data_VR6
#
_chem_comp.id VR6
_chem_comp.name N-[(furan-2-yl)methyl]-2-[(pyridin-2-yl)oxy]ethan-1-amine
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C12 H14 N2 O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2022-09-02
_chem_comp.pdbx_modified_date 2022-10-28
_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 218.252
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code VR6
_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 7FML
_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
VR6 N1 N1 N 0 1 N N N N N N 19.031 4.175 19.769 -1.283 -0.919 0.083 N1 VR6 1
VR6 C7 C1 C 0 1 N N N N N N 18.869 5.241 18.670 -2.636 -1.219 0.572 C7 VR6 2
VR6 C8 C2 C 0 1 Y N N N N N 18.112 4.696 17.546 -3.588 -0.149 0.105 C8 VR6 3
VR6 C9 C3 C 0 1 Y N N N N N 18.506 4.214 16.324 -4.289 -0.166 -1.043 C9 VR6 4
VR6 O1 O1 O 0 1 Y N N N N N 16.776 4.556 17.711 -3.885 0.981 0.766 O1 VR6 5
VR6 C1 C4 C 0 1 Y N N N N N 20.943 1.664 24.646 5.204 0.954 -0.522 C1 VR6 6
VR6 C5 C5 C 0 1 N N N N N N 17.541 2.713 21.231 1.068 -1.597 -0.006 C5 VR6 7
VR6 C6 C6 C 0 1 N N N N N N 17.868 4.170 20.789 -0.326 -1.944 0.521 C6 VR6 8
VR6 C4 C7 C 0 1 Y N N N N N 18.604 2.307 24.675 3.233 1.247 0.784 C4 VR6 9
VR6 C3 C8 C 0 1 Y N N N N N 18.676 2.310 23.290 2.743 0.070 0.233 C3 VR6 10
VR6 C2 C9 C 0 1 Y N N N N N 20.906 1.695 23.263 4.652 -0.204 -1.032 C2 VR6 11
VR6 C11 C10 C 0 1 Y N N N N N 16.327 3.959 16.595 -4.768 1.699 0.053 C11 VR6 12
VR6 C10 C11 C 0 1 Y N N N N N 17.337 3.727 15.720 -5.053 1.023 -1.075 C10 VR6 13
VR6 O O2 O 0 1 N N N N N N 17.515 2.691 22.630 1.516 -0.381 0.595 O VR6 14
VR6 C C12 C 0 1 Y N N N N N 19.789 1.974 25.352 4.487 1.696 0.405 C VR6 15
VR6 N N2 N 0 1 Y N N N N N 19.806 2.006 22.575 3.457 -0.610 -0.649 N VR6 16
VR6 H1 H1 H 0 1 N N N N N N 19.077 3.275 19.335 -1.275 -0.821 -0.921 H1 VR6 17
VR6 H3 H3 H 0 1 N N N N N N 19.863 5.556 18.320 -2.956 -2.186 0.183 H3 VR6 18
VR6 H4 H4 H 0 1 N N N N N N 18.333 6.109 19.082 -2.630 -1.250 1.661 H4 VR6 19
VR6 H5 H5 H 0 1 N N N N N N 19.505 4.210 15.913 -4.272 -0.940 -1.796 H5 VR6 20
VR6 H6 H6 H 0 1 N N N N N N 21.853 1.403 25.166 6.185 1.277 -0.838 H6 VR6 21
VR6 H7 H7 H 0 1 N N N N N N 16.561 2.411 20.833 1.760 -2.402 0.242 H7 VR6 22
VR6 H8 H8 H 0 1 N N N N N N 18.315 2.026 20.859 1.027 -1.474 -1.089 H8 VR6 23
VR6 H9 H9 H 0 1 N N N N N N 18.157 4.760 21.671 -0.304 -1.980 1.610 H9 VR6 24
VR6 H10 H10 H 0 1 N N N N N N 16.977 4.617 20.325 -0.631 -2.915 0.131 H10 VR6 25
VR6 H11 H11 H 0 1 N N N N N N 17.692 2.546 25.201 2.648 1.800 1.503 H11 VR6 26
VR6 H12 H12 H 0 1 N N N N N N 21.807 1.457 22.717 5.206 -0.786 -1.755 H12 VR6 27
VR6 H13 H13 H 0 1 N N N N N N 15.294 3.697 16.417 -5.186 2.653 0.340 H13 VR6 28
VR6 H14 H14 H 0 1 N N N N N N 17.257 3.260 14.750 -5.731 1.333 -1.857 H14 VR6 29
VR6 H15 H15 H 0 1 N N N N N N 19.802 1.959 26.432 4.897 2.604 0.823 H15 VR6 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
VR6 C10 C9 SING Y N 1
VR6 C10 C11 DOUB Y N 2
VR6 C9 C8 DOUB Y N 3
VR6 C11 O1 SING Y N 4
VR6 C8 O1 SING Y N 5
VR6 C8 C7 SING N N 6
VR6 C7 N1 SING N N 7
VR6 N1 C6 SING N N 8
VR6 C6 C5 SING N N 9
VR6 C5 O SING N N 10
VR6 N C2 DOUB Y N 11
VR6 N C3 SING Y N 12
VR6 O C3 SING N N 13
VR6 C2 C1 SING Y N 14
VR6 C3 C4 DOUB Y N 15
VR6 C1 C DOUB Y N 16
VR6 C4 C SING Y N 17
VR6 N1 H1 SING N N 18
VR6 C7 H3 SING N N 19
VR6 C7 H4 SING N N 20
VR6 C9 H5 SING N N 21
VR6 C1 H6 SING N N 22
VR6 C5 H7 SING N N 23
VR6 C5 H8 SING N N 24
VR6 C6 H9 SING N N 25
VR6 C6 H10 SING N N 26
VR6 C4 H11 SING N N 27
VR6 C2 H12 SING N N 28
VR6 C11 H13 SING N N 29
VR6 C10 H14 SING N N 30
VR6 C H15 SING N N 31
#
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
VR6 SMILES ACDLabs 12.01 C(CNCc1ccco1)Oc1ccccn1
VR6 InChI InChI 1.06 InChI=1S/C12H14N2O2/c1-2-6-14-12(5-1)16-9-7-13-10-11-4-3-8-15-11/h1-6,8,13H,7,9-10H2
VR6 InChIKey InChI 1.06 RMGIKRSEGHAEEZ-UHFFFAOYSA-N
VR6 SMILES_CANONICAL CACTVS 3.385 C(COc1ccccn1)NCc2occc2
VR6 SMILES CACTVS 3.385 C(COc1ccccn1)NCc2occc2
VR6 SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 c1ccnc(c1)OCCNCc2ccco2
VR6 SMILES "OpenEye OEToolkits" 2.0.7 c1ccnc(c1)OCCNCc2ccco2
#
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
VR6 "SYSTEMATIC NAME" ACDLabs 12.01 N-[(furan-2-yl)methyl]-2-[(pyridin-2-yl)oxy]ethan-1-amine
VR6 "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 ~{N}-(furan-2-ylmethyl)-2-pyridin-2-yloxy-ethanamine
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
VR6 'Create component' 2022-09-02 RCSB
VR6 'Initial release' 2022-11-02 RCSB
#
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
VR6 N1 N 7.972 -0.750 1
VR6 C7 C 6.673 -1.500 2
VR6 C8 C 5.374 -0.750 3
VR6 C9 C 4.004 -1.360 4
VR6 O1 O 5.217 0.742 5
VR6 C1 C 15.766 0.750 6
VR6 C5 C 10.570 -0.750 7
VR6 C6 C 9.271 -1.500 8
VR6 C4 C 13.168 0.750 9
VR6 C3 C 13.168 -0.750 10
VR6 C2 C 15.766 -0.750 11
VR6 C11 C 3.750 1.054 12
VR6 C10 C 3.000 -0.245 13
VR6 O O 11.869 -1.500 14
VR6 C C 14.467 1.500 15
VR6 N N 14.467 -1.500 16
#
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
VR6 C10 C9 SINGLE NONE 1
VR6 C10 C11 DOUBLE NONE 2
VR6 C9 C8 DOUBLE NONE 3
VR6 C11 O1 SINGLE NONE 4
VR6 C8 O1 SINGLE NONE 5
VR6 C8 C7 SINGLE NONE 6
VR6 C7 N1 SINGLE NONE 7
VR6 N1 C6 SINGLE NONE 8
VR6 C6 C5 SINGLE NONE 9
VR6 C5 O SINGLE NONE 10
VR6 N C2 SINGLE NONE 11
VR6 N C3 DOUBLE NONE 12
VR6 O C3 SINGLE NONE 13
VR6 C2 C1 DOUBLE NONE 14
VR6 C3 C4 SINGLE NONE 15
VR6 C1 C SINGLE NONE 16
VR6 C4 C DOUBLE NONE 17
#
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
VR6 MurckoScaffold S1 scaffold c1ccc(OCCNCc2ccco2)nc1 InChI=1S/C12H14N2O2/c1-2-6-14-12(5-1)16-9-7-13-10-11-4-3-8-15-11/h1-6,8,13H,7,9-10H2 RMGIKRSEGHAEEZ-UHFFFAOYSA-N
VR6 furan F1 fragment c1ccoc1 InChI=1S/C4H4O/c1-2-4-5-3-1/h1-4H YLQBMQCUIZJEEH-UHFFFAOYSA-N
VR6 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
VR6 N1 S1 1
VR6 C7 S1 1
VR6 C8 S1 1
VR6 C9 S1 1
VR6 O1 S1 1
VR6 C1 S1 1
VR6 C5 S1 1
VR6 C6 S1 1
VR6 C4 S1 1
VR6 C3 S1 1
VR6 C2 S1 1
VR6 C11 S1 1
VR6 C10 S1 1
VR6 O S1 1
VR6 C S1 1
VR6 N S1 1
VR6 C8 F1 1
VR6 C9 F1 1
VR6 C10 F1 1
VR6 C11 F1 1
VR6 O1 F1 1
VR6 C3 F2 1
VR6 C4 F2 1
VR6 C F2 1
VR6 C1 F2 1
VR6 C2 F2 1
VR6 N F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id VR6
_pdbe_chem_comp_rdkit_properties.exactmw 218.106
_pdbe_chem_comp_rdkit_properties.amw 218.256
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 1
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 6
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 16
_pdbe_chem_comp_rdkit_properties.NumAtoms 30
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.250
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 2
_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 113.988
_pdbe_chem_comp_rdkit_properties.tpsa 47.290
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.326
_pdbe_chem_comp_rdkit_properties.CrippenMR 59.271
_pdbe_chem_comp_rdkit_properties.chi0v 7.711
_pdbe_chem_comp_rdkit_properties.chi1v 3.961
_pdbe_chem_comp_rdkit_properties.chi2v 1.232
_pdbe_chem_comp_rdkit_properties.chi3v 1.232
_pdbe_chem_comp_rdkit_properties.chi4v 0.675
_pdbe_chem_comp_rdkit_properties.chi0n 21.711
_pdbe_chem_comp_rdkit_properties.chi1n 10.908
_pdbe_chem_comp_rdkit_properties.chi2n 1.232
_pdbe_chem_comp_rdkit_properties.chi3n 1.232
_pdbe_chem_comp_rdkit_properties.chi4n 0.675
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.810
_pdbe_chem_comp_rdkit_properties.kappa1 2.897
_pdbe_chem_comp_rdkit_properties.kappa2 5.924
_pdbe_chem_comp_rdkit_properties.kappa3 3.399
_pdbe_chem_comp_rdkit_properties.Phi 1.073
#
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
VR6 UniChem PDBe VR6
VR6 UniChem ZINC ZINC000035287222
VR6 UniChem eMolecules 29385391
VR6 UniChem PubChem 45259124
VR6 UniChem Mcule MCULE-8351641548
#
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
VR6 N1 -1.340 -0.516 0.590 ETKDGv3 1
VR6 C7 -2.740 -0.958 0.643 ETKDGv3 2
VR6 C8 -3.635 0.060 0.007 ETKDGv3 3
VR6 C9 -3.919 1.255 0.506 ETKDGv3 4
VR6 O1 -4.269 -0.115 -1.215 ETKDGv3 5
VR6 C1 5.544 0.331 0.516 ETKDGv3 6
VR6 C5 0.631 -0.129 -0.827 ETKDGv3 7
VR6 C6 -0.755 -0.761 -0.736 ETKDGv3 8
VR6 C4 3.712 -1.122 1.195 ETKDGv3 9
VR6 C3 2.862 -0.402 0.224 ETKDGv3 10
VR6 C2 4.747 0.962 -0.354 ETKDGv3 11
VR6 C11 -4.978 1.053 -1.457 ETKDGv3 12
VR6 C10 -4.801 1.905 -0.457 ETKDGv3 13
VR6 O 1.521 -0.771 0.082 ETKDGv3 14
VR6 C 4.994 -0.769 1.332 ETKDGv3 15
VR6 N 3.370 0.568 -0.487 ETKDGv3 16
VR6 H1 -0.807 -1.090 1.285 ETKDGv3 17
VR6 H3 -3.048 -1.079 1.705 ETKDGv3 18
VR6 H4 -2.872 -1.945 0.146 ETKDGv3 19
VR6 H5 -3.555 1.664 1.440 ETKDGv3 20
VR6 H6 6.581 0.622 0.621 ETKDGv3 21
VR6 H7 1.015 -0.245 -1.864 ETKDGv3 22
VR6 H8 0.563 0.955 -0.588 ETKDGv3 23
VR6 H9 -1.391 -0.305 -1.527 ETKDGv3 24
VR6 H10 -0.677 -1.854 -0.932 ETKDGv3 25
VR6 H11 3.299 -1.927 1.789 ETKDGv3 26
VR6 H12 5.135 1.770 -0.960 ETKDGv3 27
VR6 H13 -5.583 1.236 -2.335 ETKDGv3 28
VR6 H14 -5.234 2.893 -0.381 ETKDGv3 29
VR6 H15 5.629 -1.287 2.039 ETKDGv3 30
#