data_D6A
#
_chem_comp.id D6A
_chem_comp.name (3R,5R)-5-{3-[4-(trifluoromethyl)phenyl]-1,2,4-oxadiazol-5-yl}pyrrolidin-3-ol
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C13 H12 F3 N3 O2"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2017-10-20
_chem_comp.pdbx_modified_date 2020-04-17
_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 299.248
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code D6A
_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 5QB7
_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
D6A C4 C1 C 0 1 Y N N N N N -3.876 1.958 10.721 -1.866 1.352 -0.194 C4 D6A 1
D6A C5 C2 C 0 1 Y N N N N N -2.762 1.137 10.565 -1.043 0.257 0.058 C5 D6A 2
D6A C6 C3 C 0 1 Y N N N N N -1.456 1.717 10.230 0.430 0.427 0.107 C6 D6A 3
D6A N1 N1 N 0 1 Y N N N N N -0.364 0.998 10.198 1.089 1.543 -0.066 N1 D6A 4
D6A C7 C4 C 0 1 Y N N N N N -0.028 3.104 9.612 2.509 0.052 0.293 C7 D6A 5
D6A C8 C5 C 0 1 N N R N N N 0.719 4.196 8.894 3.854 -0.597 0.489 C8 D6A 6
D6A N2 N2 N 0 1 N N N N N N 2.158 4.240 9.328 4.759 0.294 1.260 N2 D6A 7
D6A C9 C6 C 0 1 N N N N N N 0.198 5.614 9.096 4.587 -0.759 -0.867 C9 D6A 8
D6A C10 C7 C 0 1 N N R N N N 1.092 6.282 10.125 6.074 -0.819 -0.451 C10 D6A 9
D6A C11 C8 C 0 1 N N N N N N 2.415 5.546 10.036 6.133 -0.147 0.933 C11 D6A 10
D6A C12 C9 C 0 1 N N N N N N -6.619 -0.539 11.403 -5.288 -0.235 -0.089 C12 D6A 11
D6A F2 F1 F 0 1 N N N N N N -7.486 -0.217 10.470 -5.836 0.700 -0.973 F2 D6A 12
D6A F F2 F 0 1 N N N N N N -6.609 -1.861 11.456 -5.823 -0.040 1.189 F D6A 13
D6A F1 F3 F 0 1 N N N N N N -7.149 -0.116 12.536 -5.593 -1.528 -0.530 F1 D6A 14
D6A C2 C10 C 0 1 Y N N N N N -5.273 0.044 11.147 -3.792 -0.062 -0.039 C2 D6A 15
D6A C1 C11 C 0 1 Y N N N N N -4.157 -0.773 11.009 -2.980 -1.153 0.217 C1 D6A 16
D6A C3 C12 C 0 1 Y N N N N N -5.110 1.413 11.017 -3.236 1.188 -0.238 C3 D6A 17
D6A C C13 C 0 1 Y N N N N N -2.915 -0.230 10.745 -1.609 -1.000 0.263 C D6A 18
D6A O O1 O 0 1 Y N N N N N 0.627 1.932 9.788 2.281 1.344 0.037 O D6A 19
D6A N N3 N 0 1 Y N N N N N -1.270 3.051 9.913 1.343 -0.542 0.346 N D6A 20
D6A O1 O2 O 0 1 N N N N N N 0.592 5.990 11.430 6.880 -0.100 -1.387 O1 D6A 21
D6A H1 H1 H 0 1 N N N N N N -3.774 3.027 10.610 -1.433 2.329 -0.350 H1 D6A 22
D6A H2 H2 H 0 1 N N N N N N 0.693 3.977 7.816 3.748 -1.561 0.986 H2 D6A 23
D6A H3 H3 H 0 1 N N N N N N 2.345 3.479 9.949 4.619 1.260 1.005 H3 D6A 24
D6A H5 H5 H 0 1 N N N N N N 0.238 6.168 8.147 4.286 -1.684 -1.360 H5 D6A 25
D6A H6 H6 H 0 1 N N N N N N -0.839 5.585 9.461 4.400 0.101 -1.511 H6 D6A 26
D6A H7 H7 H 0 1 N N N N N N 1.207 7.359 9.932 6.407 -1.855 -0.384 H7 D6A 27
D6A H8 H8 H 0 1 N N N N N N 2.808 5.355 11.046 6.800 0.714 0.900 H8 D6A 28
D6A H9 H9 H 0 1 N N N N N N 3.141 6.145 9.467 6.481 -0.861 1.679 H9 D6A 29
D6A H10 H10 H 0 1 N N N N N N -4.262 -1.843 11.109 -3.420 -2.125 0.380 H10 D6A 30
D6A H11 H11 H 0 1 N N N N N N -5.961 2.065 11.149 -3.874 2.038 -0.429 H11 D6A 31
D6A H12 H12 H 0 1 N N N N N N -2.053 -0.877 10.678 -0.976 -1.853 0.459 H12 D6A 32
D6A H13 H13 H 0 1 N N N N N N 1.145 6.404 12.082 7.824 -0.103 -1.177 H13 D6A 33
#
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
D6A C8 C9 SING N N 1
D6A C8 N2 SING N N 2
D6A C8 C7 SING N N 3
D6A C9 C10 SING N N 4
D6A N2 C11 SING N N 5
D6A C7 O SING Y N 6
D6A C7 N DOUB Y N 7
D6A O N1 SING Y N 8
D6A N C6 SING Y N 9
D6A C11 C10 SING N N 10
D6A C10 O1 SING N N 11
D6A N1 C6 DOUB Y N 12
D6A C6 C5 SING N N 13
D6A F2 C12 SING N N 14
D6A C5 C4 DOUB Y N 15
D6A C5 C SING Y N 16
D6A C4 C3 SING Y N 17
D6A C C1 DOUB Y N 18
D6A C1 C2 SING Y N 19
D6A C3 C2 DOUB Y N 20
D6A C2 C12 SING N N 21
D6A C12 F SING N N 22
D6A C12 F1 SING N N 23
D6A C4 H1 SING N N 24
D6A C8 H2 SING N N 25
D6A N2 H3 SING N N 26
D6A C9 H5 SING N N 27
D6A C9 H6 SING N N 28
D6A C10 H7 SING N N 29
D6A C11 H8 SING N N 30
D6A C11 H9 SING N N 31
D6A C1 H10 SING N N 32
D6A C3 H11 SING N N 33
D6A C H12 SING N N 34
D6A O1 H13 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
D6A SMILES ACDLabs 12.01 c1cc(C(F)(F)F)ccc1c2noc(n2)C3CC(O)CN3
D6A InChI InChI 1.03 InChI=1S/C13H12F3N3O2/c14-13(15,16)8-3-1-7(2-4-8)11-18-12(21-19-11)10-5-9(20)6-17-10/h1-4,9-10,17,20H,5-6H2/t9-,10-/m1/s1
D6A InChIKey InChI 1.03 BFYYUFJLDXZELT-NXEZZACHSA-N
D6A SMILES_CANONICAL CACTVS 3.385 O[C@H]1CN[C@H](C1)c2onc(n2)c3ccc(cc3)C(F)(F)F
D6A SMILES CACTVS 3.385 O[CH]1CN[CH](C1)c2onc(n2)c3ccc(cc3)C(F)(F)F
D6A SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 c1cc(ccc1c2nc(on2)[C@H]3C[C@H](CN3)O)C(F)(F)F
D6A SMILES "OpenEye OEToolkits" 2.0.6 c1cc(ccc1c2nc(on2)C3CC(CN3)O)C(F)(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
D6A "SYSTEMATIC NAME" ACDLabs 12.01 (3R,5R)-5-{3-[4-(trifluoromethyl)phenyl]-1,2,4-oxadiazol-5-yl}pyrrolidin-3-ol
D6A "SYSTEMATIC NAME" "OpenEye OEToolkits" 2.0.6 (3~{R},5~{R})-5-[3-[4-(trifluoromethyl)phenyl]-1,2,4-oxadiazol-5-yl]pyrrolidin-3-ol
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
D6A 'Create component' 2017-10-20 RCSB
D6A 'Initial release' 2020-04-22 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
D6A C4 C 3.201 -1.661 1
D6A C5 C 4.500 -0.911 2
D6A C6 C 4.500 0.589 3
D6A N1 N 3.287 1.471 4
D6A C7 C 5.250 2.897 5
D6A C8 C 6.132 4.111 6
D6A N2 N 5.668 5.537 7
D6A C9 C 7.632 4.111 8
D6A C10 C 8.095 5.537 9
D6A C11 C 6.882 6.419 10
D6A C12 C 4.500 -5.411 11
D6A F2 F 3.000 -5.411 12
D6A F F 4.500 -6.911 13
D6A F1 F 6.000 -5.411 14
D6A C2 C 4.500 -3.911 15
D6A C1 C 5.799 -3.161 16
D6A C3 C 3.201 -3.161 17
D6A C C 5.799 -1.661 18
D6A O O 3.750 2.897 19
D6A N N 5.713 1.471 20
D6A O1 O 9.522 6.001 21
#
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
D6A C8 C9 SINGLE NONE 1
D6A C8 N2 SINGLE NONE 2
D6A C8 C7 SINGLE BEGINDASH 3
D6A C9 C10 SINGLE NONE 4
D6A N2 C11 SINGLE NONE 5
D6A C7 O SINGLE NONE 6
D6A C7 N DOUBLE NONE 7
D6A O N1 SINGLE NONE 8
D6A N C6 SINGLE NONE 9
D6A C11 C10 SINGLE NONE 10
D6A C10 O1 SINGLE BEGINDASH 11
D6A N1 C6 DOUBLE NONE 12
D6A C6 C5 SINGLE NONE 13
D6A F2 C12 SINGLE NONE 14
D6A C5 C4 DOUBLE NONE 15
D6A C5 C SINGLE NONE 16
D6A C4 C3 SINGLE NONE 17
D6A C C1 DOUBLE NONE 18
D6A C1 C2 SINGLE NONE 19
D6A C3 C2 DOUBLE NONE 20
D6A C2 C12 SINGLE NONE 21
D6A C12 F SINGLE NONE 22
D6A C12 F1 SINGLE NONE 23
#
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
D6A MurckoScaffold S1 scaffold 'c1ccc(-c2noc([C@H]3CCCN3)n2)cc1' InChI=1S/C12H13N3O/c1-2-5-9(6-3-1)11-14-12(16-15-11)10-7-4-8-13-10/h1-3,5-6,10,13H,4,7-8H2/t10-/m1/s1 RJBMVNYIOPXWKS-SNVBAGLBSA-N
D6A isoxadiazole F1 fragment c1ncon1 InChI=1S/C2H2N2O/c1-3-2-5-4-1/h1-2H BBVIDBNAYOIXOE-UHFFFAOYSA-N
D6A phenyl F2 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
D6A Z57791725 F3 fragment Cc1nc(-c2ccccc2)no1 InChI=1S/C9H8N2O/c1-7-10-9(11-12-7)8-5-3-2-4-6-8/h2-6H,1H3 VRRLZUXQTZOCKJ-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
D6A C4 S1 1
D6A C5 S1 1
D6A C6 S1 1
D6A N1 S1 1
D6A C7 S1 1
D6A C8 S1 1
D6A N2 S1 1
D6A C9 S1 1
D6A C10 S1 1
D6A C11 S1 1
D6A C2 S1 1
D6A C1 S1 1
D6A C3 S1 1
D6A C S1 1
D6A O S1 1
D6A N S1 1
D6A N1 F1 1
D6A C6 F1 1
D6A N F1 1
D6A C7 F1 1
D6A O F1 1
D6A C4 F2 1
D6A C5 F2 1
D6A C F2 1
D6A C1 F2 1
D6A C2 F2 1
D6A C3 F2 1
D6A C8 F3 1
D6A C7 F3 1
D6A N F3 1
D6A C6 F3 1
D6A N1 F3 1
D6A O F3 1
D6A C5 F3 1
D6A C4 F3 1
D6A C3 F3 1
D6A C2 F3 1
D6A C1 F3 1
D6A C F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id D6A
_pdbe_chem_comp_rdkit_properties.exactmw 299.088
_pdbe_chem_comp_rdkit_properties.amw 299.252
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 2
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 3
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 21
_pdbe_chem_comp_rdkit_properties.NumAtoms 33
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 8
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.385
_pdbe_chem_comp_rdkit_properties.NumRings 3
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 2
_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 2
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 134.337
_pdbe_chem_comp_rdkit_properties.tpsa 71.180
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.661
_pdbe_chem_comp_rdkit_properties.CrippenMR 64.250
_pdbe_chem_comp_rdkit_properties.chi0v 9.792
_pdbe_chem_comp_rdkit_properties.chi1v 5.276
_pdbe_chem_comp_rdkit_properties.chi2v 2.262
_pdbe_chem_comp_rdkit_properties.chi3v 2.262
_pdbe_chem_comp_rdkit_properties.chi4v 1.359
_pdbe_chem_comp_rdkit_properties.chi0n 21.792
_pdbe_chem_comp_rdkit_properties.chi1n 11.131
_pdbe_chem_comp_rdkit_properties.chi2n 2.262
_pdbe_chem_comp_rdkit_properties.chi3n 2.262
_pdbe_chem_comp_rdkit_properties.chi4n 1.359
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.930
_pdbe_chem_comp_rdkit_properties.kappa1 5.694
_pdbe_chem_comp_rdkit_properties.kappa2 5.119
_pdbe_chem_comp_rdkit_properties.kappa3 2.906
_pdbe_chem_comp_rdkit_properties.Phi 1.388
#
_pdbe_chem_comp_external_mappings.comp_id D6A
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PubChem
_pdbe_chem_comp_external_mappings.resource_id 146020542
#
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
D6A C4 2.982 -1.338 0.786 ETKDGv3 1
D6A C5 2.075 -0.513 0.230 ETKDGv3 2
D6A C6 0.641 -0.871 0.182 ETKDGv3 3
D6A N1 0.160 -1.976 0.655 ETKDGv3 4
D6A C7 -1.446 -0.714 -0.217 ETKDGv3 5
D6A C8 -2.802 -0.271 -0.697 ETKDGv3 6
D6A N2 -2.984 1.177 -0.565 ETKDGv3 7
D6A C9 -3.942 -0.929 0.069 ETKDGv3 8
D6A C10 -5.078 0.082 -0.022 ETKDGv3 9
D6A C11 -4.432 1.381 -0.522 ETKDGv3 10
D6A C12 6.280 0.597 0.369 ETKDGv3 11
D6A F2 6.538 1.117 1.623 ETKDGv3 12
D6A F 6.580 1.554 -0.585 ETKDGv3 13
D6A F1 7.098 -0.499 0.156 ETKDGv3 14
D6A C2 4.829 0.196 0.286 ETKDGv3 15
D6A C1 3.826 1.117 -0.306 ETKDGv3 16
D6A C3 4.411 -0.963 0.826 ETKDGv3 17
D6A C 2.530 0.780 -0.337 ETKDGv3 18
D6A O -1.188 -1.918 0.413 ETKDGv3 19
D6A N -0.362 -0.032 -0.396 ETKDGv3 20
D6A O1 -5.723 0.257 1.216 ETKDGv3 21
D6A H1 2.685 -2.287 1.215 ETKDGv3 22
D6A H2 -2.888 -0.540 -1.774 ETKDGv3 23
D6A H3 -2.603 1.481 0.363 ETKDGv3 24
D6A H5 -3.654 -1.098 1.131 ETKDGv3 25
D6A H6 -4.225 -1.901 -0.390 ETKDGv3 26
D6A H7 -5.828 -0.267 -0.766 ETKDGv3 27
D6A H8 -4.792 1.608 -1.549 ETKDGv3 28
D6A H9 -4.689 2.250 0.125 ETKDGv3 29
D6A H10 4.133 2.071 -0.716 ETKDGv3 30
D6A H11 5.112 -1.638 1.300 ETKDGv3 31
D6A H12 1.816 1.466 -0.775 ETKDGv3 32
D6A H13 -5.058 0.623 1.857 ETKDGv3 33
#