~{R})-2-butanimidoyl-5-[(2~{R})-2-ethylsulfanylpropyl]-3-oxidanyl-cyclohex-2-en-1-one"
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
T9O 'Create component' 2023-04-20 PDBJ
T9O 'Initial release' 2023-12-20 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
T9O C10 C -2.258 -1.696 1
T9O C15 C -7.454 -1.691 2
T9O C17 C 5.539 1.298 3
T9O C1 C 1.641 0.551 4
T9O C2 C 1.640 -0.949 5
T9O C3 C 0.340 -1.697 6
T9O C4 C -0.958 -0.947 7
T9O C5 C -0.957 0.553 8
T9O C6 C 0.343 1.302 9
T9O C9 C 2.941 1.300 10
T9O C11 C -3.556 -0.944 11
T9O C12 C -3.555 0.556 12
T9O C14 C -6.154 -0.942 13
T9O C18 C 4.239 0.549 14
T9O C19 C 6.837 0.547 15
T9O N16 N 2.942 2.800 16
T9O O7 O 0.344 2.802 17
T9O O8 O 2.938 -1.700 18
T9O S13 S -4.856 -1.694 19
T9O H26 H 1.644 3.551 20
#
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
T9O N16 C9 DOUBLE NONE 1
T9O O8 C2 SINGLE NONE 2
T9O C19 C17 SINGLE NONE 3
T9O C9 C18 SINGLE ENDUPRIGHT 4
T9O C9 C1 SINGLE ENDDOWNRIGHT 5
T9O C2 C1 DOUBLE NONE 6
T9O C2 C3 SINGLE NONE 7
T9O C18 C17 SINGLE NONE 8
T9O C1 C6 SINGLE NONE 9
T9O C3 C4 SINGLE NONE 10
T9O C6 O7 DOUBLE NONE 11
T9O C6 C5 SINGLE NONE 12
T9O C4 C5 SINGLE NONE 13
T9O C4 C10 SINGLE BEGINWEDGE 14
T9O C15 C14 SINGLE NONE 15
T9O C11 C12 SINGLE BEGINDASH 16
T9O S13 C11 SINGLE NONE 17
T9O S13 C14 SINGLE NONE 18
T9O C10 C11 SINGLE NONE 19
#
_pdbe_chem_comp_substructure.comp_id T9O
_pdbe_chem_comp_substructure.substructure_name MurckoScaffold
_pdbe_chem_comp_substructure.id S1
_pdbe_chem_comp_substructure.substructure_type scaffold
_pdbe_chem_comp_substructure.substructure_smiles O=C1C=CCCC1
_pdbe_chem_comp_substructure.substructure_inchis InChI=1S/C6H8O/c7-6-4-2-1-3-5-6/h2,4H,1,3,5H2
_pdbe_chem_comp_substructure.substructure_inchikeys FWFSEYBSWVRWGL-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
T9O C1 S1 1
T9O C2 S1 1
T9O C3 S1 1
T9O C4 S1 1
T9O C5 S1 1
T9O C6 S1 1
T9O O7 S1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id T9O
_pdbe_chem_comp_rdkit_properties.exactmw 283.161
_pdbe_chem_comp_rdkit_properties.amw 283.437
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 11
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 19
_pdbe_chem_comp_rdkit_properties.NumAtoms 44
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.733
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_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 2
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 155.186
_pdbe_chem_comp_rdkit_properties.tpsa 61.150
_pdbe_chem_comp_rdkit_properties.CrippenClogP 4.129
_pdbe_chem_comp_rdkit_properties.CrippenMR 82.232
_pdbe_chem_comp_rdkit_properties.chi0v 9.988
_pdbe_chem_comp_rdkit_properties.chi1v 5.357
_pdbe_chem_comp_rdkit_properties.chi2v 2.149
_pdbe_chem_comp_rdkit_properties.chi3v 2.149
_pdbe_chem_comp_rdkit_properties.chi4v 1.331
_pdbe_chem_comp_rdkit_properties.chi0n 34.172
_pdbe_chem_comp_rdkit_properties.chi1n 16.896
_pdbe_chem_comp_rdkit_properties.chi2n 1.741
_pdbe_chem_comp_rdkit_properties.chi3n 1.741
_pdbe_chem_comp_rdkit_properties.chi4n 1.076
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.770
_pdbe_chem_comp_rdkit_properties.kappa1 2.896
_pdbe_chem_comp_rdkit_properties.kappa2 7.731
_pdbe_chem_comp_rdkit_properties.kappa3 4.678
_pdbe_chem_comp_rdkit_properties.Phi 1.178
#
_pdbe_chem_comp_external_mappings.comp_id T9O
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PDBe
_pdbe_chem_comp_external_mappings.resource_id T9O
#
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
T9O C10 -1.900 -1.370 0.392 ETKDGv3 1
T9O C15 -5.721 1.166 0.700 ETKDGv3 2
T9O C17 5.320 1.396 0.412 ETKDGv3 3
T9O C1 2.020 0.392 -0.557 ETKDGv3 4
T9O C2 1.883 -0.950 -0.495 ETKDGv3 5
T9O C3 0.613 -1.594 0.016 ETKDGv3 6
T9O C4 -0.630 -0.711 -0.216 ETKDGv3 7
T9O C5 -0.375 0.684 0.386 ETKDGv3 8
T9O C6 0.887 1.271 -0.176 ETKDGv3 9
T9O C9 3.290 1.000 -1.029 ETKDGv3 10
T9O C11 -3.142 -1.276 -0.525 ETKDGv3 11
T9O C12 -4.321 -2.078 0.036 ETKDGv3 12
T9O C14 -4.204 1.045 0.688 ETKDGv3 13
T9O C18 4.030 1.991 -0.168 ETKDGv3 14
T9O C19 5.043 0.329 1.471 ETKDGv3 15
T9O N16 3.783 0.680 -2.185 ETKDGv3 16
T9O O7 0.976 2.521 -0.310 ETKDGv3 17
T9O O8 2.952 -1.775 -0.848 ETKDGv3 18
T9O S13 -3.631 0.450 -0.947 ETKDGv3 19
T9O H1 -1.707 -2.454 0.558 ETKDGv3 20
T9O H2 -2.115 -0.957 1.399 ETKDGv3 21
T9O H3 -6.190 0.174 0.533 ETKDGv3 22
T9O H4 -6.055 1.866 -0.095 ETKDGv3 23
T9O H5 -6.056 1.557 1.684 ETKDGv3 24
T9O H6 5.906 2.214 0.884 ETKDGv3 25
T9O H7 5.943 0.961 -0.400 ETKDGv3 26
T9O H10 0.736 -1.798 1.102 ETKDGv3 27
T9O H11 0.469 -2.565 -0.504 ETKDGv3 28
T9O H12 -0.759 -0.602 -1.317 ETKDGv3 29
T9O H13 -1.223 1.362 0.162 ETKDGv3 30
T9O H14 -0.268 0.614 1.490 ETKDGv3 31
T9O H15 -2.873 -1.756 -1.492 ETKDGv3 32
T9O H16 -4.579 -1.757 1.066 ETKDGv3 33
T9O H17 -4.063 -3.158 0.066 ETKDGv3 34
T9O H18 -5.211 -1.955 -0.617 ETKDGv3 35
T9O H19 -3.766 2.051 0.859 ETKDGv3 36
T9O H20 -3.877 0.397 1.522 ETKDGv3 37
T9O H21 3.389 2.354 0.664 ETKDGv3 38
T9O H22 4.290 2.875 -0.789 ETKDGv3 39
T9O H23 6.003 -0.019 1.906 ETKDGv3 40
T9O H24 4.415 0.747 2.286 ETKDGv3 41
T9O H25 4.527 -0.543 1.020 ETKDGv3 42
T9O H26 3.308 0.005 -2.825 ETKDGv3 43
T9O H27 2.885 -2.783 -0.781 ETKDGv3 44
#