data_K8F
#
_chem_comp.id K8F
_chem_comp.name 6-[3-(3,3-difluoroazetidin-1-yl)propyl]-4-methylpyridin-2-amine
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C12 H17 F2 N3"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2022-02-03
_chem_comp.pdbx_modified_date 2022-07-08
_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 241.280
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code K8F
_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 7TSO
_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
K8F C02 C1 C 0 1 Y N N N N N 67.276 28.713 -188.436 3.529 -1.426 0.079 C02 K8F 1
K8F C03 C2 C 0 1 Y N N N N N 67.225 30.086 -188.633 4.611 -0.641 -0.306 C03 K8F 2
K8F C04 C3 C 0 1 Y N N N N N 66.059 30.770 -188.341 4.477 0.736 -0.306 C04 K8F 3
K8F C05 C4 C 0 1 Y N N N N N 64.953 30.075 -187.852 3.262 1.284 0.081 C05 K8F 4
K8F C06 C5 C 0 1 Y N N N N N 65.050 28.703 -187.676 2.230 0.445 0.452 C06 K8F 5
K8F C07 C6 C 0 1 N N N N N N 66.010 32.260 -188.547 5.626 1.621 -0.716 C07 K8F 6
K8F C08 C7 C 0 1 N N N N N N 63.922 27.832 -187.182 0.908 1.034 0.873 C08 K8F 7
K8F C09 C8 C 0 1 N N N N N N 62.774 28.574 -186.540 -0.212 0.435 0.019 C09 K8F 8
K8F C10 C9 C 0 1 N N N N N N 61.593 27.611 -186.466 -1.554 1.033 0.446 C10 K8F 9
K8F C12 C10 C 0 1 N N N N N N 60.337 26.305 -184.826 -3.903 1.180 -0.159 C12 K8F 10
K8F C13 C11 C 0 1 N N N N N N 59.318 27.260 -184.230 -4.568 -0.209 -0.145 C13 K8F 11
K8F C14 C12 C 0 1 N N N N N N 60.165 28.430 -184.689 -3.187 -0.757 0.259 C14 K8F 12
K8F F15 F1 F 0 1 N N N N N N 58.122 27.203 -184.793 -5.546 -0.356 0.844 F15 K8F 13
K8F F16 F2 F 0 1 N N N N N N 59.309 27.187 -182.907 -4.997 -0.639 -1.405 F16 K8F 14
K8F N01 N1 N 0 1 Y N N N N N 66.194 28.065 -187.973 2.385 -0.865 0.442 N01 K8F 15
K8F N02 N2 N 0 1 N N N N N N 68.394 28.004 -188.720 3.647 -2.811 0.078 N02 K8F 16
K8F N11 N3 N 0 1 N N N N N N 61.208 27.465 -185.064 -2.629 0.459 -0.374 N11 K8F 17
K8F H1 H1 H 0 1 N N N N N N 68.087 30.615 -189.011 5.543 -1.101 -0.601 H1 K8F 18
K8F H2 H2 H 0 1 N N N N N N 64.037 30.596 -187.615 3.125 2.355 0.093 H2 K8F 19
K8F H3 H3 H 0 1 N N N N N N 65.665 32.478 -189.568 5.578 1.803 -1.790 H3 K8F 20
K8F H4 H4 H 0 1 N N N N N N 65.315 32.708 -187.822 5.561 2.570 -0.184 H4 K8F 21
K8F H5 H5 H 0 1 N N N N N N 67.015 32.683 -188.401 6.568 1.130 -0.472 H5 K8F 22
K8F H6 H6 H 0 1 N N N N N N 63.526 27.268 -188.039 0.726 0.805 1.923 H6 K8F 23
K8F H7 H7 H 0 1 N N N N N N 64.332 27.131 -186.440 0.931 2.115 0.735 H7 K8F 24
K8F H8 H8 H 0 1 N N N N N N 63.056 28.901 -185.528 -0.030 0.664 -1.031 H8 K8F 25
K8F H9 H9 H 0 1 N N N N N N 62.506 29.451 -187.148 -0.236 -0.646 0.156 H9 K8F 26
K8F H10 H10 H 0 1 N N N N N N 60.748 28.013 -187.044 -1.736 0.804 1.496 H10 K8F 27
K8F H11 H11 H 0 1 N N N N N N 61.884 26.633 -186.876 -1.531 2.114 0.309 H11 K8F 28
K8F H12 H12 H 0 1 N N N N N N 60.002 25.790 -185.739 -4.203 1.802 -1.001 H12 K8F 29
K8F H13 H13 H 0 1 N N N N N N 60.742 25.568 -184.117 -3.958 1.702 0.797 H13 K8F 30
K8F H14 H14 H 0 1 N N N N N N 60.454 29.126 -183.888 -3.031 -0.802 1.337 H14 K8F 31
K8F H15 H15 H 0 1 N N N N N N 59.743 28.996 -185.532 -2.916 -1.682 -0.249 H15 K8F 32
K8F H16 H16 H 0 1 N N N N N N 68.233 27.036 -188.528 2.894 -3.362 0.342 H16 K8F 33
K8F H17 H17 H 0 1 N N N N N N 68.625 28.118 -189.686 4.483 -3.226 -0.187 H17 K8F 34
#
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
K8F N02 C02 SING N N 1
K8F C03 C02 DOUB Y N 2
K8F C03 C04 SING Y N 3
K8F C07 C04 SING N N 4
K8F C02 N01 SING Y N 5
K8F C04 C05 DOUB Y N 6
K8F N01 C06 DOUB Y N 7
K8F C05 C06 SING Y N 8
K8F C06 C08 SING N N 9
K8F C08 C09 SING N N 10
K8F C09 C10 SING N N 11
K8F C10 N11 SING N N 12
K8F N11 C12 SING N N 13
K8F N11 C14 SING N N 14
K8F C12 C13 SING N N 15
K8F F15 C13 SING N N 16
K8F C14 C13 SING N N 17
K8F C13 F16 SING N N 18
K8F C03 H1 SING N N 19
K8F C05 H2 SING N N 20
K8F C07 H3 SING N N 21
K8F C07 H4 SING N N 22
K8F C07 H5 SING N N 23
K8F C08 H6 SING N N 24
K8F C08 H7 SING N N 25
K8F C09 H8 SING N N 26
K8F C09 H9 SING N N 27
K8F C10 H10 SING N N 28
K8F C10 H11 SING N N 29
K8F C12 H12 SING N N 30
K8F C12 H13 SING N N 31
K8F C14 H14 SING N N 32
K8F C14 H15 SING N N 33
K8F N02 H16 SING N N 34
K8F N02 H17 SING N N 35
#
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
K8F SMILES ACDLabs 12.01 Cc1cc(nc(N)c1)CCCN1CC(F)(F)C1
K8F InChI InChI 1.03 InChI=1S/C12H17F2N3/c1-9-5-10(16-11(15)6-9)3-2-4-17-7-12(13,14)8-17/h5-6H,2-4,7-8H2,1H3,(H2,15,16)
K8F InChIKey InChI 1.03 VXUPTLRCBSMECG-UHFFFAOYSA-N
K8F SMILES_CANONICAL CACTVS 3.385 Cc1cc(N)nc(CCCN2CC(F)(F)C2)c1
K8F SMILES CACTVS 3.385 Cc1cc(N)nc(CCCN2CC(F)(F)C2)c1
K8F SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 Cc1cc(nc(c1)N)CCCN2CC(C2)(F)F
K8F SMILES "OpenEye OEToolkits" 2.0.7 Cc1cc(nc(c1)N)CCCN2CC(C2)(F)F
#
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
K8F "SYSTEMATIC NAME" ACDLabs 12.01 6-[3-(3,3-difluoroazetidin-1-yl)propyl]-4-methylpyridin-2-amine
K8F "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.7 6-[3-[3,3-bis(fluoranyl)azetidin-1-yl]propyl]-4-methyl-pyridin-2-amine
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
K8F 'Create component' 2022-02-03 RCSB
K8F 'Initial release' 2022-07-13 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
K8F C02 C 5.104 -1.035 1
K8F C03 C 5.104 0.465 2
K8F C04 C 6.404 1.215 3
K8F C05 C 7.702 0.465 4
K8F C06 C 7.702 -1.035 5
K8F C07 C 6.404 2.715 6
K8F C08 C 9.002 -1.785 7
K8F C09 C 10.301 -1.035 8
K8F C10 C 11.600 -1.785 9
K8F C12 C 14.348 -1.423 10
K8F C13 C 14.736 0.026 11
K8F C14 C 13.287 0.414 12
K8F F15 F 16.185 -0.362 13
K8F F16 F 15.124 1.474 14
K8F N01 N 6.404 -1.785 15
K8F N02 N 3.805 -1.785 16
K8F N11 N 12.899 -1.035 17
#
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
K8F N02 C02 SINGLE NONE 1
K8F C03 C02 DOUBLE NONE 2
K8F C03 C04 SINGLE NONE 3
K8F C07 C04 SINGLE NONE 4
K8F C02 N01 SINGLE NONE 5
K8F C04 C05 DOUBLE NONE 6
K8F N01 C06 DOUBLE NONE 7
K8F C05 C06 SINGLE NONE 8
K8F C06 C08 SINGLE NONE 9
K8F C08 C09 SINGLE NONE 10
K8F C09 C10 SINGLE NONE 11
K8F C10 N11 SINGLE NONE 12
K8F N11 C12 SINGLE NONE 13
K8F N11 C14 SINGLE NONE 14
K8F C12 C13 SINGLE NONE 15
K8F F15 C13 SINGLE NONE 16
K8F C14 C13 SINGLE NONE 17
K8F C13 F16 SINGLE NONE 18
#
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
K8F MurckoScaffold S1 scaffold c1ccc(CCCN2CCC2)nc1 InChI=1S/C11H16N2/c1-2-7-12-11(5-1)6-3-8-13-9-4-10-13/h1-2,5,7H,3-4,6,8-10H2 GYUODWYICYHOEI-UHFFFAOYSA-N
K8F 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
K8F C02 S1 1
K8F C03 S1 1
K8F C04 S1 1
K8F C05 S1 1
K8F C06 S1 1
K8F C08 S1 1
K8F C09 S1 1
K8F C10 S1 1
K8F C12 S1 1
K8F C13 S1 1
K8F C14 S1 1
K8F N01 S1 1
K8F N11 S1 1
K8F C02 F1 1
K8F C03 F1 1
K8F C04 F1 1
K8F C05 F1 1
K8F C06 F1 1
K8F N01 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id K8F
_pdbe_chem_comp_rdkit_properties.exactmw 241.139
_pdbe_chem_comp_rdkit_properties.amw 241.285
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 6
_pdbe_chem_comp_rdkit_properties.NumHBD 1
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 17
_pdbe_chem_comp_rdkit_properties.NumAtoms 34
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.583
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 1
_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 0
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 123.631
_pdbe_chem_comp_rdkit_properties.tpsa 42.150
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.366
_pdbe_chem_comp_rdkit_properties.CrippenMR 61.738
_pdbe_chem_comp_rdkit_properties.chi0v 8.098
_pdbe_chem_comp_rdkit_properties.chi1v 4.220
_pdbe_chem_comp_rdkit_properties.chi2v 1.551
_pdbe_chem_comp_rdkit_properties.chi3v 1.551
_pdbe_chem_comp_rdkit_properties.chi4v 0.962
_pdbe_chem_comp_rdkit_properties.chi0n 25.098
_pdbe_chem_comp_rdkit_properties.chi1n 12.614
_pdbe_chem_comp_rdkit_properties.chi2n 1.551
_pdbe_chem_comp_rdkit_properties.chi3n 1.551
_pdbe_chem_comp_rdkit_properties.chi4n 0.962
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.230
_pdbe_chem_comp_rdkit_properties.kappa1 3.017
_pdbe_chem_comp_rdkit_properties.kappa2 4.565
_pdbe_chem_comp_rdkit_properties.kappa3 3.361
_pdbe_chem_comp_rdkit_properties.Phi 0.810
#
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
K8F UniChem ChEMBL CHEMBL5204779
K8F UniChem PDBe K8F
#
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
K8F C02 2.560 1.609 1.369 ETKDGv3 1
K8F C03 3.496 1.345 0.445 ETKDGv3 2
K8F C04 3.354 0.151 -0.421 ETKDGv3 3
K8F C05 2.305 -0.667 -0.244 ETKDGv3 4
K8F C06 1.295 -0.346 0.791 ETKDGv3 5
K8F C07 4.409 -0.173 -1.436 ETKDGv3 6
K8F C08 0.082 -1.212 0.961 ETKDGv3 7
K8F C09 -1.029 -0.779 -0.002 ETKDGv3 8
K8F C10 -2.269 -1.702 0.141 ETKDGv3 9
K8F C12 -4.017 0.054 0.104 ETKDGv3 10
K8F C13 -3.902 0.762 -1.234 ETKDGv3 11
K8F C14 -3.439 -0.579 -1.774 ETKDGv3 12
K8F F15 -2.921 1.739 -1.263 ETKDGv3 13
K8F F16 -5.118 1.177 -1.749 ETKDGv3 14
K8F N01 1.433 0.727 1.517 ETKDGv3 15
K8F N02 2.670 2.759 2.209 ETKDGv3 16
K8F N11 -3.542 -1.220 -0.454 ETKDGv3 17
K8F H1 4.350 2.001 0.327 ETKDGv3 18
K8F H2 2.190 -1.556 -0.852 ETKDGv3 19
K8F H3 4.990 0.736 -1.701 ETKDGv3 20
K8F H4 5.101 -0.934 -1.021 ETKDGv3 21
K8F H5 3.946 -0.569 -2.365 ETKDGv3 22
K8F H6 0.354 -2.273 0.771 ETKDGv3 23
K8F H7 -0.279 -1.137 2.011 ETKDGv3 24
K8F H8 -0.626 -0.847 -1.034 ETKDGv3 25
K8F H9 -1.280 0.280 0.207 ETKDGv3 26
K8F H10 -2.023 -2.684 -0.317 ETKDGv3 27
K8F H11 -2.454 -1.901 1.219 ETKDGv3 28
K8F H12 -3.373 0.486 0.900 ETKDGv3 29
K8F H13 -5.074 -0.040 0.437 ETKDGv3 30
K8F H14 -4.178 -1.022 -2.476 ETKDGv3 31
K8F H15 -2.424 -0.554 -2.218 ETKDGv3 32
K8F H16 1.936 2.954 2.925 ETKDGv3 33
K8F H17 3.477 3.417 2.124 ETKDGv3 34
#