data_SJW
#
_chem_comp.id SJW
_chem_comp.name 3-pyridin-3-ylpropanal
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula 'C8 H9 N O2'
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2020-11-20
_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 151.163
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code SJW
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag Y
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 7AZL
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBE
_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_n_terminal_atom_flag
_chem_comp_atom.pdbx_backbone_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
SJW C1 C1 C 0 1 N N N N N N -30.913 59.281 40.065 0.532 -0.014 0.750 C1 SJW 1
SJW C3 C2 C 0 1 Y N N N N N -30.873 60.077 41.272 -0.922 -0.019 0.354 C3 SJW 2
SJW C4 C3 C 0 1 Y N N N N N -32.013 60.147 42.026 -1.602 1.170 0.170 C4 SJW 3
SJW C6 C4 C 0 1 Y N N N N N -30.917 61.376 43.599 -3.546 0.054 -0.360 C6 SJW 4
SJW C7 C5 C 0 1 Y N N N N N -29.748 61.320 42.890 -2.931 -1.173 -0.199 C7 SJW 5
SJW C C6 C 0 1 N N N N Y Y -30.435 57.710 38.341 2.857 0.001 -0.112 C SJW 6
SJW O O1 O 0 1 N N N N Y Y -31.694 57.516 38.304 3.165 -0.003 1.057 O SJW 7
SJW CH3 C7 C 0 1 N N N N N N -30.045 58.858 39.139 1.403 -0.004 -0.507 CH3 SJW 8
SJW C8 C8 C 0 1 Y N N N N N -29.713 60.647 41.707 -1.594 -1.217 0.164 C8 SJW 9
SJW N5 N1 N 0 1 Y N N N N N -32.016 60.802 43.164 -2.874 1.174 -0.176 N5 SJW 10
SJW H1 H1 H 0 1 N N N N N N -31.656 59.818 39.458 0.743 0.874 1.345 H1 SJW 11
SJW H2 H2 H 0 1 N N N N N N -31.347 58.336 40.425 0.752 -0.906 1.337 H2 SJW 12
SJW H3 H3 H 0 1 N N N N N N -32.915 59.661 41.683 -1.084 2.108 0.312 H3 SJW 13
SJW H4 H4 H 0 1 N N N N N N -30.937 61.905 44.540 -4.587 0.096 -0.643 H4 SJW 14
SJW H5 H5 H 0 1 N N N N N N -28.860 61.806 43.266 -3.485 -2.087 -0.355 H5 SJW 15
SJW H6 H6 H 0 1 N N N N N N -29.109 58.599 39.656 1.192 -0.893 -1.103 H6 SJW 16
SJW H7 H7 H 0 1 N N N N N N -29.863 59.695 38.449 1.183 0.887 -1.095 H7 SJW 17
SJW H8 H8 H 0 1 N N N N N N -28.801 60.568 41.134 -1.087 -2.162 0.297 H8 SJW 18
SJW OXT OXT O 0 1 N Y N N Y Y ? ? ? 3.810 0.009 -1.057 O1 SJW 19
SJW HXT HXT H 0 1 N Y N N Y Y ? ? ? 4.728 0.012 -0.754 H9 SJW 20
#
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
SJW O C DOUB N N 1
SJW C CH3 SING N N 2
SJW CH3 C1 SING N N 3
SJW C1 C3 SING N N 4
SJW C3 C8 DOUB Y N 5
SJW C3 C4 SING Y N 6
SJW C8 C7 SING Y N 7
SJW C4 N5 DOUB Y N 8
SJW C7 C6 DOUB Y N 9
SJW N5 C6 SING Y N 10
SJW C1 H1 SING N N 11
SJW C1 H2 SING N N 12
SJW C4 H3 SING N N 13
SJW C6 H4 SING N N 14
SJW C7 H5 SING N N 15
SJW CH3 H6 SING N N 16
SJW CH3 H7 SING N N 17
SJW C8 H8 SING N N 18
SJW C OXT SING N N 19
SJW OXT HXT SING N N 20
#
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
SJW InChI InChI 1.06 'InChI=1S/C8H9NO2/c10-8(11)4-3-7-2-1-5-9-6-7/h1-2,5-6H,3-4H2,(H,10,11)'
SJW InChIKey InChI 1.06 WDGXIUUWINKTGP-UHFFFAOYSA-N
SJW SMILES_CANONICAL CACTVS 3.385 'OC(=O)CCc1cccnc1'
SJW SMILES CACTVS 3.385 'OC(=O)CCc1cccnc1'
SJW SMILES_CANONICAL 'OpenEye OEToolkits' 2.0.7 'c1cc(cnc1)CCC(=O)O'
SJW SMILES 'OpenEye OEToolkits' 2.0.7 'c1cc(cnc1)CCC(=O)O'
#
_pdbx_chem_comp_identifier.comp_id SJW
_pdbx_chem_comp_identifier.type 'SYSTEMATIC NAME'
_pdbx_chem_comp_identifier.program 'OpenEye OEToolkits'
_pdbx_chem_comp_identifier.program_version 2.0.7
_pdbx_chem_comp_identifier.identifier '3-pyridin-3-ylpropanoic 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
SJW 'Create component' 2020-11-20 PDBE
SJW 'Initial release' 2021-12-01 RCSB
SJW 'Modify backbone' 2023-11-03 PDBE
SJW 'Other modification' 2024-06-28 PDBE
SJW 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id SJW
_pdbx_chem_comp_pcm.modified_residue_id ?
_pdbx_chem_comp_pcm.type None
_pdbx_chem_comp_pcm.category 'Non-standard residue'
_pdbx_chem_comp_pcm.position 'Amino-acid side chain and backbone'
_pdbx_chem_comp_pcm.polypeptide_position N-terminal
_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 ?
_pdbx_chem_comp_pcm.first_instance_model_db_code 7AZL
#
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
SJW C1 C 5.104 -0.375 1
SJW C3 C 6.404 -1.125 2
SJW C4 C 6.404 -2.625 3
SJW C6 C 9.002 -2.625 4
SJW C7 C 9.002 -1.125 5
SJW C C 3.805 1.875 6
SJW O O 3.805 3.375 7
SJW CH3 C 5.104 1.125 8
SJW C8 C 7.702 -0.375 9
SJW N5 N 7.702 -3.375 10
SJW OXT O 2.506 1.125 11
#
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
SJW O C DOUBLE NONE 1
SJW C CH3 SINGLE NONE 2
SJW CH3 C1 SINGLE NONE 3
SJW C1 C3 SINGLE NONE 4
SJW C3 C8 DOUBLE NONE 5
SJW C3 C4 SINGLE NONE 6
SJW C8 C7 SINGLE NONE 7
SJW C4 N5 DOUBLE NONE 8
SJW C7 C6 DOUBLE NONE 9
SJW N5 C6 SINGLE NONE 10
SJW C OXT SINGLE NONE 11
#
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
SJW MurckoScaffold S1 scaffold c1ccncc1 InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H JUJWROOIHBZHMG-UHFFFAOYSA-N
SJW pyridine F1 fragment c1ccncc1 InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H JUJWROOIHBZHMG-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
SJW C3 S1 1
SJW C4 S1 1
SJW C6 S1 1
SJW C7 S1 1
SJW C8 S1 1
SJW N5 S1 1
SJW C4 F1 1
SJW C3 F1 1
SJW C8 F1 1
SJW C7 F1 1
SJW C6 F1 1
SJW N5 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id SJW
_pdbe_chem_comp_rdkit_properties.exactmw 151.063
_pdbe_chem_comp_rdkit_properties.amw 151.165
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 3
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 11
_pdbe_chem_comp_rdkit_properties.NumAtoms 20
_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 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_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 77.433
_pdbe_chem_comp_rdkit_properties.tpsa 50.190
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.044
_pdbe_chem_comp_rdkit_properties.CrippenMR 39.928
_pdbe_chem_comp_rdkit_properties.chi0v 5.264
_pdbe_chem_comp_rdkit_properties.chi1v 2.605
_pdbe_chem_comp_rdkit_properties.chi2v 0.757
_pdbe_chem_comp_rdkit_properties.chi3v 0.757
_pdbe_chem_comp_rdkit_properties.chi4v 0.403
_pdbe_chem_comp_rdkit_properties.chi0n 14.264
_pdbe_chem_comp_rdkit_properties.chi1n 7.014
_pdbe_chem_comp_rdkit_properties.chi2n 0.757
_pdbe_chem_comp_rdkit_properties.chi3n 0.757
_pdbe_chem_comp_rdkit_properties.chi4n 0.403
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.380
_pdbe_chem_comp_rdkit_properties.kappa1 2.062
_pdbe_chem_comp_rdkit_properties.kappa2 3.707
_pdbe_chem_comp_rdkit_properties.kappa3 2.798
_pdbe_chem_comp_rdkit_properties.Phi 0.695
#
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
SJW UniChem ChEMBL CHEMBL1725941
SJW UniChem ChEBI 183427
SJW UniChem ZINC ZINC000000143743
SJW UniChem eMolecules 500381
SJW UniChem 'PubChem TPHARMA' 14867382
SJW UniChem Mcule MCULE-9809125467
SJW UniChem ACTor 3724-19-4
SJW UniChem Nikkaji J1.714.843E
SJW UniChem 'EPA CompTox Dashboard' DTXSID40293459
SJW UniChem ChemicalBook CB8416067
SJW UniChem SureChEMBL SCHEMBL333061
SJW UniChem PubChem 259624
SJW UniChem BRENDA 238293
#
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
SJW C1 -0.700 0.703 0.219 ETKDGv3 1
SJW C3 0.744 0.296 0.103 ETKDGv3 2
SJW C4 1.478 -0.192 1.295 ETKDGv3 3
SJW C6 3.410 -0.552 -0.072 ETKDGv3 4
SJW C7 2.781 -0.130 -1.174 ETKDGv3 5
SJW C -3.053 -0.094 0.114 ETKDGv3 6
SJW O -3.633 -0.142 1.231 ETKDGv3 7
SJW CH3 -1.618 -0.501 -0.004 ETKDGv3 8
SJW C8 1.375 0.309 -1.083 ETKDGv3 9
SJW N5 2.717 -0.579 1.187 ETKDGv3 10
SJW H1 -0.883 1.131 1.229 ETKDGv3 11
SJW H2 -0.932 1.498 -0.525 ETKDGv3 12
SJW H3 0.989 -0.231 2.259 ETKDGv3 13
SJW H4 4.440 -0.879 -0.126 ETKDGv3 14
SJW H5 3.295 -0.111 -2.126 ETKDGv3 15
SJW H6 -1.444 -0.924 -1.017 ETKDGv3 16
SJW H7 -1.395 -1.291 0.746 ETKDGv3 17
SJW H8 0.863 0.636 -1.979 ETKDGv3 18
SJW OXT -3.733 0.379 -1.004 ETKDGv3 19
SJW HXT -4.700 0.673 -0.937 ETKDGv3 20
#