data_88B
#
_chem_comp.id 88B
_chem_comp.name "4-diazanyl-4-oxidanylidene-butanoic acid"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C4 H8 N2 O3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2019-07-25
_chem_comp.pdbx_modified_date 2020-08-21
_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 132.118
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 88B
_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 6SCU
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
#
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
88B N N1 N 0 1 N N N N N N 11.652 39.800 -9.892 3.774 -0.114 -0.020 N 88B 1
88B C C1 C 0 1 N N N N N N 11.481 40.515 -7.618 1.433 0.096 -0.012 C 88B 2
88B O O1 O 0 1 N N N N N N 10.493 41.208 -7.847 1.546 1.303 -0.019 O 88B 3
88B C1 C2 C 0 1 N N N N N N 12.032 40.365 -6.225 0.063 -0.533 -0.003 C1 88B 4
88B C2 C3 C 0 1 N N N N N N 11.107 39.562 -5.342 -1.002 0.566 -0.005 C2 88B 5
88B C3 C4 C 0 1 N N N N N N 10.755 38.235 -5.947 -2.371 -0.063 0.004 C3 88B 6
88B N1 N2 N 0 1 N N N N N N 12.109 39.816 -8.557 2.532 -0.684 -0.012 N1 88B 7
88B O1 O2 O 0 1 N N N N N N 9.758 38.051 -6.596 -2.484 -1.266 0.011 O1 88B 8
88B O2 O3 O 0 1 N N N N N N 11.631 37.313 -5.722 -3.466 0.714 0.004 O2 88B 9
88B H1 H1 H 0 1 N N N N N N 12.253 39.221 -10.444 3.886 0.519 0.757 H1 88B 10
88B H2 H2 H 0 1 N N N N N N 10.721 39.437 -9.921 4.495 -0.820 -0.019 H2 88B 11
88B H3 H3 H 0 1 N N N N N N 13.005 39.855 -6.280 -0.056 -1.156 -0.889 H3 88B 12
88B H4 H4 H 0 1 N N N N N N 12.166 41.364 -5.785 -0.049 -1.146 0.891 H4 88B 13
88B H5 H5 H 0 1 N N N N N N 11.602 39.390 -4.375 -0.882 1.189 0.881 H5 88B 14
88B H6 H6 H 0 1 N N N N N N 10.182 40.136 -5.184 -0.889 1.179 -0.899 H6 88B 15
88B H7 H7 H 0 1 N N N N N N 12.923 39.290 -8.312 2.442 -1.650 -0.006 H7 88B 16
88B H8 H8 H 0 1 N N N N N N 11.357 36.506 -6.141 -4.323 0.265 0.009 H8 88B 17
#
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
88B N N1 SING N N 1
88B N1 C SING N N 2
88B O C DOUB N N 3
88B C C1 SING N N 4
88B O1 C3 DOUB N N 5
88B C1 C2 SING N N 6
88B C3 O2 SING N N 7
88B C3 C2 SING N N 8
88B N H1 SING N N 9
88B N H2 SING N N 10
88B C1 H3 SING N N 11
88B C1 H4 SING N N 12
88B C2 H5 SING N N 13
88B C2 H6 SING N N 14
88B N1 H7 SING N N 15
88B O2 H8 SING N N 16
#
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
88B InChI InChI 1.03 InChI=1S/C4H8N2O3/c5-6-3(7)1-2-4(8)9/h1-2,5H2,(H,6,7)(H,8,9)
88B InChIKey InChI 1.03 XRMBRQWBOICYRP-UHFFFAOYSA-N
88B SMILES_CANONICAL CACTVS 3.385 NNC(=O)CCC(O)=O
88B SMILES CACTVS 3.385 NNC(=O)CCC(O)=O
88B SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 C(CC(=O)O)C(=O)NN
88B SMILES "OpenEye OEToolkits" 2.0.7 C(CC(=O)O)C(=O)NN
#
_pdbx_chem_comp_identifier.comp_id 88B
_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-diazanyl-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
88B 'Create component' 2019-07-25 EBI
88B 'Initial release' 2020-08-26 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
88B N N 3.805 -0.375 1
88B C C 6.404 -0.375 2
88B O O 6.404 -1.875 3
88B C1 C 7.702 0.375 4
88B C2 C 9.002 -0.375 5
88B C3 C 10.301 0.375 6
88B N1 N 5.104 0.375 7
88B O1 O 11.600 -0.375 8
88B O2 O 10.301 1.875 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
88B N N1 SINGLE NONE 1
88B N1 C SINGLE NONE 2
88B O C DOUBLE NONE 3
88B C C1 SINGLE NONE 4
88B O1 C3 DOUBLE NONE 5
88B C1 C2 SINGLE NONE 6
88B C3 O2 SINGLE NONE 7
88B C3 C2 SINGLE NONE 8
#
_pdbe_chem_comp_substructure.comp_id 88B
_pdbe_chem_comp_substructure.substructure_name amide
_pdbe_chem_comp_substructure.id F1
_pdbe_chem_comp_substructure.substructure_type fragment
_pdbe_chem_comp_substructure.substructure_smiles CC(N)=O
_pdbe_chem_comp_substructure.substructure_inchis InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4)
_pdbe_chem_comp_substructure.substructure_inchikeys DLFVBJFMPXGRIB-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
88B N1 F1 1
88B C F1 1
88B O F1 1
88B C1 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 88B
_pdbe_chem_comp_rdkit_properties.exactmw 132.053
_pdbe_chem_comp_rdkit_properties.amw 132.119
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 9
_pdbe_chem_comp_rdkit_properties.NumAtoms 17
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.500
_pdbe_chem_comp_rdkit_properties.NumRings 0
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_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 63.312
_pdbe_chem_comp_rdkit_properties.tpsa 92.420
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.159
_pdbe_chem_comp_rdkit_properties.CrippenMR 29.200
_pdbe_chem_comp_rdkit_properties.chi0v 4.119
_pdbe_chem_comp_rdkit_properties.chi1v 1.786
_pdbe_chem_comp_rdkit_properties.chi2v 0.362
_pdbe_chem_comp_rdkit_properties.chi3v 0.362
_pdbe_chem_comp_rdkit_properties.chi4v 0.129
_pdbe_chem_comp_rdkit_properties.chi0n 12.119
_pdbe_chem_comp_rdkit_properties.chi1n 5.536
_pdbe_chem_comp_rdkit_properties.chi2n 0.362
_pdbe_chem_comp_rdkit_properties.chi3n 0.362
_pdbe_chem_comp_rdkit_properties.chi4n 0.129
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.100
_pdbe_chem_comp_rdkit_properties.kappa1 1.694
_pdbe_chem_comp_rdkit_properties.kappa2 3.849
_pdbe_chem_comp_rdkit_properties.kappa3 4.759
_pdbe_chem_comp_rdkit_properties.Phi 0.724
#
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
88B UniChem ChEMBL CHEMBL2164246
88B UniChem PDBe 88B
88B UniChem ZINC ZINC000001700248
88B UniChem SureChEMBL SCHEMBL960529
88B UniChem ACTor 4604-20-0
88B UniChem 'EPA CompTox Dashboard' DTXSID10278758
88B UniChem 'Probes And Drugs' PD119474
88B UniChem BindingDb 50395083
88B UniChem PubChem 222878
#
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
88B N -2.355 1.216 0.956 ETKDGv3 1
88B C -0.699 0.601 -0.762 ETKDGv3 2
88B O -0.714 1.777 -1.218 ETKDGv3 3
88B C1 0.220 -0.418 -1.370 ETKDGv3 4
88B C2 1.628 -0.338 -0.770 ETKDGv3 5
88B C3 1.639 -0.757 0.668 ETKDGv3 6
88B N1 -1.525 0.256 0.355 ETKDGv3 7
88B O1 1.685 -1.980 0.969 ETKDGv3 8
88B O2 1.560 0.203 1.672 ETKDGv3 9
88B H1 -2.809 0.769 1.785 ETKDGv3 10
88B H2 -3.120 1.431 0.277 ETKDGv3 11
88B H3 -0.197 -1.440 -1.231 ETKDGv3 12
88B H4 0.286 -0.235 -2.465 ETKDGv3 13
88B H5 2.304 -1.006 -1.346 ETKDGv3 14
88B H6 2.022 0.697 -0.861 ETKDGv3 15
88B H7 -1.474 -0.710 0.754 ETKDGv3 16
88B H8 1.548 -0.065 2.648 ETKDGv3 17
#