data_YX6
#
_chem_comp.id YX6
_chem_comp.name N-[(3R)-6-oxopiperidin-3-yl]-1,3-thiazole-4-carboxamide
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C9 H11 N3 O2 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2023-06-22
_chem_comp.pdbx_modified_date 2023-07-07
_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 225.268
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code YX6
_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 7G84
_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
YX6 C10 C1 C 0 1 N N N N N N -3.498 -34.642 16.806 -2.076 0.649 -0.960 C10 YX6 1
YX6 O01 O1 O 0 1 N N N N N N -4.917 -31.960 15.372 0.543 1.523 0.772 O01 YX6 2
YX6 C02 C2 C 0 1 N N N N N N -4.131 -31.520 16.162 0.840 0.435 0.316 C02 YX6 3
YX6 N03 N1 N 0 1 N N N N N N -3.654 -32.257 17.316 -0.126 -0.457 0.020 N03 YX6 4
YX6 C04 C3 C 0 1 N N R N N N -4.079 -33.596 17.692 -1.533 -0.117 0.247 C04 YX6 5
YX6 C05 C4 C 0 1 N N N N N N -3.828 -33.772 19.124 -2.351 -1.401 0.422 C05 YX6 6
YX6 C06 C5 C 0 1 N N N N N N -3.358 -35.056 19.623 -3.773 -1.016 0.838 C06 YX6 7
YX6 C07 C6 C 0 1 N N N N N N -3.716 -36.340 18.771 -4.300 0.053 -0.075 C07 YX6 8
YX6 O08 O2 O 0 1 N N N N N N -3.902 -37.417 19.252 -5.497 0.246 -0.103 O08 YX6 9
YX6 N09 N2 N 0 1 N N N N N N -3.767 -36.091 17.256 -3.522 0.803 -0.858 N09 YX6 10
YX6 C11 C7 C 0 1 Y N N N N N -3.597 -30.117 15.944 2.253 0.093 0.088 C11 YX6 11
YX6 C12 C8 C 0 1 Y N N N N N -4.041 -29.363 14.868 3.273 0.936 0.367 C12 YX6 12
YX6 S13 S1 S 0 1 Y N N N N N -3.202 -27.866 15.031 4.747 0.172 -0.037 S13 YX6 13
YX6 C14 C9 C 0 1 Y N N N N N -2.357 -28.322 16.470 3.919 -1.229 -0.555 C14 YX6 14
YX6 N15 N3 N 0 1 Y N N N N N -2.728 -29.562 16.767 2.649 -1.082 -0.409 N15 YX6 15
YX6 H1 H1 H 0 1 N N N N N N -2.409 -34.492 16.768 -1.612 1.634 -1.000 H1 YX6 16
YX6 H2 H2 H 0 1 N N N N N N -3.922 -34.512 15.799 -1.836 0.103 -1.872 H2 YX6 17
YX6 H3 H3 H 0 1 N N N N N N -2.978 -31.808 17.901 0.110 -1.325 -0.344 H3 YX6 18
YX6 H4 H4 H 0 1 N N N N N N -5.169 -33.637 17.552 -1.620 0.500 1.141 H4 YX6 19
YX6 H5 H5 H 0 1 N N N N N N -3.074 -33.024 19.410 -2.380 -1.950 -0.519 H5 YX6 20
YX6 H6 H6 H 0 1 N N N N N N -4.774 -33.556 19.642 -1.899 -2.022 1.196 H6 YX6 21
YX6 H7 H7 H 0 1 N N N N N N -3.784 -35.196 20.627 -4.418 -1.893 0.778 H7 YX6 22
YX6 H8 H8 H 0 1 N N N N N N -2.262 -35.002 19.694 -3.763 -0.643 1.862 H8 YX6 23
YX6 H9 H9 H 0 1 N N N N N N -3.962 -36.823 16.603 -3.945 1.493 -1.392 H9 YX6 24
YX6 H10 H10 H 0 1 N N N N N N -4.749 -29.648 14.104 3.171 1.930 0.777 H10 YX6 25
YX6 H11 H11 H 0 1 N N N N N N -1.658 -27.712 17.023 4.395 -2.116 -0.946 H11 YX6 26
#
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
YX6 C12 S13 SING Y N 1
YX6 C12 C11 DOUB Y N 2
YX6 S13 C14 SING Y N 3
YX6 O01 C02 DOUB N N 4
YX6 C11 C02 SING N N 5
YX6 C11 N15 SING Y N 6
YX6 C02 N03 SING N N 7
YX6 C14 N15 DOUB Y N 8
YX6 C10 N09 SING N N 9
YX6 C10 C04 SING N N 10
YX6 N09 C07 SING N N 11
YX6 N03 C04 SING N N 12
YX6 C04 C05 SING N N 13
YX6 C07 O08 DOUB N N 14
YX6 C07 C06 SING N N 15
YX6 C05 C06 SING N N 16
YX6 C10 H1 SING N N 17
YX6 C10 H2 SING N N 18
YX6 N03 H3 SING N N 19
YX6 C04 H4 SING N N 20
YX6 C05 H5 SING N N 21
YX6 C05 H6 SING N N 22
YX6 C06 H7 SING N N 23
YX6 C06 H8 SING N N 24
YX6 N09 H9 SING N N 25
YX6 C12 H10 SING N N 26
YX6 C14 H11 SING N N 27
#
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
YX6 SMILES ACDLabs 12.01 O=C(NC1CCC(=O)NC1)c1cscn1
YX6 InChI InChI 1.06 InChI=1S/C9H11N3O2S/c13-8-2-1-6(3-10-8)12-9(14)7-4-15-5-11-7/h4-6H,1-3H2,(H,10,13)(H,12,14)/t6-/m1/s1
YX6 InChIKey InChI 1.06 MTDCJLXPYPQTPX-ZCFIWIBFSA-N
YX6 SMILES_CANONICAL CACTVS 3.385 O=C1CC[C@H](CN1)NC(=O)c2cscn2
YX6 SMILES CACTVS 3.385 O=C1CC[CH](CN1)NC(=O)c2cscn2
YX6 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 c1c(ncs1)C(=O)N[C@@H]2CCC(=O)NC2
YX6 SMILES "OpenEye OEToolkits" 2.0.7 c1c(ncs1)C(=O)NC2CCC(=O)NC2
#
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
YX6 "SYSTEMATIC NAME" ACDLabs 12.01 N-[(3R)-6-oxopiperidin-3-yl]-1,3-thiazole-4-carboxamide
YX6 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 ~{N}-[(3~{R})-6-oxidanylidenepiperidin-3-yl]-1,3-thiazole-4-carboxamide
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
YX6 'Create component' 2023-06-22 RCSB
YX6 'Initial release' 2023-07-12 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
YX6 C10 C 9.271 -0.062 1
YX6 O01 O 7.972 2.188 2
YX6 C02 C 6.673 1.438 3
YX6 N03 N 6.673 -0.062 4
YX6 C04 C 7.972 -0.812 5
YX6 C05 C 7.972 -2.312 6
YX6 C06 C 9.271 -3.062 7
YX6 C07 C 10.570 -2.312 8
YX6 O08 O 11.869 -3.062 9
YX6 N09 N 10.570 -0.812 10
YX6 C11 C 5.374 2.188 11
YX6 C12 C 4.004 1.578 12
YX6 S13 S 3.000 2.693 13
YX6 C14 C 3.750 3.992 14
YX6 N15 N 5.217 3.680 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
YX6 C12 S13 SINGLE NONE 1
YX6 C12 C11 DOUBLE NONE 2
YX6 S13 C14 SINGLE NONE 3
YX6 O01 C02 DOUBLE NONE 4
YX6 C11 C02 SINGLE NONE 5
YX6 C11 N15 SINGLE NONE 6
YX6 C02 N03 SINGLE NONE 7
YX6 C14 N15 DOUBLE NONE 8
YX6 C10 N09 SINGLE NONE 9
YX6 C10 C04 SINGLE NONE 10
YX6 N09 C07 SINGLE NONE 11
YX6 C04 N03 SINGLE BEGINWEDGE 12
YX6 C04 C05 SINGLE NONE 13
YX6 C07 O08 DOUBLE NONE 14
YX6 C07 C06 SINGLE NONE 15
YX6 C05 C06 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
YX6 MurckoScaffold S1 scaffold 'O=C1CC[C@@H](NC(=O)c2cscn2)CN1' InChI=1S/C9H11N3O2S/c13-8-2-1-6(3-10-8)12-9(14)7-4-15-5-11-7/h4-6H,1-3H2,(H,10,13)(H,12,14)/t6-/m1/s1 MTDCJLXPYPQTPX-ZCFIWIBFSA-N
YX6 amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
YX6 thiazole F2 fragment c1cscn1 InChI=1S/C3H3NS/c1-2-5-3-4-1/h1-3H FZWLAAWBMGSTSO-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
YX6 C10 S1 1
YX6 O01 S1 1
YX6 C02 S1 1
YX6 N03 S1 1
YX6 C04 S1 1
YX6 C05 S1 1
YX6 C06 S1 1
YX6 C07 S1 1
YX6 O08 S1 1
YX6 N09 S1 1
YX6 C11 S1 1
YX6 C12 S1 1
YX6 S13 S1 1
YX6 C14 S1 1
YX6 N15 S1 1
YX6 N03 F1 1
YX6 C02 F1 1
YX6 O01 F1 1
YX6 C11 F1 1
YX6 N09 F1 2
YX6 C07 F1 2
YX6 O08 F1 2
YX6 C06 F1 2
YX6 C12 F2 1
YX6 C11 F2 1
YX6 N15 F2 1
YX6 C14 F2 1
YX6 S13 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id YX6
_pdbe_chem_comp_rdkit_properties.exactmw 225.057
_pdbe_chem_comp_rdkit_properties.amw 225.273
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 2
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 15
_pdbe_chem_comp_rdkit_properties.NumAtoms 26
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 2
_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 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 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 106.469
_pdbe_chem_comp_rdkit_properties.tpsa 71.090
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.097
_pdbe_chem_comp_rdkit_properties.CrippenMR 55.346
_pdbe_chem_comp_rdkit_properties.chi0v 7.883
_pdbe_chem_comp_rdkit_properties.chi1v 4.475
_pdbe_chem_comp_rdkit_properties.chi2v 1.796
_pdbe_chem_comp_rdkit_properties.chi3v 1.796
_pdbe_chem_comp_rdkit_properties.chi4v 1.146
_pdbe_chem_comp_rdkit_properties.chi0n 18.066
_pdbe_chem_comp_rdkit_properties.chi1n 9.053
_pdbe_chem_comp_rdkit_properties.chi2n 1.318
_pdbe_chem_comp_rdkit_properties.chi3n 1.318
_pdbe_chem_comp_rdkit_properties.chi4n 0.734
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.430
_pdbe_chem_comp_rdkit_properties.kappa1 3.279
_pdbe_chem_comp_rdkit_properties.kappa2 4.394
_pdbe_chem_comp_rdkit_properties.kappa3 2.528
_pdbe_chem_comp_rdkit_properties.Phi 0.961
#
_pdbe_chem_comp_external_mappings.comp_id YX6
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PubChem
_pdbe_chem_comp_external_mappings.resource_id 96463062
#
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
YX6 C10 -1.549 -0.971 0.544 ETKDGv3 1
YX6 O01 1.225 -1.557 -1.324 ETKDGv3 2
YX6 C02 1.577 -0.684 -0.485 ETKDGv3 3
YX6 N03 0.587 0.165 0.121 ETKDGv3 4
YX6 C04 -0.825 0.113 -0.268 ETKDGv3 5
YX6 C05 -1.489 1.478 -0.029 ETKDGv3 6
YX6 C06 -2.941 1.473 -0.517 ETKDGv3 7
YX6 C07 -3.687 0.273 -0.009 ETKDGv3 8
YX6 O08 -4.944 0.309 0.064 ETKDGv3 9
YX6 N09 -2.993 -0.940 0.310 ETKDGv3 10
YX6 C11 3.009 -0.574 -0.140 ETKDGv3 11
YX6 C12 3.540 0.438 0.556 ETKDGv3 12
YX6 S13 5.292 0.181 0.714 ETKDGv3 13
YX6 C14 5.167 -1.328 -0.214 ETKDGv3 14
YX6 N15 3.949 -1.573 -0.577 ETKDGv3 15
YX6 H1 -1.155 -1.971 0.259 ETKDGv3 16
YX6 H2 -1.359 -0.822 1.629 ETKDGv3 17
YX6 H3 0.841 0.722 0.966 ETKDGv3 18
YX6 H4 -0.904 -0.127 -1.353 ETKDGv3 19
YX6 H5 -0.927 2.267 -0.575 ETKDGv3 20
YX6 H6 -1.464 1.728 1.056 ETKDGv3 21
YX6 H7 -2.957 1.456 -1.628 ETKDGv3 22
YX6 H8 -3.445 2.402 -0.175 ETKDGv3 23
YX6 H9 -3.553 -1.777 0.591 ETKDGv3 24
YX6 H10 3.009 1.296 0.942 ETKDGv3 25
YX6 H11 5.995 -1.979 -0.460 ETKDGv3 26
#