data_DBU
#
_chem_comp.id DBU
_chem_comp.name '(2Z)-2-AMINOBUT-2-ENOIC ACID'
_chem_comp.type 'PEPTIDE LINKING'
_chem_comp.pdbx_type ATOMP
_chem_comp.formula 'C4 H7 N O2'
_chem_comp.mon_nstd_parent_comp_id THR
_chem_comp.pdbx_synonyms Z-DEHYDROBUTYRINE
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2004-03-16
_chem_comp.pdbx_modified_date 2024-09-27
_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 101.104
_chem_comp.one_letter_code T
_chem_comp.three_letter_code DBU
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag Y
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code ?
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
_chem_comp.pdbx_pcm Y
#
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
DBU N N N 0 1 N N N Y Y N 0.370 21.917 6.620 0.897 2.171 -1.353 N DBU 1
DBU CA CA C 0 1 N N N Y N N -0.171 23.187 6.670 2.034 1.474 -1.063 CA DBU 2
DBU CB CB C 0 1 N N N N N N 0.511 24.230 6.180 2.118 0.311 -0.392 CB DBU 3
DBU CG CG C 0 1 N N N N N N 1.866 23.988 5.602 0.973 -0.465 0.179 CG DBU 4
DBU C C C 0 1 N N N Y N Y -1.563 23.412 7.240 3.331 2.048 -1.531 C DBU 5
DBU O O O 0 1 N N N Y N Y -1.783 24.276 8.088 4.435 1.555 -1.357 O DBU 6
DBU OXT OXT O 0 1 N Y N Y N Y ? ? ? 3.131 3.215 -2.192 OXT DBU 7
DBU H H H 0 1 N N N Y Y N -0.149 21.123 6.993 0.983 3.094 -1.718 H1 DBU 8
DBU H2 H2 H 0 1 N Y N Y Y N 1.286 21.940 7.067 0.016 1.735 -1.190 H2 DBU 9
DBU HB 1HB H 0 1 N N N N N N -0.022 25.142 5.956 3.088 -0.152 -0.221 HB1 DBU 10
DBU HG1 1HG H 0 1 N N N N N N 2.615 24.111 6.366 0.000 0.000 -0.000 HG1 DBU 11
DBU HG2 2HG H 0 1 N N N N N N 2.041 24.695 4.802 1.102 -0.569 1.261 HG2 DBU 12
DBU HG3 3HG H 0 1 N N N N N N 1.922 22.983 5.214 0.952 -1.467 -0.260 HG3 DBU 13
DBU HXT HXT H 0 1 N Y N Y N Y ? ? ? 3.973 3.607 -2.507 HXT DBU 14
#
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
DBU N CA SING N N 1
DBU N H SING N N 2
DBU N H2 SING N N 3
DBU CA CB DOUB N Z 4
DBU CA C SING N N 5
DBU CB CG SING N N 6
DBU CB HB SING N N 7
DBU CG HG1 SING N N 8
DBU CG HG2 SING N N 9
DBU CG HG3 SING N N 10
DBU C O DOUB N N 11
DBU C OXT SING N N 12
DBU OXT HXT SING N N 13
#
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
DBU SMILES ACDLabs 10.04 'O=C(O)C(=C/C)/N'
DBU SMILES_CANONICAL CACTVS 3.341 'C\C=C(/N)C(O)=O'
DBU SMILES CACTVS 3.341 'CC=C(N)C(O)=O'
DBU SMILES_CANONICAL 'OpenEye OEToolkits' 1.5.0 'C\C=C(\C(=O)O)/N'
DBU SMILES 'OpenEye OEToolkits' 1.5.0 'CC=C(C(=O)O)N'
DBU InChI InChI 1.03 'InChI=1S/C4H7NO2/c1-2-3(5)4(6)7/h2H,5H2,1H3,(H,6,7)/b3-2-'
DBU InChIKey InChI 1.03 PAWSVPVNIXFKOS-IHWYPQMZSA-N
#
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
DBU 'SYSTEMATIC NAME' ACDLabs 10.04 '(2Z)-2-aminobut-2-enoic acid'
DBU 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.5.0 '(Z)-2-aminobut-2-enoic 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
DBU 'Create component' 2004-03-16 EBI
DBU 'Modify parent residue' 2011-01-07 EBI
DBU 'Modify model coordinates code' 2011-01-12 EBI
DBU 'Modify model coordinates code' 2011-01-20 EBI
DBU 'Modify name' 2011-02-09 EBI
DBU 'Modify descriptor' 2011-06-04 RCSB
DBU 'Modify synonyms' 2020-06-05 PDBE
DBU 'Modify backbone' 2023-11-03 PDBE
DBU 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id DBU
_pdbx_chem_comp_synonyms.name Z-DEHYDROBUTYRINE
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id DBU
_pdbx_chem_comp_pcm.modified_residue_id THR
_pdbx_chem_comp_pcm.type 'Dehydroamino acid'
_pdbx_chem_comp_pcm.category 'Named protein modification'
_pdbx_chem_comp_pcm.position 'Amino-acid side chain and backbone'
_pdbx_chem_comp_pcm.polypeptide_position 'Any position'
_pdbx_chem_comp_pcm.comp_id_linking_atom ?
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom ?
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession PTM-0440
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession PTM-0007
#
_pdbe_chem_comp_drugbank_details.comp_id DBU
_pdbe_chem_comp_drugbank_details.drugbank_id DB03720
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name 'alpha,beta-Dehydroaminobutyric acid'
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number 71018-10-5
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
DBU Z-DEHYDROBUTYRINE wwPDB ?
DBU '(2Z)-2-aminobut-2-enoic acid' DrugBank ?
DBU '(Z)-2-aminobutenoic acid' DrugBank ?
DBU (Z)-dehydrobutyrine DrugBank ?
DBU (Z)2,3-didehydrobutyrine DrugBank ?
DBU 2-Ammoniobut-2-enoate DrugBank ?
DBU 'alpha,beta-Dehydroaminobutyric acid' DrugBank ?
DBU Anhydrothreonine DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id DBU
_pdbe_chem_comp_drugbank_classification.drugbank_id DB03720
_pdbe_chem_comp_drugbank_classification.parent 'Alpha amino acids'
_pdbe_chem_comp_drugbank_classification.kingdom 'Organic compounds'
_pdbe_chem_comp_drugbank_classification.class 'Carboxylic acids and derivatives'
_pdbe_chem_comp_drugbank_classification.superclass 'Organic acids and derivatives'
_pdbe_chem_comp_drugbank_classification.description
'This compound belongs to the class of organic compounds known as alpha amino acids. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon).'
#
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
DBU N N 3.805 0.750 1
DBU CA C 5.104 0.000 2
DBU CB C 5.104 -1.500 3
DBU CG C 3.805 -2.250 4
DBU C C 6.404 0.750 5
DBU O O 7.702 0.000 6
DBU OXT O 6.404 2.250 7
#
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
DBU N CA SINGLE ENDUPRIGHT 1
DBU CA CB DOUBLE NONE 2
DBU CA C SINGLE ENDUPRIGHT 3
DBU CB CG SINGLE ENDDOWNRIGHT 4
DBU C O DOUBLE NONE 5
DBU C OXT SINGLE NONE 6
#
_pdbe_chem_comp_substructure.comp_id DBU
_pdbe_chem_comp_substructure.substructure_name peptide
_pdbe_chem_comp_substructure.id F1
_pdbe_chem_comp_substructure.substructure_type fragment
_pdbe_chem_comp_substructure.substructure_smiles NCC=O
_pdbe_chem_comp_substructure.substructure_inchis InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2
_pdbe_chem_comp_substructure.substructure_inchikeys LYIIBVSRGJSHAV-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
DBU O F1 1
DBU C F1 1
DBU CA F1 1
DBU N F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id DBU
_pdbe_chem_comp_rdkit_properties.exactmw 101.048
_pdbe_chem_comp_rdkit_properties.amw 101.105
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 3
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 7
_pdbe_chem_comp_rdkit_properties.NumAtoms 14
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 3
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.250
_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 51.478
_pdbe_chem_comp_rdkit_properties.tpsa 63.320
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.067
_pdbe_chem_comp_rdkit_properties.CrippenMR 25.580
_pdbe_chem_comp_rdkit_properties.chi0v 3.264
_pdbe_chem_comp_rdkit_properties.chi1v 1.382
_pdbe_chem_comp_rdkit_properties.chi2v 0.312
_pdbe_chem_comp_rdkit_properties.chi3v 0.312
_pdbe_chem_comp_rdkit_properties.chi4v 0.051
_pdbe_chem_comp_rdkit_properties.chi0n 10.264
_pdbe_chem_comp_rdkit_properties.chi1n 4.685
_pdbe_chem_comp_rdkit_properties.chi2n 0.312
_pdbe_chem_comp_rdkit_properties.chi3n 0.312
_pdbe_chem_comp_rdkit_properties.chi4n 0.051
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.990
_pdbe_chem_comp_rdkit_properties.kappa1 1.046
_pdbe_chem_comp_rdkit_properties.kappa2 2.230
_pdbe_chem_comp_rdkit_properties.kappa3 1.808
_pdbe_chem_comp_rdkit_properties.Phi 0.333
#
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
DBU UniChem DrugBank DB03720
DBU UniChem 'KEGG LIGAND' C17234
DBU UniChem ChEBI 18820
DBU UniChem fdasrs 66QL1S96RM
DBU UniChem SureChEMBL SCHEMBL360722
DBU UniChem PubChem 6449989
DBU UniChem ACTor 20748-08-7
DBU UniChem ACTor 71018-10-5
DBU UniChem Nikkaji J1.018.629C
DBU UniChem Nikkaji J19.823D
DBU UniChem BRENDA 172751
DBU UniChem BRENDA 90066
DBU UniChem 'Probes And Drugs' PD007294
DBU UniChem NMRShiftDB 70013163
#
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
DBU N 0.218 -1.630 0.433 ETKDGv3 1
DBU CA 0.407 -0.228 0.181 ETKDGv3 2
DBU CB -0.635 0.625 0.180 ETKDGv3 3
DBU CG -2.050 0.202 0.435 ETKDGv3 4
DBU C 1.774 0.278 -0.081 ETKDGv3 5
DBU O 2.752 -0.517 -0.081 ETKDGv3 6
DBU OXT 1.997 1.631 -0.330 ETKDGv3 7
DBU H -0.720 -2.044 0.624 ETKDGv3 8
DBU H2 1.030 -2.286 0.433 ETKDGv3 9
DBU HB -0.471 1.679 -0.013 ETKDGv3 10
DBU HG1 -2.720 1.086 0.380 ETKDGv3 11
DBU HG2 -2.139 -0.243 1.448 ETKDGv3 12
DBU HG3 -2.374 -0.532 -0.332 ETKDGv3 13
DBU HXT 2.931 1.979 -0.510 ETKDGv3 14
#