data_5NF
#
_chem_comp.id 5NF
_chem_comp.name (3S,4S,5S,8S)-8-[(2S)-butan-2-yl]-3-methyl-3,4-bis(oxidanyl)-1-oxa-7,10-diazaspiro[4.5]decane-6,9-dione
_chem_comp.type non-polymer
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C12 H20 N2 O5"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2021-08-23
_chem_comp.pdbx_modified_date 2023-02-10
_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 272.298
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code 5NF
_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 7V34
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site PDBJ
#
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
5NF C1 C1 C 0 1 N N N N N N 39.161 40.451 69.624 -2.063 -1.217 -1.210 C1 5NF 1
5NF C2 C2 C 0 1 N N S N N N 40.475 41.224 69.681 -3.084 -0.474 -0.319 C2 5NF 2
5NF C3 C3 C 0 1 N N S N N N 40.157 42.415 70.716 -2.217 0.498 0.514 C3 5NF 3
5NF C4 C4 C 0 1 N N S N N N 38.685 42.146 71.187 -0.779 0.229 0.025 C4 5NF 4
5NF C5 C5 C 0 1 N N N N N N 37.554 43.010 70.553 -0.115 -0.768 0.923 C5 5NF 5
5NF C6 C6 C 0 1 N N N N N N 37.455 42.531 73.362 1.251 1.570 0.312 C6 5NF 6
5NF C10 C7 C 0 1 N N N N N N 35.445 40.556 72.280 3.727 -1.332 0.151 C10 5NF 7
5NF C11 C8 C 0 1 N N N N N N 34.489 39.433 72.696 4.504 -1.935 -1.020 C11 5NF 8
5NF C12 C9 C 0 1 N N N N N N 40.925 41.681 68.278 -3.817 -1.459 0.593 C12 5NF 9
5NF C7 C10 C 0 1 N N S N N N 36.137 42.996 72.673 2.043 0.395 0.802 C7 5NF 10
5NF C8 C11 C 0 1 N N S N N N 35.027 41.924 72.845 2.914 -0.131 -0.339 C8 5NF 11
5NF C9 C12 C 0 1 N N N N N N 33.715 42.395 72.151 3.866 0.972 -0.805 C9 5NF 12
5NF N1 N1 N 0 1 N N N N N N 38.549 42.164 72.619 -0.036 1.478 -0.040 N1 5NF 13
5NF N2 N2 N 0 1 N N N N N N 36.429 43.358 71.283 1.173 -0.676 1.270 N2 5NF 14
5NF O1 O1 O 0 1 N N N N N N 41.446 40.424 70.232 -4.016 0.251 -1.123 O1 5NF 15
5NF O2 O2 O 0 1 N N N N N N 40.971 42.347 71.864 -2.591 1.852 0.252 O2 5NF 16
5NF O3 O3 O 0 1 N N N N N N 38.381 40.835 70.717 -0.930 -0.324 -1.298 O3 5NF 17
5NF O4 O4 O 0 1 N N N N N N 37.652 43.397 69.384 -0.770 -1.695 1.351 O4 5NF 18
5NF O5 O5 O 0 1 N N N N N N 37.586 42.461 74.571 1.800 2.649 0.233 O5 5NF 19
5NF H1 H1 H 0 1 N N N N N N 38.632 40.685 68.688 -1.770 -2.158 -0.746 H1 5NF 20
5NF H2 H2 H 0 1 N N N N N N 39.362 39.371 69.671 -2.483 -1.395 -2.200 H2 5NF 21
5NF H3 H3 H 0 1 N N N N N N 40.224 43.385 70.202 -2.308 0.275 1.577 H3 5NF 22
5NF H4 H4 H 0 1 N N N N N N 36.453 40.315 72.648 3.053 -2.082 0.565 H4 5NF 23
5NF H5 H5 H 0 1 N N N N N N 35.460 40.618 71.182 4.426 -1.007 0.922 H5 5NF 24
5NF H6 H6 H 0 1 N N N N N N 34.833 38.480 72.267 3.805 -2.260 -1.791 H6 5NF 25
5NF H7 H7 H 0 1 N N N N N N 34.470 39.355 73.793 5.178 -1.185 -1.434 H7 5NF 26
5NF H8 H8 H 0 1 N N N N N N 33.477 39.657 72.327 5.082 -2.790 -0.671 H8 5NF 27
5NF H9 H9 H 0 1 N N N N N N 41.873 42.233 68.358 -3.093 -1.988 1.213 H9 5NF 28
5NF H10 H10 H 0 1 N N N N N N 41.067 40.801 67.634 -4.513 -0.915 1.231 H10 5NF 29
5NF H11 H11 H 0 1 N N N N N N 40.156 42.335 67.841 -4.367 -2.177 -0.015 H11 5NF 30
5NF H12 H12 H 0 1 N N N N N N 35.799 43.900 73.200 2.685 0.715 1.623 H12 5NF 31
5NF H13 H13 H 0 1 N N N N N N 34.824 41.808 73.920 2.279 -0.438 -1.170 H13 5NF 32
5NF H14 H14 H 0 1 N N N N N N 33.417 43.373 72.555 4.487 0.597 -1.618 H14 5NF 33
5NF H15 H15 H 0 1 N N N N N N 33.884 42.482 71.068 3.287 1.827 -1.154 H15 5NF 34
5NF H16 H16 H 0 1 N N N N N N 32.917 41.662 72.339 4.502 1.279 0.026 H16 5NF 35
5NF H17 H17 H 0 1 N N N N N N 39.352 41.873 73.138 -0.492 2.275 -0.352 H17 5NF 36
5NF H18 H18 H 0 1 N N N N N N 35.744 43.915 70.812 1.545 -1.351 1.860 H18 5NF 37
5NF H19 H19 H 0 1 N N N N N N 41.171 40.141 71.096 -4.545 -0.306 -1.711 H19 5NF 38
5NF H20 H20 H 0 1 N N N N N N 40.755 43.064 72.449 -3.506 2.060 0.484 H20 5NF 39
#
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
5NF C12 C2 SING N N 1
5NF O4 C5 DOUB N N 2
5NF C1 C2 SING N N 3
5NF C1 O3 SING N N 4
5NF C2 O1 SING N N 5
5NF C2 C3 SING N N 6
5NF C5 C4 SING N N 7
5NF C5 N2 SING N N 8
5NF C3 C4 SING N N 9
5NF C3 O2 SING N N 10
5NF O3 C4 SING N N 11
5NF C4 N1 SING N N 12
5NF N2 C7 SING N N 13
5NF C9 C8 SING N N 14
5NF C10 C11 SING N N 15
5NF C10 C8 SING N N 16
5NF N1 C6 SING N N 17
5NF C7 C8 SING N N 18
5NF C7 C6 SING N N 19
5NF C6 O5 DOUB N N 20
5NF C1 H1 SING N N 21
5NF C1 H2 SING N N 22
5NF C3 H3 SING N N 23
5NF C10 H4 SING N N 24
5NF C10 H5 SING N N 25
5NF C11 H6 SING N N 26
5NF C11 H7 SING N N 27
5NF C11 H8 SING N N 28
5NF C12 H9 SING N N 29
5NF C12 H10 SING N N 30
5NF C12 H11 SING N N 31
5NF C7 H12 SING N N 32
5NF C8 H13 SING N N 33
5NF C9 H14 SING N N 34
5NF C9 H15 SING N N 35
5NF C9 H16 SING N N 36
5NF N1 H17 SING N N 37
5NF N2 H18 SING N N 38
5NF O1 H19 SING N N 39
5NF O2 H20 SING N N 40
#
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
5NF InChI InChI 1.03 InChI=1S/C12H20N2O5/c1-4-6(2)7-8(15)14-12(10(17)13-7)9(16)11(3,18)5-19-12/h6-7,9,16,18H,4-5H2,1-3H3,(H,13,17)(H,14,15)/t6-,7-,9-,11-,12-/m0/s1
5NF InChIKey InChI 1.03 AXTVENSNWFMLLA-USYUNJQESA-N
5NF SMILES_CANONICAL CACTVS 3.385 CC[C@H](C)[C@@H]1NC(=O)[C@@]2(NC1=O)OC[C@](C)(O)[C@@H]2O
5NF SMILES CACTVS 3.385 CC[CH](C)[CH]1NC(=O)[C]2(NC1=O)OC[C](C)(O)[CH]2O
5NF SMILES_CANONICAL "OpenEye OEToolkits" 2.0.7 CC[C@H](C)[C@H]1C(=O)N[C@]2([C@H]([C@@](CO2)(C)O)O)C(=O)N1
5NF SMILES "OpenEye OEToolkits" 2.0.7 CCC(C)C1C(=O)NC2(C(C(CO2)(C)O)O)C(=O)N1
#
_pdbx_chem_comp_identifier.comp_id 5NF
_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
(3~{S},4~{S},5~{S},8~{S})-8-[(2~{S})-butan-2-yl]-3-methyl-3,4-bis(oxidanyl)-1-oxa-7,10-diazaspiro[4.5]decane-6,9-dione
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
5NF 'Create component' 2021-08-23 PDBJ
5NF 'Initial release' 2023-02-15 RCSB
#
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
5NF C1 C 12.058 -1.026 1
5NF C2 C 12.058 0.474 2
5NF C3 C 10.632 0.938 3
5NF C4 C 9.750 -0.276 4
5NF C5 C 9.000 -1.575 5
5NF C6 C 7.500 1.023 6
5NF C10 C 4.500 -1.575 7
5NF C11 C 3.000 -1.575 8
5NF C12 C 13.558 0.474 9
5NF C7 C 6.750 -0.276 10
5NF C8 C 5.250 -0.276 11
5NF C9 C 4.500 1.023 12
5NF N1 N 9.000 1.023 13
5NF N2 N 7.500 -1.575 14
5NF O1 O 12.522 1.901 15
5NF O2 O 10.684 2.437 16
5NF O3 O 10.632 -1.489 17
5NF O4 O 9.750 -2.874 18
5NF O5 O 6.750 2.322 19
#
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
5NF C2 C12 SINGLE BEGINDASH 1
5NF O4 C5 DOUBLE NONE 2
5NF C1 C2 SINGLE NONE 3
5NF C1 O3 SINGLE NONE 4
5NF C2 O1 SINGLE NONE 5
5NF C2 C3 SINGLE NONE 6
5NF C5 C4 SINGLE NONE 7
5NF C5 N2 SINGLE NONE 8
5NF C3 C4 SINGLE NONE 9
5NF C3 O2 SINGLE BEGINWEDGE 10
5NF O3 C4 SINGLE NONE 11
5NF C4 N1 SINGLE BEGINWEDGE 12
5NF C7 N2 SINGLE BEGINWEDGE 13
5NF C8 C9 SINGLE BEGINDASH 14
5NF C10 C11 SINGLE NONE 15
5NF C10 C8 SINGLE NONE 16
5NF N1 C6 SINGLE NONE 17
5NF C7 C8 SINGLE NONE 18
5NF C7 C6 SINGLE NONE 19
5NF C6 O5 DOUBLE NONE 20
#
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
5NF MurckoScaffold S1 scaffold 'O=C1CNC(=O)[C@@]2(CCCO2)N1' InChI=1S/C7H10N2O3/c10-5-4-8-6(11)7(9-5)2-1-3-12-7/h1-4H2,(H,8,11)(H,9,10)/t7-/m0/s1 LEMBZAGMBZLGRU-ZETCQYMHSA-N
5NF amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
5NF peptide F2 fragment NCC=O InChI=1S/C2H5NO/c3-1-2-4/h2H,1,3H2 LYIIBVSRGJSHAV-UHFFFAOYSA-N
5NF piperazine F3 fragment C1CNCCN1 InChI=1S/C4H10N2/c1-2-6-4-3-5-1/h5-6H,1-4H2 GLUUGHFHXGJENI-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
5NF C1 S1 1
5NF C2 S1 1
5NF C3 S1 1
5NF C4 S1 1
5NF C5 S1 1
5NF C6 S1 1
5NF C7 S1 1
5NF N1 S1 1
5NF N2 S1 1
5NF O3 S1 1
5NF O4 S1 1
5NF O5 S1 1
5NF N1 F1 1
5NF C6 F1 1
5NF O5 F1 1
5NF C7 F1 1
5NF N2 F1 2
5NF C5 F1 2
5NF O4 F1 2
5NF C4 F1 2
5NF O4 F2 1
5NF C5 F2 1
5NF C4 F2 1
5NF N1 F2 1
5NF O5 F2 2
5NF C6 F2 2
5NF C7 F2 2
5NF N2 F2 2
5NF N1 F3 1
5NF C4 F3 1
5NF C5 F3 1
5NF N2 F3 1
5NF C7 F3 1
5NF C6 F3 1
#
_pdbe_chem_comp_rdkit_properties.comp_id 5NF
_pdbe_chem_comp_rdkit_properties.exactmw 272.137
_pdbe_chem_comp_rdkit_properties.amw 272.301
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 7
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 4
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 7
_pdbe_chem_comp_rdkit_properties.NumHBD 4
_pdbe_chem_comp_rdkit_properties.NumHBA 5
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 19
_pdbe_chem_comp_rdkit_properties.NumAtoms 39
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 7
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 2
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.833
_pdbe_chem_comp_rdkit_properties.NumRings 2
_pdbe_chem_comp_rdkit_properties.NumAromaticRings 0
_pdbe_chem_comp_rdkit_properties.NumAliphaticRings 2
_pdbe_chem_comp_rdkit_properties.NumSaturatedRings 2
_pdbe_chem_comp_rdkit_properties.NumHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAromaticHeterocycles 0
_pdbe_chem_comp_rdkit_properties.NumSaturatedHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumAliphaticHeterocycles 2
_pdbe_chem_comp_rdkit_properties.NumSpiroAtoms 1
_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 139.256
_pdbe_chem_comp_rdkit_properties.tpsa 107.890
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.514
_pdbe_chem_comp_rdkit_properties.CrippenMR 64.842
_pdbe_chem_comp_rdkit_properties.chi0v 8.936
_pdbe_chem_comp_rdkit_properties.chi1v 4.619
_pdbe_chem_comp_rdkit_properties.chi2v 2.297
_pdbe_chem_comp_rdkit_properties.chi3v 2.297
_pdbe_chem_comp_rdkit_properties.chi4v 1.382
_pdbe_chem_comp_rdkit_properties.chi0n 28.936
_pdbe_chem_comp_rdkit_properties.chi1n 14.330
_pdbe_chem_comp_rdkit_properties.chi2n 2.297
_pdbe_chem_comp_rdkit_properties.chi3n 2.297
_pdbe_chem_comp_rdkit_properties.chi4n 1.382
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.180
_pdbe_chem_comp_rdkit_properties.kappa1 3.345
_pdbe_chem_comp_rdkit_properties.kappa2 4.432
_pdbe_chem_comp_rdkit_properties.kappa3 2.015
_pdbe_chem_comp_rdkit_properties.Phi 0.780
#
_pdbe_chem_comp_external_mappings.comp_id 5NF
_pdbe_chem_comp_external_mappings.source UniChem
_pdbe_chem_comp_external_mappings.resource PDBe
_pdbe_chem_comp_external_mappings.resource_id 5NF
#
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
5NF C1 2.419 -0.633 -1.443 ETKDGv3 1
5NF C2 3.392 -0.242 -0.336 ETKDGv3 2
5NF C3 2.572 0.784 0.423 ETKDGv3 3
5NF C4 1.124 0.283 0.208 ETKDGv3 4
5NF C5 0.161 1.445 0.039 ETKDGv3 5
5NF C6 -0.641 -0.640 1.806 ETKDGv3 6
5NF C10 -3.350 0.213 -0.884 ETKDGv3 7
5NF C11 -4.539 0.789 -0.109 ETKDGv3 8
5NF C12 4.702 0.338 -0.906 ETKDGv3 9
5NF C7 -1.720 0.160 1.134 ETKDGv3 10
5NF C8 -2.378 -0.640 -0.028 ETKDGv3 11
5NF C9 -3.070 -1.919 0.481 ETKDGv3 12
5NF N1 0.710 -0.571 1.335 ETKDGv3 13
5NF N2 -1.140 1.407 0.637 ETKDGv3 14
5NF O1 3.657 -1.380 0.454 ETKDGv3 15
5NF O2 2.931 0.848 1.780 ETKDGv3 16
5NF O3 1.097 -0.497 -0.971 ETKDGv3 17
5NF O4 0.472 2.430 -0.685 ETKDGv3 18
5NF O5 -0.926 -1.391 2.778 ETKDGv3 19
5NF H1 2.592 -1.681 -1.771 ETKDGv3 20
5NF H2 2.537 0.025 -2.332 ETKDGv3 21
5NF H3 2.730 1.784 -0.046 ETKDGv3 22
5NF H4 -2.794 1.049 -1.359 ETKDGv3 23
5NF H5 -3.743 -0.410 -1.717 ETKDGv3 24
5NF H6 -5.151 -0.021 0.339 ETKDGv3 25
5NF H7 -5.186 1.361 -0.807 ETKDGv3 26
5NF H8 -4.198 1.482 0.686 ETKDGv3 27
5NF H9 4.500 1.198 -1.581 ETKDGv3 28
5NF H10 5.357 0.689 -0.081 ETKDGv3 29
5NF H11 5.242 -0.443 -1.482 ETKDGv3 30
5NF H12 -2.492 0.410 1.895 ETKDGv3 31
5NF H13 -1.568 -0.969 -0.717 ETKDGv3 32
5NF H14 -3.773 -1.689 1.308 ETKDGv3 33
5NF H15 -2.316 -2.645 0.850 ETKDGv3 34
5NF H16 -3.629 -2.413 -0.342 ETKDGv3 35
5NF H17 1.389 -1.261 1.726 ETKDGv3 36
5NF H18 -1.739 2.262 0.597 ETKDGv3 37
5NF H19 4.335 -1.129 1.136 ETKDGv3 38
5NF H20 2.434 1.617 2.164 ETKDGv3 39
#