data_9TY
#
_chem_comp.id 9TY
_chem_comp.name "cyclopropane-1,1-dicarboxylic acid"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C5 H6 O4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2017-06-08
_chem_comp.pdbx_modified_date 2017-10-20
_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 130.099
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 9TY
_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 5W3K
_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
9TY C02 C1 C 0 1 N N N N N N -0.172 -14.872 11.520 -1.275 0.313 -0.106 C02 9TY 1
9TY C03 C2 C 0 1 N N N N N N -0.268 -16.208 10.802 0.000 -0.466 0.089 C03 9TY 2
9TY C04 C3 C 0 1 N N N N N N -1.540 -17.030 10.953 1.275 0.314 -0.105 C04 9TY 3
9TY C07 C4 C 0 1 N N N N N N 1.060 -16.977 10.666 0.001 -1.937 -0.334 C07 9TY 4
9TY C08 C5 C 0 1 N N N N N N 0.426 -16.317 9.438 -0.000 -1.567 1.152 C08 9TY 5
9TY O01 O1 O 0 1 N N N N N N 0.935 -14.280 11.551 -2.246 -0.226 -0.582 O01 9TY 6
9TY O05 O2 O 0 1 N N N N N N -2.626 -16.520 11.381 1.331 1.607 0.250 O05 9TY 7
9TY O06 O3 O 0 1 N N N N N N -1.423 -18.242 10.631 2.247 -0.225 -0.579 O06 9TY 8
9TY O09 O4 O 0 1 N N N N N N -1.177 -14.368 12.090 -1.333 1.605 0.254 O09 9TY 9
9TY H1 H1 H 0 1 N N N N N N 1.073 -18.073 10.756 -0.921 -2.340 -0.752 H1 9TY 10
9TY H2 H2 H 0 1 N N N N N N 1.983 -16.563 11.099 0.923 -2.340 -0.752 H2 9TY 11
9TY H3 H3 H 0 1 N N N N N N 0.895 -15.430 8.988 0.922 -1.727 1.711 H3 9TY 12
9TY H4 H4 H 0 1 N N N N N N -0.015 -16.940 8.646 -0.923 -1.727 1.710 H4 9TY 13
9TY H5 H5 H 0 1 N N N N N N -3.300 -17.189 11.412 2.170 2.066 0.107 H5 9TY 14
9TY H6 H6 H 0 1 N N N N N N -0.932 -13.544 12.495 -2.173 2.062 0.113 H6 9TY 15
#
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
9TY C08 C07 SING N N 1
9TY C08 C03 SING N N 2
9TY O06 C04 DOUB N N 3
9TY C07 C03 SING N N 4
9TY C03 C04 SING N N 5
9TY C03 C02 SING N N 6
9TY C04 O05 SING N N 7
9TY C02 O01 DOUB N N 8
9TY C02 O09 SING N N 9
9TY C07 H1 SING N N 10
9TY C07 H2 SING N N 11
9TY C08 H3 SING N N 12
9TY C08 H4 SING N N 13
9TY O05 H5 SING N N 14
9TY O09 H6 SING N N 15
#
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
9TY SMILES ACDLabs 12.01 C(=O)(O)C1(C(O)=O)CC1
9TY InChI InChI 1.03 InChI=1S/C5H6O4/c6-3(7)5(1-2-5)4(8)9/h1-2H2,(H,6,7)(H,8,9)
9TY InChIKey InChI 1.03 FDKLLWKMYAMLIF-UHFFFAOYSA-N
9TY SMILES_CANONICAL CACTVS 3.385 OC(=O)C1(CC1)C(O)=O
9TY SMILES CACTVS 3.385 OC(=O)C1(CC1)C(O)=O
9TY SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 C1CC1(C(=O)O)C(=O)O
9TY SMILES "OpenEye OEToolkits" 2.0.6 C1CC1(C(=O)O)C(=O)O
#
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
9TY "SYSTEMATIC NAME" ACDLabs 12.01 "cyclopropane-1,1-dicarboxylic acid"
9TY "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 "cyclopropane-1,1-dicarboxylic 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
9TY 'Create component' 2017-06-08 RCSB
9TY 'Initial release' 2017-10-25 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
9TY C02 C 5.049 -1.702 1
9TY C03 C 4.299 -0.403 2
9TY C04 C 5.049 0.896 3
9TY C07 C 3.000 0.347 4
9TY C08 C 3.000 -1.153 5
9TY O01 O 6.549 -1.702 6
9TY O05 O 6.549 0.896 7
9TY O06 O 4.299 2.195 8
9TY O09 O 4.299 -3.001 9
#
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
9TY C08 C07 SINGLE NONE 1
9TY C08 C03 SINGLE NONE 2
9TY O06 C04 DOUBLE NONE 3
9TY C07 C03 SINGLE NONE 4
9TY C03 C04 SINGLE NONE 5
9TY C03 C02 SINGLE NONE 6
9TY C04 O05 SINGLE NONE 7
9TY C02 O01 DOUBLE NONE 8
9TY C02 O09 SINGLE NONE 9
#
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
9TY MurckoScaffold S1 scaffold C1CC1 InChI=1S/C3H6/c1-2-3-1/h1-3H2 LVZWSLJZHVFIQJ-UHFFFAOYSA-N
9TY cyclopropane F1 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
9TY C03 S1 1
9TY C07 S1 1
9TY C08 S1 1
9TY C03 F1 1
9TY C08 F1 1
9TY C07 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 9TY
_pdbe_chem_comp_rdkit_properties.exactmw 130.027
_pdbe_chem_comp_rdkit_properties.amw 130.099
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_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 9
_pdbe_chem_comp_rdkit_properties.NumAtoms 15
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.600
_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 1
_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 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 59.708
_pdbe_chem_comp_rdkit_properties.tpsa 74.600
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.064
_pdbe_chem_comp_rdkit_properties.CrippenMR 26.939
_pdbe_chem_comp_rdkit_properties.chi0v 4.133
_pdbe_chem_comp_rdkit_properties.chi1v 2.066
_pdbe_chem_comp_rdkit_properties.chi2v 0.987
_pdbe_chem_comp_rdkit_properties.chi3v 0.987
_pdbe_chem_comp_rdkit_properties.chi4v 0.350
_pdbe_chem_comp_rdkit_properties.chi0n 10.133
_pdbe_chem_comp_rdkit_properties.chi1n 4.883
_pdbe_chem_comp_rdkit_properties.chi2n 0.987
_pdbe_chem_comp_rdkit_properties.chi3n 0.987
_pdbe_chem_comp_rdkit_properties.chi4n 0.350
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.060
_pdbe_chem_comp_rdkit_properties.kappa1 1.968
_pdbe_chem_comp_rdkit_properties.kappa2 1.462
_pdbe_chem_comp_rdkit_properties.kappa3 0.667
_pdbe_chem_comp_rdkit_properties.Phi 0.320
#
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
9TY UniChem ChEMBL CHEMBL1993862
9TY UniChem PDBe 9TY
9TY UniChem ZINC ZINC000000388470
9TY UniChem eMolecules 495927
9TY UniChem 'PubChem TPHARMA' 14747648
9TY UniChem ACTor 598-10-7
9TY UniChem BindingDb 82142
9TY UniChem BRENDA 132254
9TY UniChem BRENDA 18045
9TY UniChem BRENDA 82618
9TY UniChem ChemicalBook CB9487673
9TY UniChem 'EPA CompTox Dashboard' DTXSID20208526
9TY UniChem SureChEMBL SCHEMBL106415
9TY UniChem PubChem 69017
9TY UniChem Nikkaji J6.789J
#
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
9TY C02 -1.419 0.419 0.261 ETKDGv3 1
9TY C03 -0.065 -0.048 -0.170 ETKDGv3 2
9TY C04 0.879 0.946 -0.769 ETKDGv3 3
9TY C07 0.568 -1.137 0.686 ETKDGv3 4
9TY C08 0.026 -1.474 -0.696 ETKDGv3 5
9TY O01 -2.375 0.421 -0.560 ETKDGv3 6
9TY O05 1.748 1.658 0.051 ETKDGv3 7
9TY O06 0.861 1.163 -2.010 ETKDGv3 8
9TY O09 -1.612 0.888 1.556 ETKDGv3 9
9TY H1 1.678 -1.137 0.736 ETKDGv3 10
9TY H2 -0.058 -1.535 1.514 ETKDGv3 11
9TY H3 0.821 -1.666 -1.448 ETKDGv3 12
9TY H4 -0.916 -2.064 -0.670 ETKDGv3 13
9TY H5 2.384 2.344 -0.339 ETKDGv3 14
9TY H6 -2.520 1.220 1.859 ETKDGv3 15
#