data_YFN
#
_chem_comp.id YFN
_chem_comp.name N-[(3S)-3-methyl-1,1-dioxo-1lambda~6~-thiolan-3-yl]cyclopropanecarboxamide
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C9 H15 N O3 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2023-01-26
_chem_comp.pdbx_modified_date 2023-02-10
_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 217.285
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code YFN
_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 7FSR
_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
YFN C10 C1 C 0 1 N N N N N N -3.507 -6.197 -10.755 2.134 0.230 0.161 C10 YFN 1
YFN C13 C2 C 0 1 N N N N N N -3.542 -8.544 -11.746 4.676 -0.249 -0.065 C13 YFN 2
YFN C01 C3 C 0 1 N N N N N N -3.555 -3.774 -8.826 0.015 2.261 0.402 C01 YFN 3
YFN C02 C4 C 0 1 N N S N N N -3.908 -5.241 -8.489 -0.242 0.758 0.279 C02 YFN 4
YFN C03 C5 C 0 1 N N N N N N -5.362 -5.229 -7.333 -0.473 0.412 -1.193 C03 YFN 5
YFN C04 C6 C 0 1 N N N N N N -5.385 -6.556 -6.779 -1.415 -0.818 -1.272 C04 YFN 6
YFN C08 C7 C 0 1 N N N N N N -2.888 -5.853 -7.741 -1.443 0.384 1.161 C08 YFN 7
YFN C12 C8 C 0 1 N N N N N N -4.127 -7.127 -11.814 3.350 -0.515 0.650 C12 YFN 8
YFN C14 C9 C 0 1 N N N N N N -3.281 -7.671 -12.976 3.947 -1.577 -0.275 C14 YFN 9
YFN N09 N1 N 0 1 N N N N N N -4.281 -5.993 -9.521 0.940 0.034 0.755 N09 YFN 10
YFN O06 O1 O 0 1 N N N N N N -3.596 -8.304 -7.919 -3.139 -1.605 0.616 O06 YFN 11
YFN O07 O2 O 0 1 N N N N N N -3.210 -7.433 -5.576 -3.556 0.570 -0.460 O07 YFN 12
YFN O11 O3 O 0 1 N N N N N N -2.454 -5.685 -10.930 2.231 1.009 -0.763 O11 YFN 13
YFN S05 S1 S 0 1 N N N N N N -3.750 -7.199 -6.935 -2.648 -0.407 0.029 S05 YFN 14
YFN H132 H1 H 0 0 N N N N N N -2.723 -8.767 -11.047 4.669 0.465 -0.889 H132 YFN 15
YFN H131 H2 H 0 0 N N N N N N -4.207 -9.417 -11.823 5.584 -0.262 0.538 H131 YFN 16
YFN H013 H3 H 0 0 N N N N N N -2.695 -3.751 -9.511 0.230 2.509 1.441 H013 YFN 17
YFN H012 H4 H 0 0 N N N N N N -4.419 -3.290 -9.306 0.867 2.536 -0.221 H012 YFN 18
YFN H011 H5 H 0 0 N N N N N N -3.301 -3.236 -7.901 -0.868 2.809 0.072 H011 YFN 19
YFN H031 H6 H 0 0 N N N N N N -6.293 -5.019 -7.880 -0.934 1.260 -1.700 H031 YFN 20
YFN H032 H7 H 0 0 N N N N N N -5.224 -4.478 -6.541 0.479 0.174 -1.667 H032 YFN 21
YFN H042 H8 H 0 0 N N N N N N -5.678 -6.519 -5.719 -1.888 -0.887 -2.252 H042 YFN 22
YFN H041 H9 H 0 0 N N N N N N -6.095 -7.186 -7.335 -0.881 -1.737 -1.031 H041 YFN 23
YFN H082 H10 H 0 0 N N N N N N -2.463 -5.156 -7.004 -1.138 -0.317 1.938 H082 YFN 24
YFN H081 H11 H 0 0 N N N N N N -2.087 -6.229 -8.395 -1.876 1.279 1.608 H081 YFN 25
YFN H121 H12 H 0 0 N N N N N N -5.211 -7.040 -11.982 3.385 -0.703 1.723 H121 YFN 26
YFN H142 H13 H 0 0 N N N N N N -2.275 -7.267 -13.160 3.460 -1.738 -1.237 H142 YFN 27
YFN H141 H14 H 0 0 N N N N N N -3.759 -7.917 -13.936 4.375 -2.466 0.190 H141 YFN 28
YFN H091 H15 H 0 0 N N N N N N -5.163 -6.459 -9.452 0.863 -0.586 1.497 H091 YFN 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
YFN C02 C01 SING N N 1
YFN C04 C03 SING N N 2
YFN S05 C04 SING N N 3
YFN O06 S05 DOUB N N 4
YFN O07 S05 DOUB N N 5
YFN C08 S05 SING N N 6
YFN C03 C02 SING N N 7
YFN N09 C02 SING N N 8
YFN C10 N09 SING N N 9
YFN O11 C10 DOUB N N 10
YFN C12 C10 SING N N 11
YFN C13 C12 SING N N 12
YFN C14 C13 SING N N 13
YFN C02 C08 SING N N 14
YFN C12 C14 SING N N 15
YFN C13 H132 SING N N 16
YFN C13 H131 SING N N 17
YFN C01 H013 SING N N 18
YFN C01 H012 SING N N 19
YFN C01 H011 SING N N 20
YFN C03 H031 SING N N 21
YFN C03 H032 SING N N 22
YFN C04 H042 SING N N 23
YFN C04 H041 SING N N 24
YFN C08 H082 SING N N 25
YFN C08 H081 SING N N 26
YFN C12 H121 SING N N 27
YFN C14 H142 SING N N 28
YFN C14 H141 SING N N 29
YFN N09 H091 SING N N 30
#
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
YFN SMILES ACDLabs 12.01 O=S1(=O)CCC(C)(NC(=O)C2CC2)C1
YFN InChI InChI 1.06 InChI=1S/C9H15NO3S/c1-9(4-5-14(12,13)6-9)10-8(11)7-2-3-7/h7H,2-6H2,1H3,(H,10,11)/t9-/m0/s1
YFN InChIKey InChI 1.06 LMUYJJAKMZKBHS-VIFPVBQESA-N
YFN SMILES_CANONICAL CACTVS 3.385 C[C@@]1(CC[S](=O)(=O)C1)NC(=O)C2CC2
YFN SMILES CACTVS 3.385 C[C]1(CC[S](=O)(=O)C1)NC(=O)C2CC2
YFN SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 C[C@@]1(CCS(=O)(=O)C1)NC(=O)C2CC2
YFN SMILES "OpenEye OEToolkits" 2.0.7 CC1(CCS(=O)(=O)C1)NC(=O)C2CC2
#
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
YFN "SYSTEMATIC NAME" ACDLabs 12.01 N-[(3S)-3-methyl-1,1-dioxo-1lambda~6~-thiolan-3-yl]cyclopropanecarboxamide
YFN "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 ~{N}-[(3~{S})-3-methyl-1,1-bis(oxidanylidene)thiolan-3-yl]cyclopropanecarboxamide
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
YFN 'Create component' 2023-01-26 RCSB
YFN 'Initial release' 2023-02-15 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
YFN C10 C 6.587 1.080 1
YFN C13 C 8.839 2.903 2
YFN C01 C 3.332 1.237 3
YFN C02 C 4.213 0.023 4
YFN C03 C 3.000 -0.859 5
YFN C04 C 3.463 -2.285 6
YFN C08 C 5.427 -0.859 7
YFN C12 C 7.469 2.293 8
YFN C14 C 7.625 3.785 9
YFN N09 N 5.095 1.237 10
YFN O06 O 4.963 -3.785 11
YFN O07 O 6.390 -2.749 12
YFN O11 O 7.197 -0.290 13
YFN S05 S 4.963 -2.285 14
#
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
YFN C02 C01 SINGLE BEGINWEDGE 1
YFN C04 C03 SINGLE NONE 2
YFN S05 C04 SINGLE NONE 3
YFN O06 S05 DOUBLE NONE 4
YFN O07 S05 DOUBLE NONE 5
YFN C08 S05 SINGLE NONE 6
YFN C03 C02 SINGLE NONE 7
YFN N09 C02 SINGLE NONE 8
YFN C10 N09 SINGLE NONE 9
YFN O11 C10 DOUBLE NONE 10
YFN C12 C10 SINGLE NONE 11
YFN C13 C12 SINGLE NONE 12
YFN C14 C13 SINGLE NONE 13
YFN C02 C08 SINGLE NONE 14
YFN C12 C14 SINGLE NONE 15
#
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
YFN MurckoScaffold S1 scaffold O=C(NC1CCS(=O)(=O)C1)C1CC1 InChI=1S/C8H13NO3S/c10-8(6-1-2-6)9-7-3-4-13(11,12)5-7/h6-7H,1-5H2,(H,9,10)/t7-/m0/s1 LNMJJGUUBYOTJX-ZETCQYMHSA-N
YFN amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
YFN cyclopropane F2 fragment C1CC1 InChI=1S/C3H6/c1-2-3-1/h1-3H2 LVZWSLJZHVFIQJ-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
YFN C10 S1 1
YFN C13 S1 1
YFN C02 S1 1
YFN C03 S1 1
YFN C04 S1 1
YFN C08 S1 1
YFN C12 S1 1
YFN C14 S1 1
YFN N09 S1 1
YFN O06 S1 1
YFN O07 S1 1
YFN O11 S1 1
YFN S05 S1 1
YFN N09 F1 1
YFN C10 F1 1
YFN O11 F1 1
YFN C12 F1 1
YFN C13 F2 1
YFN C12 F2 1
YFN C14 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id YFN
_pdbe_chem_comp_rdkit_properties.exactmw 217.077
_pdbe_chem_comp_rdkit_properties.amw 217.290
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_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 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 14
_pdbe_chem_comp_rdkit_properties.NumAtoms 29
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.889
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 2
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_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 105.117
_pdbe_chem_comp_rdkit_properties.tpsa 63.240
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.090
_pdbe_chem_comp_rdkit_properties.CrippenMR 52.543
_pdbe_chem_comp_rdkit_properties.chi0v 7.397
_pdbe_chem_comp_rdkit_properties.chi1v 4.876
_pdbe_chem_comp_rdkit_properties.chi2v 2.316
_pdbe_chem_comp_rdkit_properties.chi3v 2.316
_pdbe_chem_comp_rdkit_properties.chi4v 1.602
_pdbe_chem_comp_rdkit_properties.chi0n 21.580
_pdbe_chem_comp_rdkit_properties.chi1n 10.840
_pdbe_chem_comp_rdkit_properties.chi2n 1.381
_pdbe_chem_comp_rdkit_properties.chi3n 1.381
_pdbe_chem_comp_rdkit_properties.chi4n 0.784
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.580
_pdbe_chem_comp_rdkit_properties.kappa1 2.392
_pdbe_chem_comp_rdkit_properties.kappa2 2.953
_pdbe_chem_comp_rdkit_properties.kappa3 2.079
_pdbe_chem_comp_rdkit_properties.Phi 0.505
#
loop_
_pdbe_chem_comp_external_mappings.comp_id
_pdbe_chem_comp_external_mappings.source
_pdbe_chem_comp_external_mappings.resource
_pdbe_chem_comp_external_mappings.resource_id
YFN UniChem ZINC ZINC000042370297
YFN UniChem PubChem 93848777
#
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
YFN C10 1.657 -0.351 0.835 ETKDGv3 1
YFN C13 3.669 -0.001 -0.756 ETKDGv3 2
YFN C01 -0.967 -1.867 -0.053 ETKDGv3 3
YFN C02 -0.791 -0.334 0.014 ETKDGv3 4
YFN C03 -1.363 0.229 1.343 ETKDGv3 5
YFN C04 -2.884 0.339 1.240 ETKDGv3 6
YFN C08 -1.604 0.326 -1.126 ETKDGv3 7
YFN C12 3.117 0.007 0.661 ETKDGv3 8
YFN C14 3.432 1.322 -0.036 ETKDGv3 9
YFN N09 0.640 0.005 -0.128 ETKDGv3 10
YFN O06 -4.214 -0.393 -1.000 ETKDGv3 11
YFN O07 -3.689 2.010 -0.732 ETKDGv3 12
YFN O11 1.342 -0.986 1.875 ETKDGv3 13
YFN S05 -3.223 0.606 -0.471 ETKDGv3 14
YFN H132 4.741 -0.284 -0.827 ETKDGv3 15
YFN H131 2.956 -0.221 -1.576 ETKDGv3 16
YFN H013 -0.501 -2.265 -0.979 ETKDGv3 17
YFN H012 -2.042 -2.146 -0.056 ETKDGv3 18
YFN H011 -0.491 -2.367 0.816 ETKDGv3 19
YFN H031 -1.093 -0.402 2.217 ETKDGv3 20
YFN H032 -0.947 1.247 1.515 ETKDGv3 21
YFN H042 -3.267 1.181 1.855 ETKDGv3 22
YFN H041 -3.361 -0.609 1.568 ETKDGv3 23
YFN H082 -1.176 1.315 -1.396 ETKDGv3 24
YFN H081 -1.649 -0.305 -2.040 ETKDGv3 25
YFN H121 3.842 -0.292 1.449 ETKDGv3 26
YFN H142 4.365 1.812 0.314 ETKDGv3 27
YFN H141 2.573 1.912 -0.415 ETKDGv3 28
YFN H091 0.929 0.514 -0.991 ETKDGv3 29
#