data_ABA
#
_chem_comp.id ABA
_chem_comp.name 'ALPHA-AMINOBUTYRIC ACID'
_chem_comp.type 'L-PEPTIDE LINKING'
_chem_comp.pdbx_type ATOMP
_chem_comp.formula 'C4 H9 N O2'
_chem_comp.mon_nstd_parent_comp_id ALA
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_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 103.120
_chem_comp.one_letter_code A
_chem_comp.three_letter_code ABA
_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 1CWC
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
_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
ABA N N N 0 1 N N N Y Y N 8.872 35.101 18.829 -0.644 1.545 0.393 N ABA 1
ABA CA CA C 0 1 N N S Y N N 10.112 35.739 19.276 -0.299 0.117 0.432 CA ABA 2
ABA C C C 0 1 N N N Y N Y 10.743 36.533 18.128 1.141 -0.063 0.030 C ABA 3
ABA O O O 0 1 N N N Y N Y 11.507 35.962 17.351 1.707 0.803 -0.595 O ABA 4
ABA CB CB C 0 1 N N N N N N 11.098 34.657 19.740 -1.200 -0.651 -0.537 CB ABA 5
ABA CG CG C 0 1 N N N N N N 10.518 33.684 20.758 -2.651 -0.572 -0.057 CG ABA 6
ABA OXT OXT O 0 1 N Y N Y N Y 10.475 37.838 18.044 1.796 -1.186 0.364 OXT ABA 7
ABA H H H 0 1 N N N Y Y N 8.470 34.586 19.586 -0.517 1.922 -0.535 H ABA 8
ABA H2 HN2 H 0 1 N Y N Y Y N 8.228 35.802 18.523 -1.586 1.699 0.720 HN2 ABA 9
ABA HA HA H 0 1 N N N Y N N 9.905 36.420 20.114 -0.445 -0.263 1.443 HA ABA 10
ABA HB3 HB3 H 0 1 N N N N N N 11.421 34.083 18.859 -1.122 -0.213 -1.531 HB3 ABA 11
ABA HB2 HB2 H 0 1 N N N N N N 11.968 35.154 20.194 -0.887 -1.695 -0.574 HB2 ABA 12
ABA HG1 HG1 H 0 1 N N N N N N 11.284 32.945 21.037 -2.729 -1.010 0.938 HG1 ABA 13
ABA HG3 HG3 H 0 1 N N N N N N 10.199 34.237 21.654 -2.964 0.472 -0.020 HG3 ABA 14
ABA HG2 HG2 H 0 1 N N N N N N 9.652 33.167 20.319 -3.292 -1.119 -0.747 HG2 ABA 15
ABA HXT HXT H 0 1 N Y N Y N Y 10.956 38.214 17.317 2.719 -1.256 0.084 HXT ABA 16
#
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
ABA N CA SING N N 1
ABA N H SING N N 2
ABA N H2 SING N N 3
ABA CA C SING N N 4
ABA CA CB SING N N 5
ABA CA HA SING N N 6
ABA C O DOUB N N 7
ABA C OXT SING N N 8
ABA CB CG SING N N 9
ABA CB HB3 SING N N 10
ABA CB HB2 SING N N 11
ABA CG HG1 SING N N 12
ABA CG HG3 SING N N 13
ABA CG HG2 SING N N 14
ABA OXT HXT 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
ABA SMILES ACDLabs 12.01 'O=C(O)C(N)CC'
ABA InChI InChI 1.03 'InChI=1S/C4H9NO2/c1-2-3(5)4(6)7/h3H,2,5H2,1H3,(H,6,7)/t3-/m0/s1'
ABA InChIKey InChI 1.03 QWCKQJZIFLGMSD-VKHMYHEASA-N
ABA SMILES_CANONICAL CACTVS 3.385 'CC[C@H](N)C(O)=O'
ABA SMILES CACTVS 3.385 'CC[CH](N)C(O)=O'
ABA SMILES_CANONICAL 'OpenEye OEToolkits' 1.7.6 'CC[C@@H](C(=O)O)N'
ABA SMILES 'OpenEye OEToolkits' 1.7.6 'CCC(C(=O)O)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
ABA 'SYSTEMATIC NAME' ACDLabs 12.01 '(2S)-2-aminobutanoic acid'
ABA 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.7.6 '(2S)-2-azanylbutanoic 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
ABA 'Create component' 1999-07-08 RCSB
ABA 'Modify descriptor' 2011-06-04 RCSB
ABA 'Other modification' 2015-02-19 RCSB
ABA 'Modify backbone' 2023-11-03 PDBE
ABA 'Modify PCM' 2024-09-27 PDBE
#
loop_
_pdbx_chem_comp_pcm.pcm_id
_pdbx_chem_comp_pcm.comp_id
_pdbx_chem_comp_pcm.modified_residue_id
_pdbx_chem_comp_pcm.type
_pdbx_chem_comp_pcm.category
_pdbx_chem_comp_pcm.position
_pdbx_chem_comp_pcm.polypeptide_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
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession
1 ABA ? None 'Non-standard residue' 'Amino-acid side chain' 'Any position' ? ? ? ?
2 ABA LYS None Crosslinker 'Amino-acid side chain' 'Any position' CB NZ ? ?
3 ABA THR None Crosslinker 'Amino-acid backbone' N-terminal C N ? ?
#
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
ABA N N 3.805 0.750 1
ABA CA C 5.104 0.000 2
ABA C C 6.404 0.750 3
ABA O O 7.702 0.000 4
ABA CB C 5.104 -1.500 5
ABA CG C 3.805 -2.250 6
ABA 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
ABA CA N SINGLE BEGINDASH 1
ABA CA C SINGLE NONE 2
ABA CA CB SINGLE NONE 3
ABA C O DOUBLE NONE 4
ABA C OXT SINGLE NONE 5
ABA CB CG SINGLE NONE 6
#
_pdbe_chem_comp_substructure.comp_id ABA
_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
ABA O F1 1
ABA C F1 1
ABA CA F1 1
ABA N F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id ABA
_pdbe_chem_comp_rdkit_properties.exactmw 103.063
_pdbe_chem_comp_rdkit_properties.amw 103.121
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_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 16
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 3
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.750
_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 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 54.977
_pdbe_chem_comp_rdkit_properties.tpsa 63.320
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.192
_pdbe_chem_comp_rdkit_properties.CrippenMR 25.902
_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 12.264
_pdbe_chem_comp_rdkit_properties.chi1n 5.685
_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 -0.570
_pdbe_chem_comp_rdkit_properties.kappa1 0.910
_pdbe_chem_comp_rdkit_properties.kappa2 2.577
_pdbe_chem_comp_rdkit_properties.kappa3 2.167
_pdbe_chem_comp_rdkit_properties.Phi 0.335
#
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
ABA UniChem 'KEGG LIGAND' C02356
ABA UniChem ChEBI 35619
ABA UniChem ChEBI 74359
ABA UniChem ZINC ZINC000000901351
ABA UniChem eMolecules 476611
ABA UniChem fdasrs 0QAJ5KN9IM
ABA UniChem SureChEMBL SCHEMBL78599
ABA UniChem HMDB HMDB0000452
ABA UniChem 'PubChem TPHARMA' 15363447
ABA UniChem PubChem 6971252
ABA UniChem PubChem 80283
ABA UniChem NMRShiftDB 60020867
ABA UniChem Recon C02356
ABA UniChem Nikkaji J7.749F
ABA UniChem BindingDb 50357210
ABA UniChem 'EPA CompTox Dashboard' DTXSID10883684
ABA UniChem LipidMaps LMFA01100034
ABA UniChem MetaboLights MTBLC35619
ABA UniChem MetaboLights MTBLC74359
ABA UniChem BRENDA 106368
ABA UniChem BRENDA 12577
ABA UniChem BRENDA 1471
ABA UniChem BRENDA 1505
ABA UniChem BRENDA 16938
ABA UniChem BRENDA 174268
ABA UniChem BRENDA 1873
ABA UniChem BRENDA 229560
ABA UniChem BRENDA 260106
ABA UniChem BRENDA 44993
ABA UniChem BRENDA 46302
ABA UniChem BRENDA 89363
ABA UniChem BRENDA 8980
ABA UniChem BRENDA 91081
ABA UniChem BRENDA 93770
ABA UniChem BRENDA 99684
ABA UniChem Rhea 74359
ABA UniChem ChemicalBook CB3741533
ABA UniChem MedChemExpress HY-W010589
ABA UniChem 'Probes And Drugs' PD099496
ABA UniChem CCDC HUWSOI
ABA UniChem Mcule MCULE-3597025691
#
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
ABA N -0.195 1.510 0.637 ETKDGv3 1
ABA CA 0.093 0.082 0.482 ETKDGv3 2
ABA C 1.556 -0.195 0.711 ETKDGv3 3
ABA O 2.428 0.334 -0.030 ETKDGv3 4
ABA CB -0.338 -0.413 -0.911 ETKDGv3 5
ABA CG -1.848 -0.298 -1.116 ETKDGv3 6
ABA OXT 1.946 -1.040 1.745 ETKDGv3 7
ABA H 0.394 2.061 -0.030 ETKDGv3 8
ABA H2 0.070 1.803 1.606 ETKDGv3 9
ABA HA -0.489 -0.480 1.247 ETKDGv3 10
ABA HB3 -0.049 -1.480 -1.029 ETKDGv3 11
ABA HB2 0.181 0.173 -1.701 ETKDGv3 12
ABA HG1 -2.388 -0.887 -0.345 ETKDGv3 13
ABA HG3 -2.116 -0.696 -2.117 ETKDGv3 14
ABA HG2 -2.169 0.763 -1.061 ETKDGv3 15
ABA HXT 2.925 -1.238 1.912 ETKDGv3 16
#