data_ACB
#
_chem_comp.id ACB
_chem_comp.name "3-METHYL-BETA-D-ASPARTIC ACID"
_chem_comp.type "D-beta-peptide, C-gamma linking"
_chem_comp.pdbx_type ATOMP
_chem_comp.formula "C5 H9 N O4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "(3S)-3-methyl-D-aspartic acid; D-METHYL ASPARTIC ACID"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_chem_comp.pdbx_modified_date 2023-11-03
_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 147.129
_chem_comp.one_letter_code D
_chem_comp.three_letter_code ACB
_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 1FJM
_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
ACB C C1 C 0 1 N N N Y N Y 87.862 26.787 27.362 1.915 -0.019 0.017 C ACB 1
ACB O O1 O 0 1 N N N Y N Y 88.952 27.565 27.512 2.552 -0.636 -0.803 O ACB 2
ACB OXT O2 O 0 1 N N N Y N Y 87.892 25.596 27.282 2.447 1.062 0.607 OXT ACB 3
ACB CA C2 C 0 1 N N R Y N N 86.596 27.640 27.210 0.519 -0.461 0.374 CA ACB 4
ACB N N2 N 0 1 N N N Y Y N 85.391 26.753 27.159 0.337 -1.868 -0.010 N ACB 5
ACB CB C3 C 0 1 N N S N N N 86.696 28.501 25.912 -0.497 0.406 -0.372 CB ACB 6
ACB CG C C 0 1 N N N N N N 86.795 27.567 24.705 -1.893 -0.036 -0.015 CG ACB 7
ACB OD1 O O 0 1 N N N N N N 85.932 26.721 24.474 -2.059 -0.951 0.756 OD1 ACB 8
ACB C4 C4 C 0 1 N N N N N N 85.476 29.444 25.741 -0.308 1.871 0.027 C4 ACB 9
ACB OD2 OXT O 0 1 N Y N N N N 87.930 27.762 23.969 -2.953 0.587 -0.555 OD2 ACB 10
ACB HXT HO2 H 0 1 N N N Y N Y 88.792 25.297 27.340 3.344 1.309 0.343 HXT ACB 11
ACB HA H2 H 0 1 N N N Y N N 86.501 28.313 28.075 0.367 -0.355 1.448 HA ACB 12
ACB H HN21 H 0 1 N N N Y Y N 84.568 27.313 27.060 -0.569 -2.207 0.277 H ACB 13
ACB H2 HN22 H 0 1 N Y N Y Y N 85.467 26.132 26.379 0.472 -1.992 -1.002 H2 ACB 14
ACB HB3 H3 H 0 1 N N N N N N 87.592 29.134 25.989 -0.346 0.300 -1.446 HB3 ACB 15
ACB H41 H41 H 0 1 N N N N N N 85.590 30.028 24.816 0.701 2.191 -0.230 H41 ACB 16
ACB H42 H42 H 0 1 N N N N N N 84.555 28.845 25.685 -1.032 2.489 -0.504 H42 ACB 17
ACB H43 H43 H 0 1 N N N N N N 85.417 30.127 26.601 -0.459 1.977 1.102 H43 ACB 18
ACB HD2 HXT H 0 1 N Y N N N N 87.951 27.143 23.249 -3.828 0.268 -0.296 HD2 ACB 19
#
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
ACB C O DOUB N N 1
ACB C OXT SING N N 2
ACB C CA SING N N 3
ACB OXT HXT SING N N 4
ACB CA N SING N N 5
ACB CA CB SING N N 6
ACB CA HA SING N N 7
ACB N H SING N N 8
ACB N H2 SING N N 9
ACB CB CG SING N N 10
ACB CB C4 SING N N 11
ACB CB HB3 SING N N 12
ACB CG OD1 DOUB N N 13
ACB CG OD2 SING N N 14
ACB C4 H41 SING N N 15
ACB C4 H42 SING N N 16
ACB C4 H43 SING N N 17
ACB OD2 HD2 SING N N 18
#
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
ACB SMILES ACDLabs 12.01 O=C(O)C(N)C(C(=O)O)C
ACB SMILES_CANONICAL CACTVS 3.370 C[C@@H]([C@@H](N)C(O)=O)C(O)=O
ACB SMILES CACTVS 3.370 C[CH]([CH](N)C(O)=O)C(O)=O
ACB SMILES_CANONICAL "OpenEye OEToolkits" 1.7.2 C[C@@H]([C@H](C(=O)O)N)C(=O)O
ACB SMILES "OpenEye OEToolkits" 1.7.2 CC(C(C(=O)O)N)C(=O)O
ACB InChI InChI 1.03 InChI=1S/C5H9NO4/c1-2(4(7)8)3(6)5(9)10/h2-3H,6H2,1H3,(H,7,8)(H,9,10)/t2-,3+/m0/s1
ACB InChIKey InChI 1.03 LXRUAYBIUSUULX-STHAYSLISA-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
ACB "SYSTEMATIC NAME" ACDLabs 12.01 "(3S)-3-methyl-D-aspartic acid"
ACB "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.2 "(2R,3S)-2-azanyl-3-methyl-butanedioic 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
ACB 'Create component' 1999-07-08 RCSB
ACB 'Other modification' 2011-02-11 RCSB
ACB 'Other modification' 2011-02-28 RCSB
ACB 'Modify name' 2011-06-03 RCSB
ACB 'Modify descriptor' 2011-06-04 RCSB
ACB 'Modify synonyms' 2020-06-05 PDBE
ACB 'Modify backbone' 2023-11-03 PDBE
#
loop_
_pdbx_chem_comp_synonyms.ordinal
_pdbx_chem_comp_synonyms.comp_id
_pdbx_chem_comp_synonyms.name
_pdbx_chem_comp_synonyms.provenance
_pdbx_chem_comp_synonyms.type
1 ACB "(3S)-3-methyl-D-aspartic acid" ? ?
2 ACB "D-METHYL ASPARTIC ACID" ? ?
#
_pdbe_chem_comp_drugbank_details.comp_id ACB
_pdbe_chem_comp_drugbank_details.drugbank_id DB04313
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name '(3S)-3-methyl-D-aspartic acid'
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number 121570-10-3
_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
ACB '(3S)-3-methyl-D-aspartic acid' wwPDB ?
ACB 'D-METHYL ASPARTIC ACID' wwPDB ?
ACB '3-methyl-beta-D-aspartic acid' DrugBank ?
ACB 'D-methyl aspartic acid' DrugBank ?
#
_pdbe_chem_comp_drugbank_classification.comp_id ACB
_pdbe_chem_comp_drugbank_classification.drugbank_id DB04313
_pdbe_chem_comp_drugbank_classification.parent 'D-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 d-alpha-amino acids. These are alpha amino acids which have the D-configuration of the alpha-carbon atom.'
#
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
ACB C C 5.104 0.142 1
ACB O O 3.805 -0.608 2
ACB OXT O 5.104 1.643 3
ACB CA C 6.404 -0.608 4
ACB N N 6.404 -2.107 5
ACB CB C 7.702 0.142 6
ACB CG C 9.002 -0.608 7
ACB OD1 O 10.301 0.142 8
ACB C4 C 7.702 1.643 9
ACB OD2 O 9.002 -2.107 10
#
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
ACB C O DOUBLE NONE 1
ACB C OXT SINGLE NONE 2
ACB C CA SINGLE NONE 3
ACB CA N SINGLE BEGINWEDGE 4
ACB CA CB SINGLE NONE 5
ACB CB CG SINGLE NONE 6
ACB CB C4 SINGLE BEGINDASH 7
ACB CG OD1 DOUBLE NONE 8
ACB CG OD2 SINGLE NONE 9
#
_pdbe_chem_comp_substructure.comp_id ACB
_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
ACB O F1 1
ACB C F1 1
ACB CA F1 1
ACB N F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id ACB
_pdbe_chem_comp_rdkit_properties.exactmw 147.053
_pdbe_chem_comp_rdkit_properties.amw 147.130
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 10
_pdbe_chem_comp_rdkit_properties.NumAtoms 19
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.600
_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 2
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 70.385
_pdbe_chem_comp_rdkit_properties.tpsa 100.620
_pdbe_chem_comp_rdkit_properties.CrippenClogP -0.881
_pdbe_chem_comp_rdkit_properties.CrippenMR 32.411
_pdbe_chem_comp_rdkit_properties.chi0v 4.580
_pdbe_chem_comp_rdkit_properties.chi1v 2.040
_pdbe_chem_comp_rdkit_properties.chi2v 0.634
_pdbe_chem_comp_rdkit_properties.chi3v 0.634
_pdbe_chem_comp_rdkit_properties.chi4v 0.199
_pdbe_chem_comp_rdkit_properties.chi0n 13.580
_pdbe_chem_comp_rdkit_properties.chi1n 6.251
_pdbe_chem_comp_rdkit_properties.chi2n 0.634
_pdbe_chem_comp_rdkit_properties.chi3n 0.634
_pdbe_chem_comp_rdkit_properties.chi4n 0.199
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.100
_pdbe_chem_comp_rdkit_properties.kappa1 1.945
_pdbe_chem_comp_rdkit_properties.kappa2 3.166
_pdbe_chem_comp_rdkit_properties.kappa3 2.022
_pdbe_chem_comp_rdkit_properties.Phi 0.616
#
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
ACB UniChem DrugBank DB04313
ACB UniChem PDBe ACB
ACB UniChem ChEBI 194704
ACB UniChem ZINC ZINC000001677332
ACB UniChem fdasrs JVW3X5Z42K
ACB UniChem SureChEMBL SCHEMBL4330500
ACB UniChem PubChem 5287600
ACB UniChem 'Probes And Drugs' PD006022
ACB UniChem Nikkaji J748.994C
#
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
ACB C 1.817 0.410 0.380 ETKDGv3 1
ACB O 2.450 0.306 1.464 ETKDGv3 2
ACB OXT 2.045 1.502 -0.453 ETKDGv3 3
ACB CA 0.781 -0.621 0.011 ETKDGv3 4
ACB N 0.817 -0.873 -1.433 ETKDGv3 5
ACB CB -0.625 -0.157 0.478 ETKDGv3 6
ACB CG -1.098 1.068 -0.264 ETKDGv3 7
ACB OD1 -1.474 0.986 -1.465 ETKDGv3 8
ACB C4 -1.667 -1.281 0.387 ETKDGv3 9
ACB OD2 -1.093 2.304 0.374 ETKDGv3 10
ACB HXT 2.726 2.211 -0.206 ETKDGv3 11
ACB HA 1.039 -1.565 0.545 ETKDGv3 12
ACB H 1.795 -1.132 -1.700 ETKDGv3 13
ACB H2 0.241 -1.721 -1.638 ETKDGv3 14
ACB HB3 -0.550 0.109 1.557 ETKDGv3 15
ACB H41 -1.318 -2.175 0.946 ETKDGv3 16
ACB H42 -1.864 -1.569 -0.666 ETKDGv3 17
ACB H43 -2.625 -0.944 0.841 ETKDGv3 18
ACB HD2 -1.395 3.141 -0.111 ETKDGv3 19
#