data_4VU
#
_chem_comp.id 4VU
_chem_comp.name (2R)-2-(pyridin-3-yl)-1-azabicyclo[2.2.2]octane
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C12 H16 N2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2015-06-08
_chem_comp.pdbx_modified_date 2015-06-19
_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 188.269
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 4VU
_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 5BW2
_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
4VU C1 C1 C 0 1 Y N N N N N 39.055 25.472 13.510 3.088 -1.143 0.125 C1 4VU 1
4VU N1 N1 N 0 1 N N N N N N 37.248 23.533 9.933 -1.130 1.005 -0.407 N1 4VU 2
4VU C2 C2 C 0 1 Y N N N N N 38.382 25.037 14.626 3.631 0.113 0.312 C2 4VU 3
4VU N2 N2 N 0 1 Y N N N N N 37.194 24.433 14.601 2.906 1.198 0.113 N2 4VU 4
4VU C4 C3 C 0 1 Y N N N N N 36.674 24.265 13.383 1.647 1.129 -0.271 C4 4VU 5
4VU C5 C4 C 0 1 Y N N N N N 37.260 24.658 12.203 1.036 -0.094 -0.479 C5 4VU 6
4VU C6 C5 C 0 1 Y N N N N N 38.483 25.280 12.275 1.768 -1.255 -0.284 C6 4VU 7
4VU C7 C6 C 0 1 N N R N N N 36.538 24.399 10.916 -0.402 -0.163 -0.922 C7 4VU 8
4VU C9 C7 C 0 1 N N N N N N 36.234 22.976 9.013 -2.529 0.996 -0.859 C9 4VU 9
4VU C10 C8 C 0 1 N N N N N N 36.226 25.695 10.210 -1.044 -1.442 -0.376 C10 4VU 10
4VU C11 C9 C 0 1 N N N N N N 35.369 24.116 8.529 -3.230 -0.250 -0.312 C11 4VU 11
4VU C12 C10 C 0 1 N N N N N N 36.124 25.404 8.734 -2.228 -1.058 0.521 C12 4VU 12
4VU C13 C11 C 0 1 N N N N N N 38.244 24.236 9.090 -1.051 1.073 1.058 C13 4VU 13
4VU C14 C12 C 0 1 N N N N N N 37.502 25.180 8.181 -1.711 -0.171 1.660 C14 4VU 14
4VU H1 H1 H 0 1 N N N N N N 40.016 25.956 13.601 3.686 -2.027 0.290 H1 4VU 15
4VU H3 H3 H 0 1 N N N N N N 38.847 25.195 15.588 4.659 0.209 0.627 H3 4VU 16
4VU H4 H4 H 0 1 N N N N N N 35.712 23.779 13.319 1.085 2.039 -0.424 H4 4VU 17
4VU H5 H5 H 0 1 N N N N N N 38.985 25.612 11.378 1.317 -2.225 -0.439 H5 4VU 18
4VU H6 H6 H 0 1 N N N N N N 35.581 23.915 11.161 -0.447 -0.169 -2.011 H6 4VU 19
4VU H17 H7 H 0 1 N N N N N N 35.615 22.236 9.542 -3.035 1.889 -0.492 H17 4VU 20
4VU H16 H8 H 0 1 N N N N N N 36.730 22.494 8.158 -2.559 0.983 -1.948 H16 4VU 21
4VU H8 H9 H 0 1 N N N N N N 37.030 26.423 10.393 -1.397 -2.055 -1.205 H8 4VU 22
4VU H7 H10 H 0 1 N N N N N N 35.272 26.101 10.578 -0.309 -2.000 0.204 H7 4VU 23
4VU H10 H11 H 0 1 N N N N N N 34.430 24.140 9.102 -4.069 0.050 0.316 H10 4VU 24
4VU H11 H12 H 0 1 N N N N N N 35.143 23.984 7.461 -3.592 -0.859 -1.141 H11 4VU 25
4VU H9 H13 H 0 1 N N N N N N 35.625 26.233 8.210 -2.705 -1.955 0.915 H9 4VU 26
4VU H12 H14 H 0 1 N N N N N N 38.807 23.506 8.490 -0.006 1.115 1.365 H12 4VU 27
4VU H13 H15 H 0 1 N N N N N N 38.940 24.801 9.727 -1.569 1.965 1.409 H13 4VU 28
4VU H15 H16 H 0 1 N N N N N N 37.429 24.743 7.174 -2.544 0.129 2.296 H15 4VU 29
4VU H14 H17 H 0 1 N N N N N N 38.039 26.139 8.127 -0.979 -0.723 2.250 H14 4VU 30
#
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
4VU C14 C12 SING N N 1
4VU C14 C13 SING N N 2
4VU C11 C12 SING N N 3
4VU C11 C9 SING N N 4
4VU C12 C10 SING N N 5
4VU C9 N1 SING N N 6
4VU C13 N1 SING N N 7
4VU N1 C7 SING N N 8
4VU C10 C7 SING N N 9
4VU C7 C5 SING N N 10
4VU C5 C6 DOUB Y N 11
4VU C5 C4 SING Y N 12
4VU C6 C1 SING Y N 13
4VU C4 N2 DOUB Y N 14
4VU C1 C2 DOUB Y N 15
4VU N2 C2 SING Y N 16
4VU C1 H1 SING N N 17
4VU C2 H3 SING N N 18
4VU C4 H4 SING N N 19
4VU C6 H5 SING N N 20
4VU C7 H6 SING N N 21
4VU C9 H17 SING N N 22
4VU C9 H16 SING N N 23
4VU C10 H8 SING N N 24
4VU C10 H7 SING N N 25
4VU C11 H10 SING N N 26
4VU C11 H11 SING N N 27
4VU C12 H9 SING N N 28
4VU C13 H12 SING N N 29
4VU C13 H13 SING N N 30
4VU C14 H15 SING N N 31
4VU C14 H14 SING N N 32
#
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
4VU SMILES ACDLabs 12.01 c1cncc(c1)C2N3CCC(C2)CC3
4VU InChI InChI 1.03 InChI=1S/C12H16N2/c1-2-11(9-13-5-1)12-8-10-3-6-14(12)7-4-10/h1-2,5,9-10,12H,3-4,6-8H2/t12-/m1/s1
4VU InChIKey InChI 1.03 YJYPZLAZNIGNRP-GFCCVEGCSA-N
4VU SMILES_CANONICAL CACTVS 3.385 C1CN2CCC1C[C@@H]2c3cccnc3
4VU SMILES CACTVS 3.385 C1CN2CCC1C[CH]2c3cccnc3
4VU SMILES_CANONICAL "OpenEye OEToolkits" 1.9.2 c1cc(cnc1)[C@H]2CC3CCN2CC3
4VU SMILES "OpenEye OEToolkits" 1.9.2 c1cc(cnc1)C2CC3CCN2CC3
#
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
4VU "SYSTEMATIC NAME" ACDLabs 12.01 (2R)-2-(pyridin-3-yl)-1-azabicyclo[2.2.2]octane
4VU "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.9.2 (2R)-2-pyridin-3-yl-1-azabicyclo[2.2.2]octane
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
4VU 'Create component' 2015-06-08 RCSB
4VU 'Initial release' 2015-06-24 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
4VU C1 C -2.232 2.798 1
4VU N1 N 0.354 -1.709 2
4VU C2 C -3.533 2.052 3
4VU N2 N -3.537 0.552 4
4VU C4 C -2.240 -0.202 5
4VU C5 C -0.939 0.545 6
4VU C6 C -0.935 2.045 7
4VU C7 C 0.358 -0.209 8
4VU C9 C 1.579 -1.639 9
4VU C10 C 1.675 0.547 10
4VU C11 C 1.842 -0.370 11
4VU C12 C 2.972 -0.207 12
4VU C13 C 1.660 -2.479 13
4VU C14 C 2.977 -1.723 14
#
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
4VU C14 C12 SINGLE NONE 1
4VU C14 C13 SINGLE NONE 2
4VU C11 C12 SINGLE NONE 3
4VU C11 C9 SINGLE NONE 4
4VU C12 C10 SINGLE NONE 5
4VU C9 N1 SINGLE NONE 6
4VU C13 N1 SINGLE NONE 7
4VU N1 C7 SINGLE NONE 8
4VU C10 C7 SINGLE NONE 9
4VU C7 C5 SINGLE NONE 10
4VU C5 C6 SINGLE NONE 11
4VU C5 C4 DOUBLE NONE 12
4VU C6 C1 DOUBLE NONE 13
4VU C4 N2 SINGLE NONE 14
4VU C1 C2 SINGLE NONE 15
4VU N2 C2 DOUBLE NONE 16
#
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
4VU MurckoScaffold S1 scaffold 'c1cncc([C@H]2CC3CCN2CC3)c1' InChI=1S/C12H16N2/c1-2-11(9-13-5-1)12-8-10-3-6-14(12)7-4-10/h1-2,5,9-10,12H,3-4,6-8H2/t12-/m1/s1 YJYPZLAZNIGNRP-GFCCVEGCSA-N
4VU 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
4VU C1 S1 1
4VU N1 S1 1
4VU C2 S1 1
4VU N2 S1 1
4VU C4 S1 1
4VU C5 S1 1
4VU C6 S1 1
4VU C7 S1 1
4VU C9 S1 1
4VU C10 S1 1
4VU C11 S1 1
4VU C12 S1 1
4VU C13 S1 1
4VU C14 S1 1
4VU C2 F1 1
4VU C1 F1 1
4VU C6 F1 1
4VU C5 F1 1
4VU C4 F1 1
4VU N2 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 4VU
_pdbe_chem_comp_rdkit_properties.exactmw 188.131
_pdbe_chem_comp_rdkit_properties.amw 188.274
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 2
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 0
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 1
_pdbe_chem_comp_rdkit_properties.NumHBD 0
_pdbe_chem_comp_rdkit_properties.NumHBA 2
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 14
_pdbe_chem_comp_rdkit_properties.NumAtoms 30
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 2
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.583
_pdbe_chem_comp_rdkit_properties.NumRings 4
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 3
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 3
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 4
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 3
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 3
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 0
_pdbe_chem_comp_rdkit_properties.NumBridgeheadAtoms 2
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 107.433
_pdbe_chem_comp_rdkit_properties.tpsa 16.130
_pdbe_chem_comp_rdkit_properties.CrippenClogP 2.184
_pdbe_chem_comp_rdkit_properties.CrippenMR 55.626
_pdbe_chem_comp_rdkit_properties.chi0v 6.894
_pdbe_chem_comp_rdkit_properties.chi1v 3.868
_pdbe_chem_comp_rdkit_properties.chi2v 1.756
_pdbe_chem_comp_rdkit_properties.chi3v 1.756
_pdbe_chem_comp_rdkit_properties.chi4v 1.148
_pdbe_chem_comp_rdkit_properties.chi0n 22.894
_pdbe_chem_comp_rdkit_properties.chi1n 11.868
_pdbe_chem_comp_rdkit_properties.chi2n 1.756
_pdbe_chem_comp_rdkit_properties.chi3n 1.756
_pdbe_chem_comp_rdkit_properties.chi4n 1.148
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.890
_pdbe_chem_comp_rdkit_properties.kappa1 1.987
_pdbe_chem_comp_rdkit_properties.kappa2 3.354
_pdbe_chem_comp_rdkit_properties.kappa3 1.340
_pdbe_chem_comp_rdkit_properties.Phi 0.476
#
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
4VU UniChem ZINC ZINC000003828421
4VU UniChem 'PubChem TPHARMA' 15487489
4VU UniChem PubChem 10465094
4VU UniChem Nikkaji J936.728D
4VU UniChem Nikkaji J2.593.244G
#
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
4VU C1 3.641 0.956 -0.847 ETKDGv3 1
4VU N1 -0.631 -0.656 1.094 ETKDGv3 2
4VU C2 4.296 -0.205 -0.224 ETKDGv3 3
4VU N2 3.614 -0.999 0.548 ETKDGv3 4
4VU C4 2.215 -0.789 0.805 ETKDGv3 5
4VU C5 1.551 0.223 0.207 ETKDGv3 6
4VU C6 2.339 1.166 -0.632 ETKDGv3 7
4VU C7 0.087 0.519 0.518 ETKDGv3 8
4VU C9 -0.913 -1.669 0.041 ETKDGv3 9
4VU C10 -0.705 1.087 -0.703 ETKDGv3 10
4VU C11 -1.837 -1.096 -1.061 ETKDGv3 11
4VU C12 -2.081 0.397 -0.783 ETKDGv3 12
4VU C13 -1.921 -0.192 1.664 ETKDGv3 13
4VU C14 -2.779 0.522 0.587 ETKDGv3 14
4VU H1 4.214 1.639 -1.461 ETKDGv3 15
4VU H3 5.348 -0.391 -0.395 ETKDGv3 16
4VU H4 1.715 -1.461 1.490 ETKDGv3 17
4VU H5 1.869 2.039 -1.067 ETKDGv3 18
4VU H6 0.123 1.321 1.292 ETKDGv3 19
4VU H17 0.036 -2.022 -0.416 ETKDGv3 20
4VU H16 -1.387 -2.564 0.501 ETKDGv3 21
4VU H8 -0.167 0.910 -1.660 ETKDGv3 22
4VU H7 -0.840 2.185 -0.593 ETKDGv3 23
4VU H10 -1.368 -1.226 -2.061 ETKDGv3 24
4VU H11 -2.807 -1.641 -1.071 ETKDGv3 25
4VU H9 -2.703 0.850 -1.585 ETKDGv3 26
4VU H12 -1.732 0.496 2.517 ETKDGv3 27
4VU H13 -2.482 -1.058 2.081 ETKDGv3 28
4VU H15 -3.791 0.064 0.540 ETKDGv3 29
4VU H14 -2.904 1.595 0.848 ETKDGv3 30
#