data_SNN
#
_chem_comp.id SNN
_chem_comp.name L-3-AMINOSUCCINIMIDE
_chem_comp.type 'L-PEPTIDE LINKING'
_chem_comp.pdbx_type ATOMP
_chem_comp.formula 'C4 H6 N2 O2'
_chem_comp.mon_nstd_parent_comp_id ASN
_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 114.103
_chem_comp.one_letter_code N
_chem_comp.three_letter_code SNN
_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 1AT5
_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
SNN N1 N1 N 0 1 N N N N N N -3.520 27.155 32.509 0.536 -1.038 0.138 N1 SNN 1
SNN C C2 C 0 1 N N N Y N Y -4.615 27.066 31.622 -0.745 -0.739 -0.110 C2 SNN 2
SNN CA C3 C 0 1 N N S Y N N -5.572 26.141 32.190 -0.854 0.729 -0.463 C3 SNN 3
SNN N N3 N 0 1 N N N Y Y N -6.021 25.185 31.181 -1.704 1.432 0.507 N3 SNN 4
SNN C4 C4 C 0 1 N N N N N N -4.981 25.595 33.497 0.601 1.231 -0.375 C4 SNN 5
SNN C5 C5 C 0 1 N N N N N N -3.630 26.353 33.638 1.380 -0.005 0.019 C5 SNN 6
SNN O O2 O 0 1 N N N Y N Y -4.644 27.646 30.572 -1.671 -1.520 -0.060 O2 SNN 7
SNN O5 O5 O 0 1 N N N N N N -2.830 26.308 34.530 2.578 -0.053 0.198 O5 SNN 8
SNN HN HN H 0 1 N N N N N N -2.731 27.746 32.339 0.829 -1.928 0.388 HN SNN 9
SNN HA H3 H 0 1 N N N Y N N -6.519 26.616 32.487 -1.245 0.852 -1.473 H3 SNN 10
SNN H HN31 H 0 0 N N N Y Y N -6.124 25.651 30.302 -2.641 1.058 0.505 HN31 SNN 11
SNN H2 HN32 H 0 0 N Y N Y Y N -5.346 24.452 31.093 -1.302 1.396 1.433 HN32 SNN 12
SNN H41 H41 H 0 1 N N N N N N -5.644 25.794 34.352 0.937 1.605 -1.342 H41 SNN 13
SNN H42 H42 H 0 1 N N N N N N -4.853 24.503 33.480 0.695 2.003 0.389 H42 SNN 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
SNN N1 C SING N N 1
SNN N1 C5 SING N N 2
SNN N1 HN SING N N 3
SNN C CA SING N N 4
SNN C O DOUB N N 5
SNN CA N SING N N 6
SNN CA C4 SING N N 7
SNN CA HA SING N N 8
SNN N H SING N N 9
SNN N H2 SING N N 10
SNN C4 C5 SING N N 11
SNN C4 H41 SING N N 12
SNN C4 H42 SING N N 13
SNN C5 O5 DOUB N N 14
#
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
SNN SMILES ACDLabs 10.04 'O=C1NC(=O)C(N)C1'
SNN SMILES_CANONICAL CACTVS 3.341 'N[C@H]1CC(=O)NC1=O'
SNN SMILES CACTVS 3.341 'N[CH]1CC(=O)NC1=O'
SNN SMILES_CANONICAL 'OpenEye OEToolkits' 1.5.0 'C1[C@@H](C(=O)NC1=O)N'
SNN SMILES 'OpenEye OEToolkits' 1.5.0 'C1C(C(=O)NC1=O)N'
SNN InChI InChI 1.03 'InChI=1S/C4H6N2O2/c5-2-1-3(7)6-4(2)8/h2H,1,5H2,(H,6,7,8)/t2-/m0/s1'
SNN InChIKey InChI 1.03 YDNMHDRXNOHCJH-REOHCLBHSA-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
SNN 'SYSTEMATIC NAME' ACDLabs 10.04 '(3S)-3-aminopyrrolidine-2,5-dione'
SNN 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.5.0 '(3S)-3-aminopyrrolidine-2,5-dione'
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
SNN 'Create component' 1999-07-08 RCSB
SNN 'Modify descriptor' 2011-06-04 RCSB
SNN 'Modify backbone' 2023-11-03 PDBE
SNN '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 SNN ASN 'Succinamide ring' 'Named protein modification' 'Amino-acid side chain and backbone' 'Any position' ? ? ? ?
2 SNN ASP 'Succinamide ring' 'Named protein modification' 'Amino-acid side chain and backbone' 'Any position' ? ? ? ?
#
_pdbe_chem_comp_drugbank_details.comp_id SNN
_pdbe_chem_comp_drugbank_details.drugbank_id DB03487
_pdbe_chem_comp_drugbank_details.type 'small molecule'
_pdbe_chem_comp_drugbank_details.name (S)-Aspartimide
_pdbe_chem_comp_drugbank_details.description ?
_pdbe_chem_comp_drugbank_details.cas_number 73537-92-5
_pdbe_chem_comp_drugbank_details.mechanism_of_action ?
#
_pdbe_chem_comp_synonyms.comp_id SNN
_pdbe_chem_comp_synonyms.name 3-aminosuccinimide
_pdbe_chem_comp_synonyms.provenance DrugBank
_pdbe_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_drugbank_classification.comp_id SNN
_pdbe_chem_comp_drugbank_classification.drugbank_id DB03487
_pdbe_chem_comp_drugbank_classification.parent 'Alpha amino acids 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 alpha amino acids and derivatives. These are amino acids in which the amino group is attached to the carbon atom immediately adjacent to the carboxylate group (alpha carbon), or a derivative thereof.'
#
loop_
_pdbe_chem_comp_drugbank_targets.comp_id
_pdbe_chem_comp_drugbank_targets.drugbank_id
_pdbe_chem_comp_drugbank_targets.name
_pdbe_chem_comp_drugbank_targets.organism
_pdbe_chem_comp_drugbank_targets.uniprot_id
_pdbe_chem_comp_drugbank_targets.pharmacologically_active
_pdbe_chem_comp_drugbank_targets.ordinal
SNN DB03487 'Lysozyme C' Humans P61626 unknown 1
SNN DB03487 'Chemotaxis protein CheY' 'Escherichia coli (strain K12)' P0AE67 unknown 2
#
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
SNN N1 N 6.390 0.588 1
SNN C C 4.890 0.588 2
SNN CA C 4.427 -0.839 3
SNN N N 3.000 -1.303 4
SNN C4 C 5.640 -1.721 5
SNN C5 C 6.854 -0.839 6
SNN O O 4.008 1.801 7
SNN O5 O 8.280 -1.303 8
#
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
SNN N1 C SINGLE NONE 1
SNN N1 C5 SINGLE NONE 2
SNN C CA SINGLE NONE 3
SNN C O DOUBLE NONE 4
SNN CA N SINGLE BEGINDASH 5
SNN CA C4 SINGLE NONE 6
SNN C4 C5 SINGLE NONE 7
SNN C5 O5 DOUBLE 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
SNN MurckoScaffold S1 scaffold O=C1CCC(=O)N1 InChI=1S/C4H5NO2/c6-3-1-2-4(7)5-3/h1-2H2,(H,5,6,7) KZNICNPSHKQLFF-UHFFFAOYSA-N
SNN amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
SNN barbiturates F2 fragment NC1CC(=O)NC1=O InChI=1S/C4H6N2O2/c5-2-1-3(7)6-4(2)8/h2H,1,5H2,(H,6,7,8) YDNMHDRXNOHCJH-UHFFFAOYSA-N
SNN peptide F3 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
SNN succinimide F4 fragment O=C1CCC(=O)N1 InChI=1S/C4H5NO2/c6-3-1-2-4(7)5-3/h1-2H2,(H,5,6,7) KZNICNPSHKQLFF-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
SNN N1 S1 1
SNN C S1 1
SNN CA S1 1
SNN C4 S1 1
SNN C5 S1 1
SNN O S1 1
SNN O5 S1 1
SNN N1 F1 1
SNN C F1 1
SNN O F1 1
SNN CA F1 1
SNN N1 F1 2
SNN C5 F1 2
SNN O5 F1 2
SNN C4 F1 2
SNN C4 F2 1
SNN C5 F2 1
SNN O5 F2 1
SNN N1 F2 1
SNN C F2 1
SNN O F2 1
SNN CA F2 1
SNN N F2 1
SNN O F3 1
SNN C F3 1
SNN CA F3 1
SNN N F3 1
SNN CA F4 1
SNN C F4 1
SNN O F4 1
SNN N1 F4 1
SNN C5 F4 1
SNN O5 F4 1
SNN C4 F4 1
#
_pdbe_chem_comp_rdkit_properties.comp_id SNN
_pdbe_chem_comp_rdkit_properties.exactmw 114.043
_pdbe_chem_comp_rdkit_properties.amw 114.104
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 1
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 8
_pdbe_chem_comp_rdkit_properties.NumAtoms 14
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 2
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.500
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 1
_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 54.645
_pdbe_chem_comp_rdkit_properties.tpsa 72.190
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.640
_pdbe_chem_comp_rdkit_properties.CrippenMR 25.742
_pdbe_chem_comp_rdkit_properties.chi0v 3.711
_pdbe_chem_comp_rdkit_properties.chi1v 1.829
_pdbe_chem_comp_rdkit_properties.chi2v 0.631
_pdbe_chem_comp_rdkit_properties.chi3v 0.631
_pdbe_chem_comp_rdkit_properties.chi4v 0.328
_pdbe_chem_comp_rdkit_properties.chi0n 9.711
_pdbe_chem_comp_rdkit_properties.chi1n 4.671
_pdbe_chem_comp_rdkit_properties.chi2n 0.631
_pdbe_chem_comp_rdkit_properties.chi3n 0.631
_pdbe_chem_comp_rdkit_properties.chi4n 0.328
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.900
_pdbe_chem_comp_rdkit_properties.kappa1 1.539
_pdbe_chem_comp_rdkit_properties.kappa2 1.555
_pdbe_chem_comp_rdkit_properties.kappa3 0.696
_pdbe_chem_comp_rdkit_properties.Phi 0.299
#
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
SNN UniChem DrugBank DB03487
SNN UniChem ChEBI 46749
SNN UniChem ZINC ZINC000005134830
SNN UniChem 'Probes And Drugs' PD059737
SNN UniChem 'EPA CompTox Dashboard' DTXSID40538594
SNN UniChem SureChEMBL SCHEMBL168361
SNN UniChem PubChem 13373305
SNN UniChem Nikkaji J2.701.538G
#
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
SNN N1 1.720 0.392 0.039 ETKDGv3 1
SNN C 0.597 0.764 0.811 ETKDGv3 2
SNN CA -0.638 -0.014 0.475 ETKDGv3 3
SNN N -1.688 0.880 -0.011 ETKDGv3 4
SNN C4 -0.166 -0.977 -0.642 ETKDGv3 5
SNN C5 1.277 -0.638 -0.819 ETKDGv3 6
SNN O 0.650 1.651 1.702 ETKDGv3 7
SNN O5 2.036 -1.208 -1.645 ETKDGv3 8
SNN HN 2.684 0.788 0.101 ETKDGv3 9
SNN HA -0.987 -0.582 1.367 ETKDGv3 10
SNN H -1.980 1.500 0.779 ETKDGv3 11
SNN H2 -2.525 0.296 -0.243 ETKDGv3 12
SNN H41 -0.270 -2.035 -0.318 ETKDGv3 13
SNN H42 -0.711 -0.816 -1.597 ETKDGv3 14
#