data_S34
#
_chem_comp.id S34
_chem_comp.name 2-cyano-~{N}-(pyridin-4-ylmethyl)ethanamide
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C9 H9 N3 O"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2020-03-03
_chem_comp.pdbx_modified_date 2020-06-26
_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 175.187
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code S34
_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 5R5R
_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
S34 N1 N1 N 0 1 Y N N N N N 15.073 22.163 11.818 -4.255 -0.004 -0.546 N1 S34 1
S34 N3 N2 N 0 1 N N N N N N 18.825 22.482 5.366 5.396 -0.001 -0.152 N3 S34 2
S34 C4 C1 C 0 1 Y N N N N N 15.214 20.229 10.433 -2.362 1.192 0.163 C4 S34 3
S34 C5 C2 C 0 1 Y N N N N N 14.463 20.842 9.444 -1.698 0.003 0.421 C5 S34 4
S34 C6 C3 C 0 1 N N N N N N 14.158 20.125 8.152 -0.289 0.006 0.955 C6 S34 5
S34 C7 C4 C 0 1 N N N N N N 15.830 20.945 6.556 1.984 0.001 0.075 C7 S34 6
S34 C8 C5 C 0 1 N N N N N N 17.088 20.595 5.774 2.957 -0.007 -1.076 C8 S34 7
S34 C1 C6 C 0 1 Y N N N N N 14.030 22.137 9.674 -2.362 -1.190 0.177 C1 S34 8
S34 C2 C7 C 0 1 Y N N N N N 14.348 22.753 10.865 -3.654 -1.154 -0.312 C2 S34 9
S34 C3 C8 C 0 1 Y N N N N N 15.497 20.917 11.597 -3.655 1.150 -0.324 C3 S34 10
S34 C9 C9 C 0 1 N N N N N N 18.041 21.685 5.629 4.333 -0.003 -0.554 C9 S34 11
S34 N2 N3 N 0 1 N N N N N N 15.340 19.963 7.317 0.657 -0.001 -0.164 N2 S34 12
S34 O1 O1 O 0 1 N N N N N N 15.294 22.051 6.484 2.394 0.008 1.216 O1 S34 13
S34 H1 H1 H 0 1 N N N N N N 15.576 19.221 10.295 -1.876 2.140 0.342 H1 S34 14
S34 H2 H2 H 0 1 N N N N N N 13.408 20.705 7.594 -0.131 0.900 1.558 H2 S34 15
S34 H3 H3 H 0 1 N N N N N N 13.752 19.130 8.387 -0.131 -0.880 1.569 H3 S34 16
S34 H4 H4 H 0 1 N N N N N N 16.786 20.269 4.768 2.799 -0.900 -1.679 H4 S34 17
S34 H5 H5 H 0 1 N N N N N N 17.593 19.766 6.292 2.799 0.879 -1.691 H5 S34 18
S34 H6 H6 H 0 1 N N N N N N 13.449 22.659 8.928 -1.875 -2.135 0.365 H6 S34 19
S34 H7 H7 H 0 1 N N N N N N 13.994 23.759 11.035 -4.177 -2.079 -0.506 H7 S34 20
S34 H8 H8 H 0 1 N N N N N N 16.085 20.427 12.359 -4.179 2.072 -0.527 H8 S34 21
S34 H9 H9 H 0 1 N N N N N N 15.805 19.078 7.313 0.329 -0.007 -1.077 H9 S34 22
#
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
S34 N3 C9 TRIP N N 1
S34 C9 C8 SING N N 2
S34 C8 C7 SING N N 3
S34 O1 C7 DOUB N N 4
S34 C7 N2 SING N N 5
S34 N2 C6 SING N N 6
S34 C6 C5 SING N N 7
S34 C5 C1 DOUB Y N 8
S34 C5 C4 SING Y N 9
S34 C1 C2 SING Y N 10
S34 C4 C3 DOUB Y N 11
S34 C2 N1 DOUB Y N 12
S34 C3 N1 SING Y N 13
S34 C4 H1 SING N N 14
S34 C6 H2 SING N N 15
S34 C6 H3 SING N N 16
S34 C8 H4 SING N N 17
S34 C8 H5 SING N N 18
S34 C1 H6 SING N N 19
S34 C2 H7 SING N N 20
S34 C3 H8 SING N N 21
S34 N2 H9 SING N N 22
#
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
S34 InChI InChI 1.03 InChI=1S/C9H9N3O/c10-4-1-9(13)12-7-8-2-5-11-6-3-8/h2-3,5-6H,1,7H2,(H,12,13)
S34 InChIKey InChI 1.03 ACPRFCGKSGKRCH-UHFFFAOYSA-N
S34 SMILES_CANONICAL CACTVS 3.385 "O=C(CC#N)NCc1ccncc1"
S34 SMILES CACTVS 3.385 "O=C(CC#N)NCc1ccncc1"
S34 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "c1cnccc1CNC(=O)CC#N"
S34 SMILES "OpenEye OEToolkits" 2.0.6 "c1cnccc1CNC(=O)CC#N"
#
_pdbx_chem_comp_identifier.comp_id S34
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.6
_pdbx_chem_comp_identifier.identifier 2-cyano-~{N}-(pyridin-4-ylmethyl)ethanamide
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
S34 'Create component' 2020-03-03 RCSB
S34 'Initial release' 2020-07-01 RCSB
#
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
S34 N1 N 4.299 -5.250 1
S34 N3 N 6.897 5.250 2
S34 C4 C 3.000 -3.000 3
S34 C5 C 4.299 -2.250 4
S34 C6 C 4.299 -0.750 5
S34 C7 C 5.598 1.500 6
S34 C8 C 6.897 2.250 7
S34 C1 C 5.598 -3.000 8
S34 C2 C 5.598 -4.500 9
S34 C3 C 3.000 -4.500 10
S34 C9 C 6.897 3.750 11
S34 N2 N 5.598 0.000 12
S34 O1 O 4.299 2.250 13
#
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
S34 N3 C9 TRIPLE NONE 1
S34 C9 C8 SINGLE NONE 2
S34 C8 C7 SINGLE NONE 3
S34 O1 C7 DOUBLE NONE 4
S34 C7 N2 SINGLE NONE 5
S34 N2 C6 SINGLE NONE 6
S34 C6 C5 SINGLE NONE 7
S34 C5 C1 DOUBLE NONE 8
S34 C5 C4 SINGLE NONE 9
S34 C1 C2 SINGLE NONE 10
S34 C4 C3 DOUBLE NONE 11
S34 C2 N1 DOUBLE NONE 12
S34 C3 N1 SINGLE NONE 13
#
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
S34 MurckoScaffold S1 scaffold c1ccncc1 InChI=1S/C5H5N/c1-2-4-6-5-3-1/h1-5H JUJWROOIHBZHMG-UHFFFAOYSA-N
S34 amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
S34 pyridine F2 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
S34 N1 S1 1
S34 C4 S1 1
S34 C5 S1 1
S34 C1 S1 1
S34 C2 S1 1
S34 C3 S1 1
S34 N2 F1 1
S34 C7 F1 1
S34 O1 F1 1
S34 C8 F1 1
S34 C2 F2 1
S34 C1 F2 1
S34 C5 F2 1
S34 C4 F2 1
S34 C3 F2 1
S34 N1 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id S34
_pdbe_chem_comp_rdkit_properties.exactmw 175.075
_pdbe_chem_comp_rdkit_properties.amw 175.191
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_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 13
_pdbe_chem_comp_rdkit_properties.NumAtoms 22
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.222
_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 88.918
_pdbe_chem_comp_rdkit_properties.tpsa 65.780
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.557
_pdbe_chem_comp_rdkit_properties.CrippenMR 46.048
_pdbe_chem_comp_rdkit_properties.chi0v 6.250
_pdbe_chem_comp_rdkit_properties.chi1v 3.072
_pdbe_chem_comp_rdkit_properties.chi2v 0.906
_pdbe_chem_comp_rdkit_properties.chi3v 0.906
_pdbe_chem_comp_rdkit_properties.chi4v 0.465
_pdbe_chem_comp_rdkit_properties.chi0n 15.250
_pdbe_chem_comp_rdkit_properties.chi1n 7.519
_pdbe_chem_comp_rdkit_properties.chi2n 0.906
_pdbe_chem_comp_rdkit_properties.chi3n 0.906
_pdbe_chem_comp_rdkit_properties.chi4n 0.465
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.890
_pdbe_chem_comp_rdkit_properties.kappa1 2.808
_pdbe_chem_comp_rdkit_properties.kappa2 4.882
_pdbe_chem_comp_rdkit_properties.kappa3 3.340
_pdbe_chem_comp_rdkit_properties.Phi 1.054
#
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
S34 UniChem ZINC ZINC000000372245
S34 UniChem eMolecules 29549596
S34 UniChem Mcule MCULE-3043653055
S34 UniChem 'EPA CompTox Dashboard' DTXSID50308043
S34 UniChem SureChEMBL SCHEMBL2266663
S34 UniChem PubChem 304876
S34 UniChem ACTor 15029-28-4
#
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
S34 N1 -3.648 -0.068 -0.028 ETKDGv3 1
S34 N3 5.017 0.902 -0.767 ETKDGv3 2
S34 C4 -1.682 -1.451 -0.143 ETKDGv3 3
S34 C5 -1.018 -0.514 0.794 ETKDGv3 4
S34 C6 0.409 -0.757 1.203 ETKDGv3 5
S34 C7 1.608 0.821 -0.383 ETKDGv3 6
S34 C8 2.518 1.018 -1.554 ETKDGv3 7
S34 C1 -1.695 0.559 1.236 ETKDGv3 8
S34 C2 -3.087 0.773 0.792 ETKDGv3 9
S34 C3 -2.943 -1.220 -0.524 ETKDGv3 10
S34 C9 3.914 0.953 -1.114 ETKDGv3 11
S34 N2 1.307 -0.503 0.079 ETKDGv3 12
S34 O1 1.139 1.827 0.216 ETKDGv3 13
S34 H1 -1.151 -2.317 -0.519 ETKDGv3 14
S34 H2 0.704 -0.127 2.072 ETKDGv3 15
S34 H3 0.511 -1.817 1.521 ETKDGv3 16
S34 H4 2.335 0.228 -2.312 ETKDGv3 17
S34 H5 2.329 2.007 -2.024 ETKDGv3 18
S34 H6 -1.238 1.271 1.912 ETKDGv3 19
S34 H7 -3.642 1.631 1.146 ETKDGv3 20
S34 H8 -3.437 -1.898 -1.207 ETKDGv3 21
S34 H9 1.752 -1.320 -0.397 ETKDGv3 22
#