data_LKV # _chem_comp.id LKV _chem_comp.name "(2~{S})-2-[[(2~{S})-3-methyl-2-(3-oxidanylidene-1~{H}-isoindol-2-yl)butanoyl]amino]propanoic acid" _chem_comp.type non-polymer _chem_comp.pdbx_type HETAIN _chem_comp.formula "C16 H20 N2 O4" _chem_comp.mon_nstd_parent_comp_id ? _chem_comp.pdbx_synonyms ? _chem_comp.pdbx_formal_charge 0 _chem_comp.pdbx_initial_date 2022-07-06 _chem_comp.pdbx_modified_date 2023-04-21 _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 304.341 _chem_comp.one_letter_code ? _chem_comp.three_letter_code LKV _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 8AAI _chem_comp.pdbx_subcomponent_list ? _chem_comp.pdbx_processing_site PDBE # 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 LKV C4 C1 C 0 1 N N N N N N -14.007 -2.780 -0.424 -1.192 -0.109 0.001 C4 LKV 1 LKV C5 C2 C 0 1 N N S N N N -16.016 -2.673 -1.820 -3.400 -1.138 -0.082 C5 LKV 2 LKV C7 C3 C 0 1 N N N N N N -16.928 -3.880 -1.962 -4.812 -0.611 -0.113 C7 LKV 3 LKV C8 C4 C 0 1 N N N N N N -12.324 -0.949 1.344 2.043 0.081 1.521 C8 LKV 4 LKV C10 C5 C 0 1 Y N N N N N -11.111 1.002 2.622 4.531 -0.817 1.401 C10 LKV 5 LKV C12 C6 C 0 1 Y N N N N N -9.201 1.944 1.508 5.383 -1.102 -0.824 C12 LKV 6 LKV C13 C7 C 0 1 Y N N N N N -9.386 1.082 0.436 4.185 -0.663 -1.350 C13 LKV 7 LKV C15 C8 C 0 1 N N N N N N -10.869 -0.847 -0.513 1.778 0.200 -0.747 C15 LKV 8 LKV C1 C9 C 0 1 N N N N N N -11.817 -4.002 0.099 -0.384 2.225 -0.216 C1 LKV 9 LKV O3 O1 O 0 1 N N N N N N -10.417 -1.068 -1.620 1.299 0.385 -1.848 O3 LKV 10 LKV C14 C10 C 0 1 Y N N N N N -10.450 0.180 0.467 3.145 -0.296 -0.494 C14 LKV 11 LKV C11 C11 C 0 1 Y N N N N N -10.062 1.908 2.593 5.558 -1.180 0.546 C11 LKV 12 LKV C9 C12 C 0 1 Y N N N N N -11.305 0.133 1.554 3.333 -0.378 0.888 C9 LKV 13 LKV N1 N1 N 0 1 N N N N N N -11.914 -1.512 0.053 1.140 0.419 0.416 N1 LKV 14 LKV C3 C13 C 0 1 N N S N N N -12.474 -2.741 -0.529 -0.233 0.912 0.555 C3 LKV 15 LKV C2 C14 C 0 1 N N N N N N -10.415 -4.235 -0.454 -1.783 2.796 0.019 C2 LKV 16 LKV C C15 C 0 1 N N N N N N -12.672 -5.248 -0.114 0.664 3.227 0.273 C LKV 17 LKV O O2 O 0 1 N N N N N N -14.579 -2.580 0.645 -0.795 -0.964 -0.761 O LKV 18 LKV N N2 N 0 1 N N N N N N -14.651 -3.098 -1.555 -2.492 -0.075 0.357 N LKV 19 LKV C6 C16 C 0 1 N N N N N N -16.073 -1.839 -3.092 -3.316 -2.316 0.890 C6 LKV 20 LKV O1 O3 O 0 1 N N N N N N -16.681 -4.785 -2.738 -5.036 0.534 0.201 O1 LKV 21 LKV O2 O4 O 0 1 N N N N N N -17.988 -3.838 -1.184 -5.819 -1.415 -0.488 O2 LKV 22 LKV H1 H1 H 0 1 N N N N N N -16.377 -2.058 -0.982 -3.114 -1.470 -1.081 H1 LKV 23 LKV H14 H2 H 0 1 N N N N N N -13.342 -0.535 1.294 1.615 -0.721 2.123 H14 LKV 24 LKV H15 H3 H 0 1 N N N N N N -12.275 -1.704 2.142 2.223 0.960 2.141 H15 LKV 25 LKV H16 H4 H 0 1 N N N N N N -11.776 0.971 3.472 4.670 -0.878 2.470 H16 LKV 26 LKV H18 H5 H 0 1 N N N N N N -8.381 2.647 1.496 6.188 -1.388 -1.486 H18 LKV 27 LKV H19 H6 H 0 1 N N N N N N -8.716 1.109 -0.410 4.052 -0.604 -2.420 H19 LKV 28 LKV H5 H7 H 0 1 N N N N N N -11.731 -3.829 1.182 -0.241 2.040 -1.280 H5 LKV 29 LKV H17 H8 H 0 1 N N N N N N -9.915 2.588 3.419 6.499 -1.524 0.950 H17 LKV 30 LKV H H9 H 0 1 N N N N N N -12.224 -2.751 -1.600 -0.452 1.082 1.610 H LKV 31 LKV H7 H10 H 0 1 N N N N N N -9.981 -5.133 0.011 -1.947 2.930 1.088 H7 LKV 32 LKV H6 H11 H 0 1 N N N N N N -10.470 -4.376 -1.544 -1.872 3.758 -0.485 H6 LKV 33 LKV H8 H12 H 0 1 N N N N N N -9.783 -3.364 -0.229 -2.528 2.107 -0.379 H8 LKV 34 LKV H4 H13 H 0 1 N N N N N N -12.175 -6.117 0.343 0.581 3.342 1.354 H4 LKV 35 LKV H3 H14 H 0 1 N N N N N N -13.657 -5.101 0.353 1.661 2.862 0.022 H3 LKV 36 LKV H2 H15 H 0 1 N N N N N N -12.800 -5.424 -1.192 0.498 4.190 -0.209 H2 LKV 37 LKV H9 H16 H 0 1 N N N N N N -14.176 -3.648 -2.242 -2.826 0.652 0.905 H9 LKV 38 LKV H12 H17 H 0 1 N N N N N N -15.413 -0.966 -2.988 -2.294 -2.696 0.912 H12 LKV 39 LKV H11 H18 H 0 1 N N N N N N -15.742 -2.449 -3.945 -3.601 -1.984 1.888 H11 LKV 40 LKV H10 H19 H 0 1 N N N N N N -17.105 -1.500 -3.262 -3.991 -3.106 0.563 H10 LKV 41 LKV H13 H20 H 0 1 N N N N N N -18.516 -4.615 -1.326 -6.707 -1.032 -0.492 H13 LKV 42 # 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 LKV C6 C5 SING N N 1 LKV O1 C7 DOUB N N 2 LKV C7 C5 SING N N 3 LKV C7 O2 SING N N 4 LKV C5 N SING N N 5 LKV O3 C15 DOUB N N 6 LKV N C4 SING N N 7 LKV C3 C4 SING N N 8 LKV C3 N1 SING N N 9 LKV C3 C1 SING N N 10 LKV C15 N1 SING N N 11 LKV C15 C14 SING N N 12 LKV C2 C1 SING N N 13 LKV C4 O DOUB N N 14 LKV C C1 SING N N 15 LKV N1 C8 SING N N 16 LKV C13 C14 DOUB Y N 17 LKV C13 C12 SING Y N 18 LKV C14 C9 SING Y N 19 LKV C8 C9 SING N N 20 LKV C12 C11 DOUB Y N 21 LKV C9 C10 DOUB Y N 22 LKV C11 C10 SING Y N 23 LKV C5 H1 SING N N 24 LKV C8 H14 SING N N 25 LKV C8 H15 SING N N 26 LKV C10 H16 SING N N 27 LKV C12 H18 SING N N 28 LKV C13 H19 SING N N 29 LKV C1 H5 SING N N 30 LKV C11 H17 SING N N 31 LKV C3 H SING N N 32 LKV C2 H7 SING N N 33 LKV C2 H6 SING N N 34 LKV C2 H8 SING N N 35 LKV C H4 SING N N 36 LKV C H3 SING N N 37 LKV C H2 SING N N 38 LKV N H9 SING N N 39 LKV C6 H12 SING N N 40 LKV C6 H11 SING N N 41 LKV C6 H10 SING N N 42 LKV O2 H13 SING N N 43 # 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 LKV InChI InChI 1.06 InChI=1S/C16H20N2O4/c1-9(2)13(14(19)17-10(3)16(21)22)18-8-11-6-4-5-7-12(11)15(18)20/h4-7,9-10,13H,8H2,1-3H3,(H,17,19)(H,21,22)/t10-,13-/m0/s1 LKV InChIKey InChI 1.06 ZLJCDMXBPPBVSF-GWCFXTLKSA-N LKV SMILES_CANONICAL CACTVS 3.385 CC(C)[C@H](N1Cc2ccccc2C1=O)C(=O)N[C@@H](C)C(O)=O LKV SMILES CACTVS 3.385 CC(C)[CH](N1Cc2ccccc2C1=O)C(=O)N[CH](C)C(O)=O LKV SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 C[C@@H](C(=O)O)NC(=O)[C@H](C(C)C)N1Cc2ccccc2C1=O LKV SMILES "OpenEye OEToolkits" 2.0.7 CC(C)C(C(=O)NC(C)C(=O)O)N1Cc2ccccc2C1=O # _pdbx_chem_comp_identifier.comp_id LKV _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 "(2~{S})-2-[[(2~{S})-3-methyl-2-(3-oxidanylidene-1~{H}-isoindol-2-yl)butanoyl]amino]propanoic acid" # loop_ _pdbx_chem_comp_audit.comp_id _pdbx_chem_comp_audit.action_type _pdbx_chem_comp_audit.date _pdbx_chem_comp_audit.processing_site LKV 'Create component' 2022-07-06 PDBE LKV 'Modify descriptor' 2022-08-22 RCSB LKV 'Initial release' 2023-04-26 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 LKV C4 C 10.143 -0.667 1 LKV C5 C 12.393 -1.966 2 LKV C7 C 13.893 -1.966 3 LKV C8 C 7.018 -0.575 4 LKV C10 C 4.299 -0.868 5 LKV C12 C 3.000 1.382 6 LKV C13 C 4.299 2.132 7 LKV C15 C 7.018 1.839 8 LKV C1 C 10.143 1.931 9 LKV O3 O 7.483 3.265 10 LKV C14 C 5.598 1.382 11 LKV C11 C 3.000 -0.118 12 LKV C9 C 5.598 -0.118 13 LKV N1 N 7.893 0.632 14 LKV C3 C 9.393 0.632 15 LKV C2 C 11.643 1.931 16 LKV C C 9.393 3.230 17 LKV O O 9.393 -1.966 18 LKV N N 11.643 -0.667 19 LKV C6 C 11.643 -3.265 20 LKV O1 O 14.643 -3.265 21 LKV O2 O 14.643 -0.667 22 # 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 LKV C5 C6 SINGLE BEGINDASH 1 LKV O1 C7 DOUBLE NONE 2 LKV C7 C5 SINGLE NONE 3 LKV C7 O2 SINGLE NONE 4 LKV C5 N SINGLE NONE 5 LKV O3 C15 DOUBLE NONE 6 LKV N C4 SINGLE NONE 7 LKV C3 C4 SINGLE NONE 8 LKV C3 N1 SINGLE NONE 9 LKV C3 C1 SINGLE BEGINWEDGE 10 LKV C15 N1 SINGLE NONE 11 LKV C15 C14 SINGLE NONE 12 LKV C2 C1 SINGLE NONE 13 LKV C4 O DOUBLE NONE 14 LKV C C1 SINGLE NONE 15 LKV N1 C8 SINGLE NONE 16 LKV C13 C14 DOUBLE NONE 17 LKV C13 C12 SINGLE NONE 18 LKV C14 C9 SINGLE NONE 19 LKV C8 C9 SINGLE NONE 20 LKV C12 C11 DOUBLE NONE 21 LKV C9 C10 DOUBLE NONE 22 LKV C11 C10 SINGLE NONE 23 # 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 LKV MurckoScaffold S1 scaffold O=C1NCc2ccccc21 InChI=1S/C8H7NO/c10-8-7-4-2-1-3-6(7)5-9-8/h1-4H,5H2,(H,9,10) PXZQEOJJUGGUIB-UHFFFAOYSA-N LKV amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N LKV peptide F2 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N LKV phenyl F3 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 LKV C8 S1 1 LKV C10 S1 1 LKV C12 S1 1 LKV C13 S1 1 LKV C15 S1 1 LKV O3 S1 1 LKV C14 S1 1 LKV C11 S1 1 LKV C9 S1 1 LKV N1 S1 1 LKV N1 F1 1 LKV C15 F1 1 LKV O3 F1 1 LKV C14 F1 1 LKV N F1 2 LKV C4 F1 2 LKV O F1 2 LKV C3 F1 2 LKV O F2 1 LKV C4 F2 1 LKV C3 F2 1 LKV N1 F2 1 LKV O1 F2 2 LKV C7 F2 2 LKV C5 F2 2 LKV N F2 2 LKV C10 F3 1 LKV C9 F3 1 LKV C14 F3 1 LKV C13 F3 1 LKV C12 F3 1 LKV C11 F3 1 # _pdbe_chem_comp_rdkit_properties.comp_id LKV _pdbe_chem_comp_rdkit_properties.exactmw 304.142 _pdbe_chem_comp_rdkit_properties.amw 304.346 _pdbe_chem_comp_rdkit_properties.lipinskiHBA 6 _pdbe_chem_comp_rdkit_properties.lipinskiHBD 2 _pdbe_chem_comp_rdkit_properties.NumRotatableBonds 8 _pdbe_chem_comp_rdkit_properties.NumHBD 2 _pdbe_chem_comp_rdkit_properties.NumHBA 4 _pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 22 _pdbe_chem_comp_rdkit_properties.NumAtoms 42 _pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6 _pdbe_chem_comp_rdkit_properties.NumAmideBonds 2 _pdbe_chem_comp_rdkit_properties.FractionCSP3 0.438 _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 0 _pdbe_chem_comp_rdkit_properties.NumHeterocycles 1 _pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0 _pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 0 _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 2 _pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0 _pdbe_chem_comp_rdkit_properties.labuteASA 156.908 _pdbe_chem_comp_rdkit_properties.tpsa 86.710 _pdbe_chem_comp_rdkit_properties.CrippenClogP 1.147 _pdbe_chem_comp_rdkit_properties.CrippenMR 79.650 _pdbe_chem_comp_rdkit_properties.chi0v 10.527 _pdbe_chem_comp_rdkit_properties.chi1v 5.435 _pdbe_chem_comp_rdkit_properties.chi2v 2.398 _pdbe_chem_comp_rdkit_properties.chi3v 2.398 _pdbe_chem_comp_rdkit_properties.chi4v 1.503 _pdbe_chem_comp_rdkit_properties.chi0n 30.527 _pdbe_chem_comp_rdkit_properties.chi1n 15.290 _pdbe_chem_comp_rdkit_properties.chi2n 2.398 _pdbe_chem_comp_rdkit_properties.chi3n 2.398 _pdbe_chem_comp_rdkit_properties.chi4n 1.503 _pdbe_chem_comp_rdkit_properties.hallKierAlpha -2.370 _pdbe_chem_comp_rdkit_properties.kappa1 4.127 _pdbe_chem_comp_rdkit_properties.kappa2 6.172 _pdbe_chem_comp_rdkit_properties.kappa3 2.954 _pdbe_chem_comp_rdkit_properties.Phi 1.158 # _pdbe_chem_comp_external_mappings.comp_id LKV _pdbe_chem_comp_external_mappings.source UniChem _pdbe_chem_comp_external_mappings.resource PubChem _pdbe_chem_comp_external_mappings.resource_id 132352592 # 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 LKV C4 -1.101 0.245 0.038 ETKDGv3 1 LKV C5 -3.495 1.073 0.174 ETKDGv3 2 LKV C7 -3.999 0.127 1.225 ETKDGv3 3 LKV C8 2.152 -0.287 0.732 ETKDGv3 4 LKV C10 4.393 0.787 1.335 ETKDGv3 5 LKV C12 5.229 2.562 -0.155 ETKDGv3 6 LKV C13 4.017 2.385 -0.998 ETKDGv3 7 LKV C15 1.882 1.049 -1.205 ETKDGv3 8 LKV C1 -0.132 -2.089 -0.407 ETKDGv3 9 LKV O3 1.361 1.549 -2.237 ETKDGv3 10 LKV C14 3.133 1.459 -0.622 ETKDGv3 11 LKV C11 5.407 1.805 0.949 ETKDGv3 12 LKV C9 3.314 0.644 0.559 ETKDGv3 13 LKV N1 1.295 -0.007 -0.436 ETKDGv3 14 LKV C3 -0.048 -0.555 -0.692 ETKDGv3 15 LKV C2 -0.406 -2.446 1.067 ETKDGv3 16 LKV C -1.197 -2.756 -1.293 ETKDGv3 17 LKV O -0.864 0.690 1.194 ETKDGv3 18 LKV N -2.387 0.456 -0.562 ETKDGv3 19 LKV C6 -4.633 1.444 -0.780 ETKDGv3 20 LKV O1 -4.228 0.544 2.391 ETKDGv3 21 LKV O2 -4.239 -1.206 0.904 ETKDGv3 22 LKV H1 -3.134 2.010 0.654 ETKDGv3 23 LKV H14 1.622 -0.044 1.676 ETKDGv3 24 LKV H15 2.499 -1.342 0.719 ETKDGv3 25 LKV H16 4.525 0.181 2.222 ETKDGv3 26 LKV H18 5.969 3.301 -0.430 ETKDGv3 27 LKV H19 3.861 2.985 -1.885 ETKDGv3 28 LKV H5 0.843 -2.543 -0.690 ETKDGv3 29 LKV H17 6.290 1.939 1.560 ETKDGv3 30 LKV H -0.240 -0.419 -1.780 ETKDGv3 31 LKV H7 0.337 -1.986 1.744 ETKDGv3 32 LKV H6 -1.421 -2.116 1.374 ETKDGv3 33 LKV H8 -0.345 -3.547 1.205 ETKDGv3 34 LKV H4 -1.201 -3.855 -1.128 ETKDGv3 35 LKV H3 -0.978 -2.577 -2.367 ETKDGv3 36 LKV H2 -2.208 -2.359 -1.060 ETKDGv3 37 LKV H9 -2.543 0.125 -1.541 ETKDGv3 38 LKV H12 -5.032 0.539 -1.286 ETKDGv3 39 LKV H11 -5.456 1.937 -0.220 ETKDGv3 40 LKV H10 -4.261 2.152 -1.552 ETKDGv3 41 LKV H13 -4.583 -1.855 1.603 ETKDGv3 42 #