data_SRK
#
_chem_comp.id SRK
_chem_comp.name "4-(2,3-dihydroindol-1-yl)-4-oxidanylidene-butanoic acid"
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C12 H13 N O3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2020-11-30
_chem_comp.pdbx_modified_date 2021-07-30
_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 219.237
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code SRK
_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 7B37
_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
SRK C02 C1 C 0 1 N N N N N N 23.070 67.894 72.926 3.751 -0.561 -0.002 C02 SRK 1
SRK C04 C2 C 0 1 N N N N N N 23.193 67.181 71.598 2.828 0.631 -0.001 C04 SRK 2
SRK C05 C3 C 0 1 N N N N N N 24.391 66.232 71.493 1.375 0.150 -0.001 C05 SRK 3
SRK C06 C4 C 0 1 N N N N N N 25.730 66.750 72.017 0.453 1.342 -0.001 C06 SRK 4
SRK C09 C5 C 0 1 N N N N N N 26.736 64.498 71.439 -1.877 2.237 0.000 C09 SRK 5
SRK C10 C6 C 0 1 N N N N N N 28.123 63.957 71.269 -3.240 1.526 0.001 C10 SRK 6
SRK C11 C7 C 0 1 Y N N N N N 29.019 64.889 72.073 -2.902 0.052 0.001 C11 SRK 7
SRK C12 C8 C 0 1 Y N N N N N 30.356 64.752 72.429 -3.715 -1.065 0.001 C12 SRK 8
SRK C13 C9 C 0 1 Y N N N N N 30.943 65.748 73.199 -3.158 -2.330 -0.000 C13 SRK 9
SRK C14 C10 C 0 1 Y N N N N N 30.210 66.873 73.564 -1.783 -2.476 -0.001 C14 SRK 10
SRK C15 C11 C 0 1 Y N N N N N 28.881 67.010 73.205 -0.967 -1.364 0.000 C15 SRK 11
SRK C16 C12 C 0 1 Y N N N N N 28.275 66.020 72.422 -1.523 -0.083 0.000 C16 SRK 12
SRK N08 N1 N 0 1 N N N N N N 26.869 65.853 71.942 -0.883 1.160 -0.000 N08 SRK 13
SRK O01 O1 O 0 1 N N N N N N 23.069 67.195 73.988 5.081 -0.380 0.004 O01 SRK 14
SRK O03 O2 O 0 1 N N N N N N 22.968 69.158 72.971 3.293 -1.679 -0.001 O03 SRK 15
SRK O07 O3 O 0 1 N N N N N N 25.848 67.847 72.445 0.912 2.465 -0.001 O07 SRK 16
SRK H1 H1 H 0 1 N N N N N N 23.287 67.941 70.808 3.012 1.232 0.889 H1 SRK 17
SRK H2 H2 H 0 1 N N N N N N 22.276 66.595 71.437 3.011 1.232 -0.891 H2 SRK 18
SRK H3 H3 H 0 1 N N N N N N 24.144 65.320 72.057 1.191 -0.451 -0.891 H3 SRK 19
SRK H4 H4 H 0 1 N N N N N N 24.524 65.981 70.430 1.192 -0.451 0.889 H4 SRK 20
SRK H5 H5 H 0 1 N N N N N N 26.211 64.503 70.472 -1.771 2.850 -0.895 H5 SRK 21
SRK H6 H6 H 0 1 N N N N N N 26.175 63.882 72.157 -1.769 2.851 0.894 H6 SRK 22
SRK H7 H7 H 0 1 N N N N N N 28.187 62.930 71.659 -3.805 1.786 0.896 H7 SRK 23
SRK H8 H8 H 0 1 N N N N N N 28.412 63.965 70.208 -3.805 1.786 -0.894 H8 SRK 24
SRK H9 H9 H 0 1 N N N N N N 30.926 63.890 72.114 -4.789 -0.949 0.001 H9 SRK 25
SRK H10 H10 H 0 1 N N N N N N 31.971 65.649 73.515 -3.795 -3.202 0.000 H10 SRK 26
SRK H11 H11 H 0 1 N N N N N N 30.687 67.653 74.138 -1.346 -3.463 -0.001 H11 SRK 27
SRK H12 H12 H 0 1 N N N N N N 28.316 67.873 73.526 0.106 -1.485 0.000 H12 SRK 28
SRK H13 H13 H 0 1 N N N N N N 22.984 67.765 74.743 5.632 -1.174 0.007 H13 SRK 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
SRK C10 C09 SING N N 1
SRK C10 C11 SING N N 2
SRK C09 N08 SING N N 3
SRK C05 C04 SING N N 4
SRK C05 C06 SING N N 5
SRK C04 C02 SING N N 6
SRK N08 C06 SING N N 7
SRK N08 C16 SING N N 8
SRK C06 O07 DOUB N N 9
SRK C11 C16 DOUB Y N 10
SRK C11 C12 SING Y N 11
SRK C16 C15 SING Y N 12
SRK C12 C13 DOUB Y N 13
SRK C02 O03 DOUB N N 14
SRK C02 O01 SING N N 15
SRK C13 C14 SING Y N 16
SRK C15 C14 DOUB Y N 17
SRK C04 H1 SING N N 18
SRK C04 H2 SING N N 19
SRK C05 H3 SING N N 20
SRK C05 H4 SING N N 21
SRK C09 H5 SING N N 22
SRK C09 H6 SING N N 23
SRK C10 H7 SING N N 24
SRK C10 H8 SING N N 25
SRK C12 H9 SING N N 26
SRK C13 H10 SING N N 27
SRK C14 H11 SING N N 28
SRK C15 H12 SING N N 29
SRK O01 H13 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
SRK InChI InChI 1.03 InChI=1S/C12H13NO3/c14-11(5-6-12(15)16)13-8-7-9-3-1-2-4-10(9)13/h1-4H,5-8H2,(H,15,16)
SRK InChIKey InChI 1.03 SWNRXQYQTQVWKA-UHFFFAOYSA-N
SRK SMILES_CANONICAL CACTVS 3.385 OC(=O)CCC(=O)N1CCc2ccccc12
SRK SMILES CACTVS 3.385 OC(=O)CCC(=O)N1CCc2ccccc12
SRK SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 c1ccc2c(c1)CCN2C(=O)CCC(=O)O
SRK SMILES "OpenEye OEToolkits" 2.0.7 c1ccc2c(c1)CCN2C(=O)CCC(=O)O
#
_pdbx_chem_comp_identifier.comp_id SRK
_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 "4-(2,3-dihydroindol-1-yl)-4-oxidanylidene-butanoic 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
SRK 'Create component' 2020-11-30 PDBE
SRK 'Initial release' 2021-08-04 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
SRK C02 C 10.885 -2.280 1
SRK C04 C 9.417 -1.971 2
SRK C05 C 8.951 -0.545 3
SRK C06 C 7.483 -0.235 4
SRK C09 C 7.893 2.397 5
SRK C10 C 7.018 3.604 6
SRK C11 C 5.598 3.147 7
SRK C12 C 4.299 3.897 8
SRK C13 C 3.000 3.147 9
SRK C14 C 3.000 1.647 10
SRK C15 C 4.299 0.897 11
SRK C16 C 5.598 1.647 12
SRK N08 N 7.018 1.190 13
SRK O01 O 11.887 -1.163 14
SRK O03 O 11.351 -3.706 15
SRK O07 O 6.482 -1.352 16
#
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
SRK C10 C09 SINGLE NONE 1
SRK C10 C11 SINGLE NONE 2
SRK C09 N08 SINGLE NONE 3
SRK C05 C04 SINGLE NONE 4
SRK C05 C06 SINGLE NONE 5
SRK C04 C02 SINGLE NONE 6
SRK N08 C06 SINGLE NONE 7
SRK N08 C16 SINGLE NONE 8
SRK C06 O07 DOUBLE NONE 9
SRK C11 C16 DOUBLE NONE 10
SRK C11 C12 SINGLE NONE 11
SRK C16 C15 SINGLE NONE 12
SRK C12 C13 DOUBLE NONE 13
SRK C02 O03 DOUBLE NONE 14
SRK C02 O01 SINGLE NONE 15
SRK C13 C14 SINGLE NONE 16
SRK C15 C14 DOUBLE NONE 17
#
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
SRK MurckoScaffold S1 scaffold c1ccc2c(c1)CCN2 InChI=1S/C8H9N/c1-2-4-8-7(3-1)5-6-9-8/h1-4,9H,5-6H2 LPAGFVYQRIESJQ-UHFFFAOYSA-N
SRK amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
SRK phenyl F2 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
SRK C09 S1 1
SRK C10 S1 1
SRK C11 S1 1
SRK C12 S1 1
SRK C13 S1 1
SRK C14 S1 1
SRK C15 S1 1
SRK C16 S1 1
SRK N08 S1 1
SRK N08 F1 1
SRK C06 F1 1
SRK O07 F1 1
SRK C05 F1 1
SRK C11 F2 1
SRK C16 F2 1
SRK C15 F2 1
SRK C14 F2 1
SRK C13 F2 1
SRK C12 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id SRK
_pdbe_chem_comp_rdkit_properties.exactmw 219.090
_pdbe_chem_comp_rdkit_properties.amw 219.240
_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 16
_pdbe_chem_comp_rdkit_properties.NumAtoms 29
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.333
_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 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 111.844
_pdbe_chem_comp_rdkit_properties.tpsa 57.610
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.005
_pdbe_chem_comp_rdkit_properties.CrippenMR 58.279
_pdbe_chem_comp_rdkit_properties.chi0v 7.672
_pdbe_chem_comp_rdkit_properties.chi1v 4.033
_pdbe_chem_comp_rdkit_properties.chi2v 1.659
_pdbe_chem_comp_rdkit_properties.chi3v 1.659
_pdbe_chem_comp_rdkit_properties.chi4v 1.044
_pdbe_chem_comp_rdkit_properties.chi0n 20.672
_pdbe_chem_comp_rdkit_properties.chi1n 10.441
_pdbe_chem_comp_rdkit_properties.chi2n 1.659
_pdbe_chem_comp_rdkit_properties.chi3n 1.659
_pdbe_chem_comp_rdkit_properties.chi4n 1.044
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.840
_pdbe_chem_comp_rdkit_properties.kappa1 3.093
_pdbe_chem_comp_rdkit_properties.kappa2 4.346
_pdbe_chem_comp_rdkit_properties.kappa3 2.053
_pdbe_chem_comp_rdkit_properties.Phi 0.840
#
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
SRK UniChem ChEMBL CHEMBL357516
SRK UniChem PDBe SRK
SRK UniChem ZINC ZINC000000143134
SRK UniChem eMolecules 828224
SRK UniChem BindingDb 50136875
SRK UniChem 'EPA CompTox Dashboard' DTXSID10352628
SRK UniChem SureChEMBL SCHEMBL2278917
SRK UniChem 'PubChem TPHARMA' 16288889
SRK UniChem PubChem 730429
SRK UniChem Mcule MCULE-8578773876
SRK UniChem Nikkaji J1.861.082E
#
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
SRK C02 4.285 0.397 0.282 ETKDGv3 1
SRK C04 2.919 0.009 -0.190 ETKDGv3 2
SRK C05 2.045 1.251 -0.376 ETKDGv3 3
SRK C06 0.670 0.860 -0.840 ETKDGv3 4
SRK C09 -0.292 0.659 1.535 ETKDGv3 5
SRK C10 -1.624 0.111 2.084 ETKDGv3 6
SRK C11 -2.290 -0.431 0.870 ETKDGv3 7
SRK C12 -3.593 -1.119 0.804 ETKDGv3 8
SRK C13 -4.020 -1.582 -0.382 ETKDGv3 9
SRK C14 -3.182 -1.409 -1.597 ETKDGv3 10
SRK C15 -1.997 -0.779 -1.522 ETKDGv3 11
SRK C16 -1.551 -0.256 -0.208 ETKDGv3 12
SRK N08 -0.327 0.405 0.094 ETKDGv3 13
SRK O01 5.277 0.703 -0.644 ETKDGv3 14
SRK O03 4.525 0.485 1.516 ETKDGv3 15
SRK O07 0.411 0.913 -2.071 ETKDGv3 16
SRK H1 2.455 -0.678 0.550 ETKDGv3 17
SRK H2 3.010 -0.534 -1.156 ETKDGv3 18
SRK H3 2.511 1.923 -1.131 ETKDGv3 19
SRK H4 1.979 1.818 0.577 ETKDGv3 20
SRK H5 0.568 0.127 1.997 ETKDGv3 21
SRK H6 -0.215 1.751 1.728 ETKDGv3 22
SRK H7 -1.450 -0.700 2.824 ETKDGv3 23
SRK H8 -2.239 0.922 2.530 ETKDGv3 24
SRK H9 -4.193 -1.249 1.695 ETKDGv3 25
SRK H10 -4.972 -2.091 -0.454 ETKDGv3 26
SRK H11 -3.526 -1.802 -2.545 ETKDGv3 27
SRK H12 -1.389 -0.683 -2.409 ETKDGv3 28
SRK H13 6.202 0.982 -0.341 ETKDGv3 29
#