data_PF5
#
_chem_comp.id PF5
_chem_comp.name 2,3,4,5,6-PENTAFLUORO-L-PHENYLALANINE
_chem_comp.type 'L-PEPTIDE LINKING'
_chem_comp.pdbx_type ATOMP
_chem_comp.formula 'C9 H6 F5 N O2'
_chem_comp.mon_nstd_parent_comp_id PHE
_chem_comp.pdbx_synonyms 'FLUORINATED PHENYLALANINE'
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2006-09-12
_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 255.141
_chem_comp.one_letter_code F
_chem_comp.three_letter_code PF5
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details ?
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code 2JM0
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
_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_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
PF5 N N N 0 1 N N N Y Y N 3.338 -4.144 -2.024 -0.040 -1.210 0.053 N PF5 1
PF5 CA CA C 0 1 N N S Y N N 3.460 -3.105 -3.087 1.172 -1.709 0.652 CA PF5 2
PF5 CB CB C 0 1 N N N N N N 2.790 -1.824 -2.595 1.484 -0.975 1.962 CB PF5 3
PF5 CG CG C 0 1 Y N N N N N 1.400 -2.185 -2.139 2.940 -1.060 2.353 CG PF5 4
PF5 CD1 CD1 C 0 1 Y N N N N N 1.172 -2.555 -0.810 3.821 -0.086 1.907 CD1 PF5 5
PF5 FD1 FD1 F 0 1 N N N N N N 2.180 -2.509 0.085 3.401 0.927 1.137 FD1 PF5 6
PF5 CD2 CD2 C 0 1 Y N N N N N 0.354 -2.225 -3.068 3.370 -2.109 3.149 CD2 PF5 7
PF5 FD2 FD2 F 0 1 N N N N N N 0.580 -1.883 -4.353 2.514 -3.048 3.578 FD2 PF5 8
PF5 CE1 CE1 C 0 1 Y N N N N N -0.100 -2.980 -0.411 5.166 -0.165 2.268 CE1 PF5 9
PF5 FE1 FE1 F 0 1 N N N N N N -0.317 -3.353 0.866 6.028 0.768 1.845 FE1 PF5 10
PF5 CE2 CE2 C 0 1 Y N N N N N -0.926 -2.617 -2.663 4.715 -2.188 3.510 CE2 PF5 11
PF5 FE2 FE2 F 0 1 N N N N N N -1.941 -2.619 -3.549 5.144 -3.196 4.280 FE2 PF5 12
PF5 CZ CZ C 0 1 Y N N N N N -1.150 -3.011 -1.337 5.613 -1.216 3.069 CZ PF5 13
PF5 FZ FZ F 0 1 N N N N N N -2.374 -3.425 -0.955 6.904 -1.291 3.416 FZ PF5 14
PF5 C C C 0 1 N N N Y N Y 4.928 -2.848 -3.422 1.083 -3.207 0.905 C PF5 15
PF5 O O O 0 1 N N N Y N Y 5.249 -2.300 -4.458 0.040 -3.770 1.222 O PF5 16
PF5 OXT OXT O 0 1 N Y N Y N Y 5.878 -3.327 -2.576 2.247 -3.882 0.744 OXT PF5 17
PF5 H 1HN H 0 1 N N N Y Y N 3.311 -5.051 -2.445 -0.102 -1.155 -0.950 H PF5 18
PF5 H2 2HN H 0 1 N Y N Y Y N 4.125 -4.086 -1.409 -0.715 -0.741 0.634 H2 PF5 19
PF5 HA HA H 0 1 N N N Y N N 2.964 -3.454 -4.005 1.965 -1.558 -0.089 HA PF5 20
PF5 HB2 1HB H 0 1 N N N N N N 3.363 -1.394 -1.760 1.215 0.087 1.879 HB2 PF5 21
PF5 HB3 2HB H 0 1 N N N N N N 2.750 -1.075 -3.400 0.859 -1.368 2.775 HB3 PF5 22
PF5 HXT HOXT H 0 1 N Y N Y N Y 6.740 -3.155 -2.937 2.188 -4.848 0.901 HXT PF5 23
#
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
PF5 N CA SING N N 1
PF5 N H SING N N 2
PF5 N H2 SING N N 3
PF5 CA C SING N N 4
PF5 CA CB SING N N 5
PF5 CA HA SING N N 6
PF5 CB CG SING N N 7
PF5 CB HB2 SING N N 8
PF5 CB HB3 SING N N 9
PF5 CG CD2 SING Y N 10
PF5 CG CD1 DOUB Y N 11
PF5 CD1 CE1 SING Y N 12
PF5 CD1 FD1 SING N N 13
PF5 CD2 FD2 SING N N 14
PF5 CD2 CE2 DOUB Y N 15
PF5 CE1 CZ DOUB Y N 16
PF5 CE1 FE1 SING N N 17
PF5 CE2 FE2 SING N N 18
PF5 CE2 CZ SING Y N 19
PF5 CZ FZ SING N N 20
PF5 C O DOUB N N 21
PF5 C OXT SING N N 22
PF5 OXT HXT SING N N 23
#
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
PF5 SMILES ACDLabs 10.04 'Fc1c(c(F)c(F)c(F)c1F)CC(C(=O)O)N'
PF5 SMILES_CANONICAL CACTVS 3.341 'N[C@@H](Cc1c(F)c(F)c(F)c(F)c1F)C(O)=O'
PF5 SMILES CACTVS 3.341 'N[CH](Cc1c(F)c(F)c(F)c(F)c1F)C(O)=O'
PF5 SMILES_CANONICAL 'OpenEye OEToolkits' 1.5.0 'C(c1c(c(c(c(c1F)F)F)F)F)[C@@H](C(=O)O)N'
PF5 SMILES 'OpenEye OEToolkits' 1.5.0 'C(c1c(c(c(c(c1F)F)F)F)F)C(C(=O)O)N'
PF5 InChI InChI 1.03 'InChI=1S/C9H6F5NO2/c10-4-2(1-3(15)9(16)17)5(11)7(13)8(14)6(4)12/h3H,1,15H2,(H,16,17)/t3-/m0/s1'
PF5 InChIKey InChI 1.03 YYTDJPUFAVPHQA-VKHMYHEASA-N
#
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
PF5 'SYSTEMATIC NAME' ACDLabs 10.04 2,3,4,5,6-pentafluoro-L-phenylalanine
PF5 'SYSTEMATIC NAME' 'OpenEye OEToolkits' 1.5.0 '(2S)-2-amino-3-(2,3,4,5,6-pentafluorophenyl)propanoic 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
PF5 'Create component' 2006-09-12 EBI
PF5 'Modify descriptor' 2011-06-04 RCSB
PF5 'Modify synonyms' 2021-03-01 PDBE
PF5 'Modify backbone' 2023-11-03 PDBE
PF5 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id PF5
_pdbx_chem_comp_synonyms.name 'FLUORINATED PHENYLALANINE'
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id PF5
_pdbx_chem_comp_pcm.modified_residue_id PHE
_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 ?
#
_pdbe_chem_comp_synonyms.comp_id PF5
_pdbe_chem_comp_synonyms.name 'FLUORINATED PHENYLALANINE'
_pdbe_chem_comp_synonyms.provenance wwPDB
_pdbe_chem_comp_synonyms.type ?
#
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
PF5 N N 7.848 2.350 1
PF5 CA C 6.348 2.350 2
PF5 CB C 5.598 1.052 3
PF5 CG C 5.598 -0.449 4
PF5 CD1 C 4.299 -1.198 5
PF5 FD1 F 3.000 -0.449 6
PF5 CD2 C 6.897 -1.198 7
PF5 FD2 F 8.196 -0.449 8
PF5 CE1 C 4.299 -2.699 9
PF5 FE1 F 3.000 -3.449 10
PF5 CE2 C 6.897 -2.699 11
PF5 FE2 F 8.196 -3.449 12
PF5 CZ C 5.598 -3.449 13
PF5 FZ F 5.598 -4.949 14
PF5 C C 5.598 3.650 15
PF5 O O 6.348 4.949 16
PF5 OXT O 4.098 3.650 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
PF5 CA N SINGLE BEGINWEDGE 1
PF5 CA C SINGLE NONE 2
PF5 CA CB SINGLE NONE 3
PF5 CB CG SINGLE NONE 4
PF5 CG CD2 DOUBLE NONE 5
PF5 CG CD1 SINGLE NONE 6
PF5 CD1 CE1 DOUBLE NONE 7
PF5 CD1 FD1 SINGLE NONE 8
PF5 CD2 FD2 SINGLE NONE 9
PF5 CD2 CE2 SINGLE NONE 10
PF5 CE1 CZ SINGLE NONE 11
PF5 CE1 FE1 SINGLE NONE 12
PF5 CE2 FE2 SINGLE NONE 13
PF5 CE2 CZ DOUBLE NONE 14
PF5 CZ FZ SINGLE NONE 15
PF5 C O DOUBLE NONE 16
PF5 C OXT SINGLE 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
PF5 MurckoScaffold S1 scaffold c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-UHFFFAOYSA-N
PF5 peptide F1 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
PF5 phenyl F2 fragment c1ccccc1 InChI=1S/C6H6/c1-2-4-6-5-3-1/h1-6H UHOVQNZJYSORNB-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
PF5 CG S1 1
PF5 CD1 S1 1
PF5 CD2 S1 1
PF5 CE1 S1 1
PF5 CE2 S1 1
PF5 CZ S1 1
PF5 O F1 1
PF5 C F1 1
PF5 CA F1 1
PF5 N F1 1
PF5 CG F2 1
PF5 CD2 F2 1
PF5 CE2 F2 1
PF5 CZ F2 1
PF5 CE1 F2 1
PF5 CD1 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id PF5
_pdbe_chem_comp_rdkit_properties.exactmw 255.032
_pdbe_chem_comp_rdkit_properties.amw 255.142
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 2
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 17
_pdbe_chem_comp_rdkit_properties.NumAtoms 23
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 8
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.222
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 1
_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 1
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 100.282
_pdbe_chem_comp_rdkit_properties.tpsa 63.320
_pdbe_chem_comp_rdkit_properties.CrippenClogP 1.282
_pdbe_chem_comp_rdkit_properties.CrippenMR 45.281
_pdbe_chem_comp_rdkit_properties.chi0v 7.654
_pdbe_chem_comp_rdkit_properties.chi1v 3.827
_pdbe_chem_comp_rdkit_properties.chi2v 1.647
_pdbe_chem_comp_rdkit_properties.chi3v 1.647
_pdbe_chem_comp_rdkit_properties.chi4v 0.884
_pdbe_chem_comp_rdkit_properties.chi0n 13.654
_pdbe_chem_comp_rdkit_properties.chi1n 6.629
_pdbe_chem_comp_rdkit_properties.chi2n 1.647
_pdbe_chem_comp_rdkit_properties.chi3n 1.647
_pdbe_chem_comp_rdkit_properties.chi4n 0.884
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.700
_pdbe_chem_comp_rdkit_properties.kappa1 6.896
_pdbe_chem_comp_rdkit_properties.kappa2 4.659
_pdbe_chem_comp_rdkit_properties.kappa3 2.356
_pdbe_chem_comp_rdkit_properties.Phi 1.890
#
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
PF5 UniChem ZINC ZINC000002515995
PF5 UniChem eMolecules 6283239
PF5 UniChem fdasrs VJJ37GCZ42
PF5 UniChem 'PubChem TPHARMA' 14798780
PF5 UniChem ACTor 34702-59-5
PF5 UniChem 'EPA CompTox Dashboard' DTXSID00375801
PF5 UniChem BRENDA 55026
PF5 UniChem Nikkaji J694.750F
PF5 UniChem SureChEMBL SCHEMBL158168
PF5 UniChem PubChem 2761496
PF5 UniChem PubChem 7015671
#
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
PF5 N -3.086 -0.537 1.083 ETKDGv3 1
PF5 CA -1.810 0.004 0.609 ETKDGv3 2
PF5 CB -0.790 -1.127 0.355 ETKDGv3 3
PF5 CG 0.588 -0.580 0.059 ETKDGv3 4
PF5 CD1 1.459 -0.142 1.182 ETKDGv3 5
PF5 FD1 1.032 -0.263 2.465 ETKDGv3 6
PF5 CD2 1.026 -0.438 -1.209 ETKDGv3 7
PF5 FD2 0.251 -0.805 -2.261 ETKDGv3 8
PF5 CE1 2.670 0.376 0.934 ETKDGv3 9
PF5 FE1 3.463 0.775 1.960 ETKDGv3 10
PF5 CE2 2.365 0.132 -1.474 ETKDGv3 11
PF5 FE2 2.798 0.265 -2.752 ETKDGv3 12
PF5 CZ 3.145 0.518 -0.457 ETKDGv3 13
PF5 FZ 4.372 1.042 -0.700 ETKDGv3 14
PF5 C -2.038 0.822 -0.631 ETKDGv3 15
PF5 O -2.681 0.342 -1.604 ETKDGv3 16
PF5 OXT -1.504 2.104 -0.720 ETKDGv3 17
PF5 H -2.933 -0.981 2.018 ETKDGv3 18
PF5 H2 -3.411 -1.290 0.433 ETKDGv3 19
PF5 HA -1.409 0.677 1.399 ETKDGv3 20
PF5 HB2 -1.144 -1.784 -0.470 ETKDGv3 21
PF5 HB3 -0.728 -1.771 1.259 ETKDGv3 22
PF5 HXT -1.633 2.664 -1.555 ETKDGv3 23
#