data_DSG
#
_chem_comp.id DSG
_chem_comp.name D-ASPARAGINE
_chem_comp.type "D-PEPTIDE LINKING"
_chem_comp.pdbx_type ATOMP
_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 2004-06-28
_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 132.118
_chem_comp.one_letter_code N
_chem_comp.three_letter_code DSG
_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 1T5M
_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
DSG N N N 0 1 N N N Y Y N 3.388 -4.181 1.786 0.856 0.396 0.043 N DSG 1
DSG CA CA C 0 1 N N R Y N N 3.907 -2.888 1.256 1.491 1.310 -0.872 CA DSG 2
DSG C C C 0 1 N N N Y N Y 3.208 -2.284 -0.013 0.564 2.493 -1.081 C DSG 3
DSG O O O 0 1 N N N Y N Y 2.968 -1.076 -0.019 -0.146 2.993 -0.219 O DSG 4
DSG CB CB C 0 1 N N N N N N 4.024 -1.899 2.455 2.883 1.733 -0.406 CB DSG 5
DSG CG CG C 0 1 N N N N N N 2.746 -1.720 3.308 3.596 2.635 -1.397 CG DSG 6
DSG OD1 OD1 O 0 1 N N N N N N 2.803 -1.420 4.499 3.951 3.776 -1.110 OD1 DSG 7
DSG ND2 ND2 N 0 1 N N N N N N 1.573 -1.908 2.722 3.816 2.047 -2.621 ND2 DSG 8
DSG OXT OXT O 0 1 N Y N Y N Y ? ? ? 0.576 2.926 -2.369 OXT DSG 9
DSG H H H 0 1 N N N Y Y N 2.656 -4.194 2.505 -0.123 0.507 0.243 H DSG 10
DSG H2 HN2 H 0 1 N Y N Y Y N 3.391 -4.875 1.038 1.431 -0.200 0.615 H2 DSG 11
DSG HA HA H 0 1 N N N Y N N 4.954 -3.086 0.961 1.566 0.762 -1.819 HA DSG 12
DSG HB2 1HB H 0 1 N N N N N N 4.840 -2.209 3.133 3.516 0.849 -0.262 HB2 DSG 13
DSG HB3 2HB H 0 1 N N N N N N 4.353 -0.904 2.090 2.823 2.240 0.564 HB3 DSG 14
DSG HD21 1HD2 H 0 0 N N N N N N 1.582 -2.082 1.711 4.289 2.551 -3.364 HD21 DSG 15
DSG HD22 2HD2 H 0 0 N N N N N N 0.747 -1.867 3.330 3.521 1.099 -2.832 HD22 DSG 16
DSG HXT HXT H 0 1 N Y N Y N Y -0.423 0.365 -0.768 -0.028 3.674 -2.563 HXT DSG 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
DSG N CA SING N N 1
DSG N H SING N N 2
DSG N H2 SING N N 3
DSG CA C SING N N 4
DSG CA CB SING N N 5
DSG CA HA SING N N 6
DSG C O DOUB N N 7
DSG C OXT SING N N 8
DSG CB CG SING N N 9
DSG CB HB2 SING N N 10
DSG CB HB3 SING N N 11
DSG CG OD1 DOUB N N 12
DSG CG ND2 SING N N 13
DSG ND2 HD21 SING N N 14
DSG ND2 HD22 SING N N 15
DSG OXT HXT 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
DSG SMILES ACDLabs 10.04 O=C(N)CC(N)C(=O)O
DSG SMILES_CANONICAL CACTVS 3.341 N[C@H](CC(N)=O)C(O)=O
DSG SMILES CACTVS 3.341 N[CH](CC(N)=O)C(O)=O
DSG SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C([C@H](C(=O)O)N)C(=O)N
DSG SMILES "OpenEye OEToolkits" 1.5.0 C(C(C(=O)O)N)C(=O)N
DSG InChI InChI 1.03 InChI=1S/C4H8N2O3/c5-2(4(8)9)1-3(6)7/h2H,1,5H2,(H2,6,7)(H,8,9)/t2-/m1/s1
DSG InChIKey InChI 1.03 DCXYFEDJOCDNAF-UWTATZPHSA-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
DSG "SYSTEMATIC NAME" ACDLabs 10.04 D-asparagine
DSG "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(2R)-2,4-diamino-4-oxo-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
DSG 'Create component' 2004-06-28 RCSB
DSG 'Modify descriptor' 2011-06-04 RCSB
DSG 'Modify backbone' 2023-11-03 PDBE
#
_pdbe_chem_comp_drugbank_details.comp_id DSG
_pdbe_chem_comp_drugbank_details.drugbank_id DB03943
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name D-Asparagine
_pdbe_chem_comp_drugbank_details.description
'A non-essential amino acid that is involved in the metabolic control of cell functions in nerve and brain tissue. It is biosynthesized from ASPARTIC ACID and AMMONIA by asparagine synthetase. (From Concise Encyclopedia Biochemistry and Molecular Biology, 3rd ed)'
_pdbe_chem_comp_drugbank_details.cas_number 2058-58-4
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
_pdbe_chem_comp_drugbank_classification.comp_id DSG
_pdbe_chem_comp_drugbank_classification.drugbank_id DB03943
_pdbe_chem_comp_drugbank_classification.parent 'Asparagine and derivatives'
_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 asparagine and derivatives. These are compounds containing asparagine or a derivative thereof resulting from reaction of asparagine at the amino group or the carboxy group, or from the replacement of any hydrogen of glycine by a heteroatom.'
#
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
DSG N N 3.805 1.732 1
DSG CA C 5.104 0.983 2
DSG C C 6.404 1.732 3
DSG O O 7.702 0.983 4
DSG CB C 5.104 -0.517 5
DSG CG C 6.404 -1.268 6
DSG OD1 O 7.702 -0.517 7
DSG ND2 N 6.404 -2.768 8
DSG OXT O 6.404 3.232 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
DSG CA N SINGLE BEGINWEDGE 1
DSG CA C SINGLE NONE 2
DSG CA CB SINGLE NONE 3
DSG C O DOUBLE NONE 4
DSG C OXT SINGLE NONE 5
DSG CB CG SINGLE NONE 6
DSG CG OD1 DOUBLE NONE 7
DSG CG ND2 SINGLE NONE 8
#
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
DSG amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
DSG peptide F2 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 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
DSG ND2 F1 1
DSG CG F1 1
DSG OD1 F1 1
DSG CB F1 1
DSG O F2 1
DSG C F2 1
DSG CA F2 1
DSG N F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id DSG
_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 5
_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 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 63.190
_pdbe_chem_comp_rdkit_properties.tpsa 106.410
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.726
_pdbe_chem_comp_rdkit_properties.CrippenMR 29.423
_pdbe_chem_comp_rdkit_properties.chi0v 4.119
_pdbe_chem_comp_rdkit_properties.chi1v 1.810
_pdbe_chem_comp_rdkit_properties.chi2v 0.419
_pdbe_chem_comp_rdkit_properties.chi3v 0.419
_pdbe_chem_comp_rdkit_properties.chi4v 0.152
_pdbe_chem_comp_rdkit_properties.chi0n 12.119
_pdbe_chem_comp_rdkit_properties.chi1n 5.507
_pdbe_chem_comp_rdkit_properties.chi2n 0.419
_pdbe_chem_comp_rdkit_properties.chi3n 0.419
_pdbe_chem_comp_rdkit_properties.chi4n 0.152
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.100
_pdbe_chem_comp_rdkit_properties.kappa1 1.694
_pdbe_chem_comp_rdkit_properties.kappa2 3.032
_pdbe_chem_comp_rdkit_properties.kappa3 3.480
_pdbe_chem_comp_rdkit_properties.Phi 0.571
#
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
DSG UniChem ChEMBL CHEMBL1232369
DSG UniChem DrugBank DB03943
DSG UniChem PDBe DSG
DSG UniChem 'KEGG LIGAND' C01905
DSG UniChem ChEBI 28159
DSG UniChem ChEBI 74337
DSG UniChem ZINC ZINC000001529313
DSG UniChem eMolecules 478692
DSG UniChem fdasrs T6QV1010K6
DSG UniChem SureChEMBL SCHEMBL92738
DSG UniChem HMDB HMDB0033780
DSG UniChem NMRShiftDB 80024925
DSG UniChem 'EPA CompTox Dashboard' DTXSID30872479
DSG UniChem MetaboLights MTBLC28159
DSG UniChem MetaboLights MTBLC74337
DSG UniChem BRENDA 2194
DSG UniChem BRENDA 2293
DSG UniChem BRENDA 96332
DSG UniChem Rhea 74337
DSG UniChem ChemicalBook CB4444817
DSG UniChem MedChemExpress HY-W010378
DSG UniChem 'Probes And Drugs' PD006622
DSG UniChem Nikkaji J9.207J
DSG UniChem 'PubChem TPHARMA' 14747676
DSG UniChem PubChem 439600
DSG UniChem PubChem 6991971
DSG UniChem Mcule MCULE-5685974579
DSG UniChem Mcule MCULE-6923060287
DSG UniChem ACTor 2058-58-4
#
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
DSG N -0.867 -1.084 0.868 ETKDGv3 1
DSG CA -0.745 -0.589 -0.505 ETKDGv3 2
DSG C -1.519 0.691 -0.670 ETKDGv3 3
DSG O -2.062 0.959 -1.775 ETKDGv3 4
DSG CB 0.734 -0.392 -0.889 ETKDGv3 5
DSG CG 1.448 0.571 0.019 ETKDGv3 6
DSG OD1 1.492 1.795 -0.276 ETKDGv3 7
DSG ND2 2.052 0.114 1.229 ETKDGv3 8
DSG OXT -1.599 1.602 0.379 ETKDGv3 9
DSG H -1.878 -1.272 1.061 ETKDGv3 10
DSG H2 -0.386 -2.012 0.926 ETKDGv3 11
DSG HA -1.178 -1.349 -1.197 ETKDGv3 12
DSG HB2 0.799 -0.026 -1.938 ETKDGv3 13
DSG HB3 1.255 -1.373 -0.860 ETKDGv3 14
DSG HD21 2.023 -0.897 1.491 ETKDGv3 15
DSG HD22 2.532 0.788 1.865 ETKDGv3 16
DSG HXT -2.102 2.475 0.272 ETKDGv3 17
#