data_IF7
#
_chem_comp.id IF7
_chem_comp.name (3S,4S,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)piperidin-2-one
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C6 H11 N O4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms "ISO-GALACTO-FAGOMINE LACTAM"
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2015-03-17
_chem_comp.pdbx_modified_date 2020-06-17
_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 161.156
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code IF7
_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 4UFJ
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
#
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
IF7 O O O 0 1 N N N N N N 75.928 90.855 19.724 -2.638 -1.259 -0.132 O IF7 1
IF7 C2 C2 C 0 1 N N N N N N 76.986 90.292 19.427 -1.505 -0.826 -0.117 C2 IF7 2
IF7 C3 C3 C 0 1 N N S N N N 78.082 90.315 20.484 -1.260 0.544 -0.681 C3 IF7 3
IF7 O3 O3 O 0 1 N N N N N N 77.527 90.109 21.773 -2.303 1.425 -0.258 O3 IF7 4
IF7 C4 C4 C 0 1 N N S N N N 79.166 89.279 20.201 0.087 1.077 -0.188 C4 IF7 5
IF7 O2 O2 O 0 1 N N N N N N 78.683 87.981 20.531 0.001 1.390 1.203 O2 IF7 6
IF7 C5 C5 C 0 1 N N R N N N 79.599 89.338 18.736 1.148 -0.008 -0.409 C5 IF7 7
IF7 C6 C6 C 0 1 N N N N N N 80.710 88.355 18.433 2.534 0.558 -0.095 C6 IF7 8
IF7 O1 O1 O 0 1 N N N N N N 81.202 88.540 17.121 3.530 -0.417 -0.412 O1 IF7 9
IF7 C1 C1 C 0 1 N N N N N N 78.403 89.037 17.822 0.850 -1.181 0.526 C1 IF7 10
IF7 N N N 0 1 N N N N N N 77.176 89.729 18.241 -0.544 -1.590 0.405 N IF7 11
IF7 H3 H3 H 0 1 N N N N N N 78.555 91.308 20.452 -1.251 0.490 -1.770 H3 IF7 12
IF7 H H H 0 1 N N N N N N 76.426 89.779 17.581 -0.788 -2.474 0.722 H IF7 13
IF7 HA HA H 0 1 N N N N N N 76.592 90.273 21.745 -3.187 1.153 -0.541 HA IF7 14
IF7 H4 H4 H 0 1 N N N N N N 80.039 89.516 20.826 0.355 1.972 -0.750 H4 IF7 15
IF7 H2 H2 H 0 1 N N N N N N 79.359 87.337 20.354 -0.664 2.060 1.415 H2 IF7 16
IF7 H5 H5 H 0 1 N N N N N N 79.957 90.355 18.518 1.116 -0.346 -1.445 H5 IF7 17
IF7 H61C H61C H 0 0 N N N N N N 81.530 88.506 19.150 2.703 1.456 -0.690 H61C IF7 18
IF7 H62C H62C H 0 0 N N N N N N 80.321 87.331 18.531 2.594 0.807 0.964 H62C IF7 19
IF7 H11C H11C H 0 0 N N N N N N 78.654 89.355 16.799 1.497 -2.020 0.269 H11C IF7 20
IF7 H12C H12C H 0 0 N N N N N N 78.216 87.953 17.833 1.045 -0.881 1.555 H12C IF7 21
IF7 H1 H1 H 0 1 N N N N N N 81.897 87.915 16.952 4.435 -0.126 -0.238 H1 IF7 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
IF7 O C2 DOUB N N 1
IF7 C2 C3 SING N N 2
IF7 C2 N SING N N 3
IF7 C3 O3 SING N N 4
IF7 C3 C4 SING N N 5
IF7 C4 O2 SING N N 6
IF7 C4 C5 SING N N 7
IF7 C5 C6 SING N N 8
IF7 C5 C1 SING N N 9
IF7 C6 O1 SING N N 10
IF7 C1 N SING N N 11
IF7 C3 H3 SING N N 12
IF7 N H SING N N 13
IF7 O3 HA SING N N 14
IF7 C4 H4 SING N N 15
IF7 O2 H2 SING N N 16
IF7 C5 H5 SING N N 17
IF7 C6 H61C SING N N 18
IF7 C6 H62C SING N N 19
IF7 C1 H11C SING N N 20
IF7 C1 H12C SING N N 21
IF7 O1 H1 SING N N 22
#
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
IF7 InChI InChI 1.03 InChI=1S/C6H11NO4/c8-2-3-1-7-6(11)5(10)4(3)9/h3-5,8-10H,1-2H2,(H,7,11)/t3-,4+,5+/m1/s1
IF7 InChIKey InChI 1.03 ARBXEMIAJIJEQI-WISUUJSJSA-N
IF7 SMILES_CANONICAL CACTVS 3.385 OC[C@H]1CNC(=O)[C@@H](O)[C@H]1O
IF7 SMILES CACTVS 3.385 OC[CH]1CNC(=O)[CH](O)[CH]1O
IF7 SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 C1[C@@H]([C@@H]([C@@H](C(=O)N1)O)O)CO
IF7 SMILES "OpenEye OEToolkits" 1.7.6 C1C(C(C(C(=O)N1)O)O)CO
#
_pdbx_chem_comp_identifier.comp_id IF7
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 1.7.6
_pdbx_chem_comp_identifier.identifier (3S,4S,5R)-5-(hydroxymethyl)-3,4-bis(oxidanyl)piperidin-2-one
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
IF7 'Create component' 2015-03-17 EBI
IF7 'Initial release' 2015-03-25 RCSB
IF7 'Other modification' 2016-11-01 EBI
IF7 'Modify synonyms' 2020-06-05 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id IF7
_pdbx_chem_comp_synonyms.name "ISO-GALACTO-FAGOMINE LACTAM"
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_synonyms.comp_id IF7
_pdbe_chem_comp_synonyms.name 'ISO-GALACTO-FAGOMINE LACTAM'
_pdbe_chem_comp_synonyms.provenance wwPDB
_pdbe_chem_comp_synonyms.type ?
#
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
IF7 O O 10.301 -2.018 1
IF7 C2 C 9.002 -1.268 2
IF7 C3 C 9.002 0.233 3
IF7 O3 O 10.301 0.983 4
IF7 C4 C 7.702 0.983 5
IF7 O2 O 7.702 2.482 6
IF7 C5 C 6.404 0.233 7
IF7 C6 C 5.104 0.983 8
IF7 O1 O 3.805 0.233 9
IF7 C1 C 6.404 -1.268 10
IF7 N N 7.702 -2.018 11
#
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
IF7 O C2 DOUBLE NONE 1
IF7 C2 C3 SINGLE NONE 2
IF7 C2 N SINGLE NONE 3
IF7 C3 O3 SINGLE BEGINDASH 4
IF7 C3 C4 SINGLE NONE 5
IF7 C4 O2 SINGLE BEGINDASH 6
IF7 C4 C5 SINGLE NONE 7
IF7 C5 C6 SINGLE BEGINDASH 8
IF7 C5 C1 SINGLE NONE 9
IF7 C6 O1 SINGLE NONE 10
IF7 C1 N SINGLE NONE 11
#
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
IF7 MurckoScaffold S1 scaffold O=C1CCCCN1 InChI=1S/C5H9NO/c7-5-3-1-2-4-6-5/h1-4H2,(H,6,7) XUWHAWMETYGRKB-UHFFFAOYSA-N
IF7 amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-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
IF7 O S1 1
IF7 C2 S1 1
IF7 C3 S1 1
IF7 C4 S1 1
IF7 C5 S1 1
IF7 C1 S1 1
IF7 N S1 1
IF7 N F1 1
IF7 C2 F1 1
IF7 O F1 1
IF7 C3 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id IF7
_pdbe_chem_comp_rdkit_properties.exactmw 161.069
_pdbe_chem_comp_rdkit_properties.amw 161.157
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 5
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 11
_pdbe_chem_comp_rdkit_properties.NumAtoms 22
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 5
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_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 3
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 79.425
_pdbe_chem_comp_rdkit_properties.tpsa 89.790
_pdbe_chem_comp_rdkit_properties.CrippenClogP -2.554
_pdbe_chem_comp_rdkit_properties.CrippenMR 35.599
_pdbe_chem_comp_rdkit_properties.chi0v 5.080
_pdbe_chem_comp_rdkit_properties.chi1v 2.514
_pdbe_chem_comp_rdkit_properties.chi2v 0.999
_pdbe_chem_comp_rdkit_properties.chi3v 0.999
_pdbe_chem_comp_rdkit_properties.chi4v 0.488
_pdbe_chem_comp_rdkit_properties.chi0n 16.080
_pdbe_chem_comp_rdkit_properties.chi1n 7.686
_pdbe_chem_comp_rdkit_properties.chi2n 0.999
_pdbe_chem_comp_rdkit_properties.chi3n 0.999
_pdbe_chem_comp_rdkit_properties.chi4n 0.488
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.650
_pdbe_chem_comp_rdkit_properties.kappa1 1.985
_pdbe_chem_comp_rdkit_properties.kappa2 3.166
_pdbe_chem_comp_rdkit_properties.kappa3 1.500
_pdbe_chem_comp_rdkit_properties.Phi 0.571
#
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
IF7 UniChem PDBe IF7
IF7 UniChem 'PubChem TPHARMA' 15339498
IF7 UniChem PubChem 10329574
IF7 UniChem Nikkaji J1.571.321F
#
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
IF7 O 3.169 1.173 -0.131 ETKDGv3 1
IF7 C2 1.980 0.769 -0.238 ETKDGv3 2
IF7 C3 1.708 -0.673 -0.583 ETKDGv3 3
IF7 O3 2.690 -1.529 -0.050 ETKDGv3 4
IF7 C4 0.291 -1.115 -0.151 ETKDGv3 5
IF7 O2 0.212 -1.368 1.233 ETKDGv3 6
IF7 C5 -0.768 -0.080 -0.602 ETKDGv3 7
IF7 C6 -2.192 -0.569 -0.274 ETKDGv3 8
IF7 O1 -3.151 0.270 -0.864 ETKDGv3 9
IF7 C1 -0.494 1.306 0.020 ETKDGv3 10
IF7 N 0.904 1.711 -0.135 ETKDGv3 11
IF7 H3 1.764 -0.752 -1.691 ETKDGv3 12
IF7 H 1.140 2.715 0.034 ETKDGv3 13
IF7 HA 2.744 -1.361 0.927 ETKDGv3 14
IF7 H4 0.078 -2.074 -0.673 ETKDGv3 15
IF7 H2 0.543 -0.568 1.716 ETKDGv3 16
IF7 H5 -0.694 0.021 -1.709 ETKDGv3 17
IF7 H61C -2.344 -0.634 0.828 ETKDGv3 18
IF7 H62C -2.333 -1.590 -0.688 ETKDGv3 19
IF7 H11C -1.138 2.064 -0.476 ETKDGv3 20
IF7 H12C -0.749 1.305 1.101 ETKDGv3 21
IF7 H1 -3.360 0.979 -0.202 ETKDGv3 22
#