data_O0B
#
_chem_comp.id O0B
_chem_comp.name '(2~{S},3~{S})-2-azanyl-5,5,5-tris(fluoranyl)-3-methyl-pentanal'
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula 'C6 H10 F3 N O2'
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2020-01-13
_chem_comp.pdbx_modified_date 2024-09-27
_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 185.144
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code O0B
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag Y
_chem_comp.pdbx_ideal_coordinates_details Corina
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 6TVW
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBE
_chem_comp.pdbx_pcm Y
#
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_n_terminal_atom_flag
_chem_comp_atom.pdbx_backbone_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
O0B C4 C4 C 0 1 N N N N N N -17.514 -6.500 -12.727 -2.254 0.044 -0.051 C4 O0B 1
O0B CA C5 C 0 1 N N S N Y N -15.185 -4.885 -11.400 1.510 0.496 0.613 CA O0B 2
O0B C C6 C 0 1 N N N N Y Y -13.934 -5.014 -10.511 2.721 -0.090 -0.065 C O0B 3
O0B N N1 N 0 1 N N N Y Y N -15.335 -3.484 -11.876 1.516 1.957 0.451 N O0B 4
O0B C3 C3 C 0 1 N N N N N N -16.363 -5.890 -13.453 -0.988 0.514 0.669 C3 O0B 5
O0B C1 C1 C 0 1 N N N N N N -14.587 -7.153 -12.207 0.235 -1.602 0.150 C1 O0B 6
O0B C2 C2 C 0 1 N N S N N N -15.069 -5.797 -12.638 0.242 -0.081 -0.019 C2 O0B 7
O0B F1 F1 F 0 1 N N N N N N -18.512 -6.836 -13.546 -3.367 0.696 0.489 F1 O0B 8
O0B F2 F2 F 0 1 N N N N N N -18.036 -5.649 -11.845 -2.153 0.343 -1.414 F2 O0B 9
O0B F3 F3 F 0 1 N N N N N N -17.191 -7.603 -12.054 -2.397 -1.338 0.113 F3 O0B 10
O0B O O1 O 0 1 N N N N Y Y -13.968 -5.478 -9.329 3.305 0.544 -0.912 O O0B 11
O0B HA H7 H 0 1 N N N N Y N -16.072 -5.178 -10.819 1.531 0.249 1.674 HA O0B 12
O0B H2 H10 H 0 1 N N N Y Y N -15.412 -2.871 -11.090 2.311 2.368 0.917 H2 O0B 13
O0B H H8 H 0 1 N N N Y Y N -14.535 -3.229 -12.420 1.496 2.212 -0.525 H O0B 14
O0B H6 H6 H 0 1 N N N N N N -16.162 -6.497 -14.348 -0.933 1.602 0.634 H6 O0B 15
O0B H5 H5 H 0 1 N N N N N N -16.650 -4.873 -13.757 -1.018 0.186 1.708 H5 O0B 16
O0B H13 H3 H 0 1 N N N N N N -13.659 -7.045 -11.626 1.166 -2.014 -0.238 H13 O0B 17
O0B H11 H1 H 0 1 N N N N Y N -15.355 -7.634 -11.584 0.140 -1.849 1.207 H11 O0B 18
O0B H12 H2 H 0 1 N N N N N N -14.394 -7.773 -13.095 -0.607 -2.024 -0.400 H12 O0B 19
O0B H4 H4 H 0 1 N N N N N N -14.300 -5.361 -13.293 0.220 0.167 -1.080 H4 O0B 20
O0B OXT OXT O 0 1 N Y N N Y Y ? ? ? 3.151 -1.316 0.273 O1 O0B 21
O0B HXT HXT H 0 1 N Y N N Y Y ? ? ? 3.932 -1.650 -0.190 H1 O0B 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
O0B F1 C4 SING N N 1
O0B C3 C4 SING N N 2
O0B C3 C2 SING N N 3
O0B C4 F3 SING N N 4
O0B C4 F2 SING N N 5
O0B C2 C1 SING N N 6
O0B C2 CA SING N N 7
O0B N CA SING N N 8
O0B CA C SING N N 9
O0B C O DOUB N N 10
O0B CA HA SING N N 11
O0B N H2 SING N N 12
O0B N H SING N N 13
O0B C3 H6 SING N N 14
O0B C3 H5 SING N N 15
O0B C1 H13 SING N N 16
O0B C1 H11 SING N N 17
O0B C1 H12 SING N N 18
O0B C2 H4 SING N N 19
O0B C OXT SING N N 20
O0B OXT HXT SING N N 21
#
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
O0B InChI InChI 1.06 'InChI=1S/C6H10F3NO2/c1-3(2-6(7,8)9)4(10)5(11)12/h3-4H,2,10H2,1H3,(H,11,12)/t3-,4-/m0/s1'
O0B InChIKey InChI 1.06 IISHLMOFSAYIEX-IMJSIDKUSA-N
O0B SMILES_CANONICAL CACTVS 3.385 'C[C@@H](CC(F)(F)F)[C@H](N)C(O)=O'
O0B SMILES CACTVS 3.385 'C[CH](CC(F)(F)F)[CH](N)C(O)=O'
O0B SMILES_CANONICAL 'OpenEye OEToolkits' 2.0.7 'C[C@@H](CC(F)(F)F)[C@@H](C(=O)O)N'
O0B SMILES 'OpenEye OEToolkits' 2.0.7 'CC(CC(F)(F)F)C(C(=O)O)N'
#
_pdbx_chem_comp_identifier.comp_id O0B
_pdbx_chem_comp_identifier.type 'SYSTEMATIC NAME'
_pdbx_chem_comp_identifier.program 'OpenEye OEToolkits'
_pdbx_chem_comp_identifier.program_version 2.0.7
_pdbx_chem_comp_identifier.identifier '(2~{S},3~{S})-2-azanyl-5,5,5-tris(fluoranyl)-3-methyl-pentanoic acid'
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
O0B 'Create component' 2020-01-13 PDBE
O0B 'Initial release' 2021-01-27 RCSB
O0B 'Modify backbone' 2023-11-03 PDBE
O0B 'Other modification' 2024-06-28 PDBE
O0B 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id O0B
_pdbx_chem_comp_pcm.modified_residue_id ILE
_pdbx_chem_comp_pcm.type Fluorination
_pdbx_chem_comp_pcm.category 'Named protein modification'
_pdbx_chem_comp_pcm.position 'Amino-acid side chain'
_pdbx_chem_comp_pcm.polypeptide_position 'Any position'
_pdbx_chem_comp_pcm.comp_id_linking_atom ?
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom ?
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ?
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
#
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
O0B C4 C 4.299 -0.750 1
O0B CA C 8.196 0.000 2
O0B C C 8.196 1.500 3
O0B N N 9.495 -0.750 4
O0B C3 C 5.598 0.000 5
O0B C1 C 6.897 -2.250 6
O0B C2 C 6.897 -0.750 7
O0B F1 F 5.049 -2.049 8
O0B F2 F 3.549 0.549 9
O0B F3 F 3.000 -1.500 10
O0B O O 9.495 2.250 11
O0B OXT O 6.897 2.250 12
#
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
O0B F1 C4 SINGLE NONE 1
O0B C3 C4 SINGLE NONE 2
O0B C3 C2 SINGLE NONE 3
O0B C4 F3 SINGLE NONE 4
O0B C4 F2 SINGLE NONE 5
O0B C2 C1 SINGLE BEGINWEDGE 6
O0B C2 CA SINGLE NONE 7
O0B CA N SINGLE BEGINWEDGE 8
O0B CA C SINGLE NONE 9
O0B C O DOUBLE NONE 10
O0B C OXT SINGLE NONE 11
#
_pdbe_chem_comp_substructure.comp_id O0B
_pdbe_chem_comp_substructure.substructure_name peptide
_pdbe_chem_comp_substructure.id F1
_pdbe_chem_comp_substructure.substructure_type fragment
_pdbe_chem_comp_substructure.substructure_smiles NCC=O
_pdbe_chem_comp_substructure.substructure_inchis InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2
_pdbe_chem_comp_substructure.substructure_inchikeys LYIIBVSRGJSHAV-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
O0B O F1 1
O0B C F1 1
O0B CA F1 1
O0B N F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id O0B
_pdbe_chem_comp_rdkit_properties.exactmw 185.066
_pdbe_chem_comp_rdkit_properties.amw 185.145
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 12
_pdbe_chem_comp_rdkit_properties.NumAtoms 22
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 6
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.833
_pdbe_chem_comp_rdkit_properties.NumRings 0
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 0
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_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 2
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 81.609
_pdbe_chem_comp_rdkit_properties.tpsa 63.320
_pdbe_chem_comp_rdkit_properties.CrippenClogP 0.987
_pdbe_chem_comp_rdkit_properties.CrippenMR 35.447
_pdbe_chem_comp_rdkit_properties.chi0v 5.398
_pdbe_chem_comp_rdkit_properties.chi1v 2.449
_pdbe_chem_comp_rdkit_properties.chi2v 0.697
_pdbe_chem_comp_rdkit_properties.chi3v 0.697
_pdbe_chem_comp_rdkit_properties.chi4v 0.303
_pdbe_chem_comp_rdkit_properties.chi0n 15.398
_pdbe_chem_comp_rdkit_properties.chi1n 7.251
_pdbe_chem_comp_rdkit_properties.chi2n 0.697
_pdbe_chem_comp_rdkit_properties.chi3n 0.697
_pdbe_chem_comp_rdkit_properties.chi4n 0.303
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.780
_pdbe_chem_comp_rdkit_properties.kappa1 2.866
_pdbe_chem_comp_rdkit_properties.kappa2 3.750
_pdbe_chem_comp_rdkit_properties.kappa3 4.172
_pdbe_chem_comp_rdkit_properties.Phi 0.896
#
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
O0B UniChem SureChEMBL SCHEMBL3512022
O0B UniChem PubChem 87452334
O0B UniChem Nikkaji J2.955.582F
#
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
O0B C4 2.669 0.280 -0.566 ETKDGv3 1
O0B CA -0.966 0.106 0.960 ETKDGv3 2
O0B C -1.859 0.821 -0.027 ETKDGv3 3
O0B N -1.692 -0.946 1.680 ETKDGv3 4
O0B C3 1.253 0.710 -0.152 ETKDGv3 5
O0B C1 0.048 -1.443 -0.837 ETKDGv3 6
O0B C2 0.334 -0.453 0.310 ETKDGv3 7
O0B F1 3.219 -0.570 0.377 ETKDGv3 8
O0B F2 2.648 -0.349 -1.797 ETKDGv3 9
O0B F3 3.471 1.403 -0.668 ETKDGv3 10
O0B O -2.639 0.174 -0.777 ETKDGv3 11
O0B HA -0.655 0.857 1.722 ETKDGv3 12
O0B H2 -2.424 -0.494 2.277 ETKDGv3 13
O0B H -2.197 -1.569 1.010 ETKDGv3 14
O0B H6 1.359 1.434 0.685 ETKDGv3 15
O0B H5 0.782 1.254 -0.999 ETKDGv3 16
O0B H13 0.973 -1.989 -1.114 ETKDGv3 17
O0B H11 -0.337 -0.912 -1.734 ETKDGv3 18
O0B H12 -0.687 -2.213 -0.531 ETKDGv3 19
O0B H4 0.869 -1.015 1.108 ETKDGv3 20
O0B OXT -1.795 2.207 -0.132 ETKDGv3 21
O0B HXT -2.375 2.706 -0.797 ETKDGv3 22
#