data_F8F
#
_chem_comp.id F8F
_chem_comp.name '(2S,5S)-5-azanyl-3,4,6-tris(oxidanyl)oxane-2-carboxylic acid'
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula 'C6 H11 N O6'
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2020-04-14
_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 193.155
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code F8F
_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 6M5E
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBJ
_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
F8F N N1 N 0 1 N N N N N N -60.208 39.789 16.802 -1.755 1.437 1.330 N F8F 1
F8F C12 C1 C 0 1 N N S N N N -60.306 40.391 15.477 -1.971 0.345 0.371 C12 F8F 2
F8F C13 C2 C 0 1 N N S N N N -59.035 41.197 15.223 -1.329 0.708 -0.971 C13 F8F 3
F8F C14 C3 C 0 1 N N R N N N -58.047 40.457 14.357 0.184 0.852 -0.780 C14 F8F 4
F8F C15 C4 C 0 1 N N S N N N -58.650 40.062 13.026 0.743 -0.451 -0.202 C15 F8F 5
F8F C16 C5 C 0 1 N N S N N N -60.658 39.438 14.305 -1.329 -0.939 0.905 C16 F8F 6
F8F C87 C6 C 0 1 N N N N N N -57.811 40.067 11.754 2.222 -0.297 0.045 C87 F8F 7
F8F O1 O1 O 0 1 N N N N N N -59.893 39.341 13.099 0.083 -0.746 1.030 O1 F8F 8
F8F O24 O2 O 0 1 N N N N N N -56.829 40.786 11.651 3.059 -0.115 -0.988 O24 F8F 9
F8F O25 O3 O 0 1 N N N N N N -58.228 39.227 10.832 2.653 -0.337 1.173 O25 F8F 10
F8F O26 O4 O 0 1 N N N N N N -56.739 40.172 14.840 0.450 1.928 0.122 O26 F8F 11
F8F O27 O5 O 0 1 N N N N N N -58.833 42.538 15.674 -1.595 -0.325 -1.923 O27 F8F 12
F8F H1 H1 H 0 1 N N N N N N -59.978 40.494 17.473 -2.209 2.284 1.021 H1 F8F 13
F8F H2 H2 H 0 1 N N N N N N -61.084 39.372 17.044 -2.067 1.175 2.253 H2 F8F 14
F8F H4 H4 H 0 1 N N N N N N -61.125 41.124 15.522 -3.040 0.187 0.233 H4 F8F 15
F8F H5 H5 H 0 1 N N N N N N -58.571 40.795 16.136 -1.744 1.650 -1.331 H5 F8F 16
F8F H6 H6 H 0 1 N N N N N N -57.695 41.407 13.928 0.655 1.057 -1.741 H6 F8F 17
F8F H7 H7 H 0 1 N N N N N N -59.114 41.042 12.837 0.575 -1.264 -0.909 H7 F8F 18
F8F H8 H8 H 0 1 N N N N N N -60.124 38.596 14.770 -1.753 -1.178 1.881 H8 F8F 19
F8F H10 H10 H 0 1 N N N N N N -56.418 40.643 10.806 3.999 -0.021 -0.780 H10 F8F 20
F8F H11 H11 H 0 1 N N N N N N -56.634 40.543 15.708 1.391 2.076 0.290 H11 F8F 21
F8F H12 H12 H 0 1 N N N N N N -59.573 42.809 16.204 -1.217 -0.160 -2.798 H12 F8F 22
F8F O2 O6 O 0 1 N N N N N N -61.912 38.809 14.458 -1.585 -2.013 -0.002 O2 F8F 23
F8F H3 H3 H 0 1 N N N N N N -62.255 38.993 15.324 -1.207 -2.859 0.274 H3 F8F 24
#
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
F8F O25 C87 DOUB N N 1
F8F O24 C87 SING N N 2
F8F C87 C15 SING N N 3
F8F C15 O1 SING N N 4
F8F C15 C14 SING N N 5
F8F O1 C16 SING N N 6
F8F C16 C12 SING N N 7
F8F C14 O26 SING N N 8
F8F C14 C13 SING N N 9
F8F C13 C12 SING N N 10
F8F C13 O27 SING N N 11
F8F C12 N SING N N 12
F8F N H1 SING N N 13
F8F N H2 SING N N 14
F8F C12 H4 SING N N 15
F8F C13 H5 SING N N 16
F8F C14 H6 SING N N 17
F8F C15 H7 SING N N 18
F8F C16 H8 SING N N 19
F8F O24 H10 SING N N 20
F8F O26 H11 SING N N 21
F8F O27 H12 SING N N 22
F8F C16 O2 SING N N 23
F8F O2 H3 SING N N 24
#
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
F8F InChI InChI 1.03 'InChI=1S/C6H11NO6/c7-1-2(8)3(9)4(5(10)11)13-6(1)12/h1-4,6,8-9,12H,7H2,(H,10,11)/t1-,2-,3+,4-,6-/m0/s1'
F8F InChIKey InChI 1.03 CRIPFXSBMSGPKB-WAXACMCWSA-N
F8F SMILES_CANONICAL CACTVS 3.385 'N[C@@H]1[C@@H](O)O[C@@H]([C@H](O)[C@H]1O)C(O)=O'
F8F SMILES CACTVS 3.385 'N[CH]1[CH](O)O[CH]([CH](O)[CH]1O)C(O)=O'
F8F SMILES_CANONICAL 'OpenEye OEToolkits' 2.0.7 '[C@@H]1(C(C([C@H](OC1O)C(=O)O)O)O)N'
F8F SMILES 'OpenEye OEToolkits' 2.0.7 'C1(C(C(C(OC1O)C(=O)O)O)O)N'
#
_pdbx_chem_comp_identifier.comp_id F8F
_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},5~{S})-5-azanyl-3,4,6-tris(oxidanyl)oxane-2-carboxylic 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
F8F 'Create component' 2020-04-14 PDBJ
F8F 'Initial release' 2020-11-18 RCSB
F8F 'Modify PCM' 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id F8F
_pdbx_chem_comp_pcm.modified_residue_id D4P
_pdbx_chem_comp_pcm.type None
_pdbx_chem_comp_pcm.category 'Covalent chemical 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 C16
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom O4
_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
F8F N N 3.099 1.555 1
F8F C12 C 1.799 0.806 2
F8F C13 C 0.501 1.557 3
F8F C14 C -0.799 0.808 4
F8F C15 C -0.800 -0.692 5
F8F C16 C 1.798 -0.694 6
F8F C87 C -2.100 -1.441 7
F8F O1 O 0.498 -1.443 8
F8F O24 O -2.101 -2.941 9
F8F O25 O -3.398 -0.689 10
F8F O26 O -2.097 1.559 11
F8F O27 O 0.502 3.057 12
F8F O2 O 3.096 -1.445 13
#
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
F8F O25 C87 DOUBLE NONE 1
F8F O24 C87 SINGLE NONE 2
F8F C15 C87 SINGLE BEGINDASH 3
F8F C15 O1 SINGLE NONE 4
F8F C15 C14 SINGLE NONE 5
F8F O1 C16 SINGLE NONE 6
F8F C16 C12 SINGLE NONE 7
F8F C14 O26 SINGLE BEGINDASH 8
F8F C14 C13 SINGLE NONE 9
F8F C13 C12 SINGLE NONE 10
F8F C13 O27 SINGLE BEGINWEDGE 11
F8F C12 N SINGLE BEGINDASH 12
F8F C16 O2 SINGLE BEGINWEDGE 13
#
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
F8F MurckoScaffold S1 scaffold C1CCOCC1 InChI=1S/C5H10O/c1-2-4-6-5-3-1/h1-5H2 DHXVGJBLRPWPCS-UHFFFAOYSA-N
F8F pyranose F1 fragment OC1CCCCO1 InChI=1S/C5H10O2/c6-5-3-1-2-4-7-5/h5-6H,1-4H2 CELWCAITJAEQNL-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
F8F C12 S1 1
F8F C13 S1 1
F8F C14 S1 1
F8F C15 S1 1
F8F C16 S1 1
F8F O1 S1 1
F8F C14 F1 1
F8F C15 F1 1
F8F O1 F1 1
F8F C16 F1 1
F8F C12 F1 1
F8F C13 F1 1
F8F H1 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id F8F
_pdbe_chem_comp_rdkit_properties.exactmw 193.059
_pdbe_chem_comp_rdkit_properties.amw 193.155
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 7
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 6
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 5
_pdbe_chem_comp_rdkit_properties.NumHBD 5
_pdbe_chem_comp_rdkit_properties.NumHBA 7
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 13
_pdbe_chem_comp_rdkit_properties.NumAtoms 24
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 7
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.833
_pdbe_chem_comp_rdkit_properties.NumRings 1
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 1
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 1
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 1
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_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 5
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 89.267
_pdbe_chem_comp_rdkit_properties.tpsa 133.240
_pdbe_chem_comp_rdkit_properties.CrippenClogP -3.163
_pdbe_chem_comp_rdkit_properties.CrippenMR 38.505
_pdbe_chem_comp_rdkit_properties.chi0v 5.897
_pdbe_chem_comp_rdkit_properties.chi1v 2.902
_pdbe_chem_comp_rdkit_properties.chi2v 1.201
_pdbe_chem_comp_rdkit_properties.chi3v 1.201
_pdbe_chem_comp_rdkit_properties.chi4v 0.625
_pdbe_chem_comp_rdkit_properties.chi0n 16.897
_pdbe_chem_comp_rdkit_properties.chi1n 7.930
_pdbe_chem_comp_rdkit_properties.chi2n 1.201
_pdbe_chem_comp_rdkit_properties.chi3n 1.201
_pdbe_chem_comp_rdkit_properties.chi4n 0.625
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.730
_pdbe_chem_comp_rdkit_properties.kappa1 2.878
_pdbe_chem_comp_rdkit_properties.kappa2 3.561
_pdbe_chem_comp_rdkit_properties.kappa3 1.789
_pdbe_chem_comp_rdkit_properties.Phi 0.788
#
#
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
F8F N -2.702 0.106 -0.161 ETKDGv3 1
F8F C12 -1.396 0.190 0.500 ETKDGv3 2
F8F C13 -0.556 -1.075 0.234 ETKDGv3 3
F8F C14 0.860 -0.891 0.811 ETKDGv3 4
F8F C15 1.479 0.465 0.385 ETKDGv3 5
F8F C16 -0.634 1.440 0.012 ETKDGv3 6
F8F C87 2.001 0.529 -1.034 ETKDGv3 7
F8F O1 0.616 1.555 0.674 ETKDGv3 8
F8F O24 2.919 1.518 -1.374 ETKDGv3 9
F8F O25 1.595 -0.272 -1.918 ETKDGv3 10
F8F O26 1.698 -1.947 0.413 ETKDGv3 11
F8F O27 -1.177 -2.178 0.843 ETKDGv3 12
F8F H1 -2.568 -0.094 -1.179 ETKDGv3 13
F8F H2 -3.240 -0.691 0.250 ETKDGv3 14
F8F H4 -1.559 0.290 1.597 ETKDGv3 15
F8F H5 -0.493 -1.238 -0.867 ETKDGv3 16
F8F H6 0.782 -0.876 1.926 ETKDGv3 17
F8F H7 2.376 0.598 1.029 ETKDGv3 18
F8F H8 -0.479 1.385 -1.093 ETKDGv3 19
F8F H10 3.275 1.594 -2.319 ETKDGv3 20
F8F H11 1.516 -2.709 1.023 ETKDGv3 21
F8F H12 -0.875 -2.988 0.354 ETKDGv3 22
F8F O2 -1.385 2.588 0.309 ETKDGv3 23
F8F H3 -2.052 2.700 -0.418 ETKDGv3 24
#