data_NK1
#
_chem_comp.id NK1
_chem_comp.name (1R,5S,6S,7R,8S)-1-THIONIABICYCLO[4.3.0]NONAN-5,7,8-TRIOL
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C8 H15 O3 S"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms ?
_chem_comp.pdbx_formal_charge 1
_chem_comp.pdbx_initial_date 2007-03-08
_chem_comp.pdbx_modified_date 2011-06-04
_chem_comp.pdbx_ambiguous_flag ?
_chem_comp.pdbx_release_status REL
_chem_comp.pdbx_replaced_by ?
_chem_comp.pdbx_replaces ?
_chem_comp.formula_weight 191.268
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code NK1
_chem_comp.pdbx_model_coordinates_details ?
_chem_comp.pdbx_model_coordinates_missing_flag N
_chem_comp.pdbx_ideal_coordinates_details "OpenEye OEToolkits"
_chem_comp.pdbx_ideal_coordinates_missing_flag N
_chem_comp.pdbx_model_coordinates_db_code ?
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
#
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
NK1 O7 O7 O 0 1 N N N N N N 31.855 67.378 5.779 1.676 -3.574 -3.912 O7 NK1 1
NK1 C7 C7 C 0 1 N N N N N N 31.727 66.985 7.153 2.059 -2.420 -3.180 C7 NK1 2
NK1 C6 C6 C 0 1 N N N N N N 30.916 65.706 7.211 1.538 -2.501 -1.747 C6 NK1 3
NK1 C5 C5 C 0 1 N N N N N N 29.473 65.789 6.731 0.024 -2.346 -1.574 C5 NK1 4
NK1 O5 O5 O 0 1 N N N N N N 28.926 64.468 6.811 -0.338 -2.690 -0.233 O5 NK1 5
NK1 C4 C4 C 0 1 N N N N N N 28.562 66.708 7.572 -0.532 -0.954 -1.873 C4 NK1 6
NK1 C3 C3 C 0 1 N N N N N N 28.531 66.340 9.054 0.160 0.150 -1.074 C3 NK1 7
NK1 C2 C2 C 0 1 N N N N N N 29.892 66.439 9.739 1.643 0.215 -1.394 C2 NK1 8
NK1 S1 S1 S 1 1 N N N N N N 31.068 65.310 8.960 2.505 -1.269 -0.781 S1 NK1 9
NK1 C9 C9 C 0 1 N N N N N N 32.679 66.066 9.208 3.869 -1.239 -2.027 C9 NK1 10
NK1 C8 C8 C 0 1 N N N N N N 33.038 66.731 7.871 3.578 -2.329 -3.053 C8 NK1 11
NK1 O8 O8 O 0 1 N N N N N N 33.904 65.857 7.134 4.105 -3.571 -2.586 O8 NK1 12
NK1 HO7 HO7 H 0 1 N N N N N N 31.883 68.326 5.722 2.455 -3.857 -4.420 HO7 NK1 13
NK1 H7 H7 H 0 1 N N N N N N 31.246 67.832 7.665 1.673 -1.544 -3.711 H7 NK1 14
NK1 H6 H6 H 0 1 N N N N N N 31.286 64.940 6.513 1.816 -3.472 -1.316 H6 NK1 15
NK1 H5 H5 H 0 1 N N N N N N 29.500 66.212 5.716 -0.487 -3.071 -2.218 H5 NK1 16
NK1 HO5 HO5 H 0 1 N N N N N N 28.805 64.121 5.935 -0.885 -1.962 0.096 HO5 NK1 17
NK1 H41 1H4 H 0 1 N N N N N N 28.937 67.738 7.482 -1.601 -0.931 -1.627 H41 NK1 18
NK1 H42 2H4 H 0 1 N N N N N N 27.538 66.595 7.186 -0.446 -0.740 -2.945 H42 NK1 19
NK1 H31 1H3 H 0 1 N N N N N N 27.841 67.030 9.563 -0.302 1.111 -1.332 H31 NK1 20
NK1 H32 2H3 H 0 1 N N N N N N 28.210 65.290 9.121 0.000 -0.000 -0.000 H32 NK1 21
NK1 H21 1H2 H 0 1 N N N N N N 30.267 67.469 9.652 1.790 0.344 -2.470 H21 NK1 22
NK1 H22 2H2 H 0 1 N N N N N N 29.781 66.166 10.799 2.100 1.073 -0.892 H22 NK1 23
NK1 H91 1H9 H 0 1 N N N N N N 32.639 66.812 10.015 4.801 -1.425 -1.485 H91 NK1 24
NK1 H92 2H9 H 0 1 N N N N N N 33.433 65.322 9.504 3.918 -0.249 -2.487 H92 NK1 25
NK1 H8 H8 H 0 1 N N N N N N 33.576 67.682 7.998 4.059 -2.125 -4.014 H8 NK1 26
NK1 HO8 HO8 H 0 1 N N N N N N 34.095 66.241 6.286 3.876 -3.630 -1.646 HO8 NK1 27
#
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
NK1 O7 C7 SING N N 1
NK1 O7 HO7 SING N N 2
NK1 C7 C6 SING N N 3
NK1 C7 C8 SING N N 4
NK1 C7 H7 SING N N 5
NK1 C6 C5 SING N N 6
NK1 C6 S1 SING N N 7
NK1 C6 H6 SING N N 8
NK1 C5 O5 SING N N 9
NK1 C5 C4 SING N N 10
NK1 C5 H5 SING N N 11
NK1 O5 HO5 SING N N 12
NK1 C4 C3 SING N N 13
NK1 C4 H41 SING N N 14
NK1 C4 H42 SING N N 15
NK1 C3 C2 SING N N 16
NK1 C3 H31 SING N N 17
NK1 C3 H32 SING N N 18
NK1 C2 S1 SING N N 19
NK1 C2 H21 SING N N 20
NK1 C2 H22 SING N N 21
NK1 S1 C9 SING N N 22
NK1 C9 C8 SING N N 23
NK1 C9 H91 SING N N 24
NK1 C9 H92 SING N N 25
NK1 C8 O8 SING N N 26
NK1 C8 H8 SING N N 27
NK1 O8 HO8 SING N N 28
#
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
NK1 SMILES ACDLabs 10.04 OC1CCC[S+]2C1C(O)C(O)C2
NK1 SMILES_CANONICAL CACTVS 3.341 O[C@H]1CCC[S@+]2C[C@@H](O)[C@@H](O)[C@H]12
NK1 SMILES CACTVS 3.341 O[CH]1CCC[S+]2C[CH](O)[CH](O)[CH]12
NK1 SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 C1C[C@@H]([C@H]2[C@@H]([C@@H](C[S@+]2C1)O)O)O
NK1 SMILES "OpenEye OEToolkits" 1.5.0 C1CC(C2C(C(C[S+]2C1)O)O)O
NK1 InChI InChI 1.03 InChI=1S/C8H15O3S/c9-5-2-1-3-12-4-6(10)7(11)8(5)12/h5-11H,1-4H2/q+1/t5-,6+,7+,8-,12+/m0/s1
NK1 InChIKey InChI 1.03 YXHBFMXISHCSIQ-OZFRBSTCSA-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
NK1 "SYSTEMATIC NAME" ACDLabs 10.04 "(1R,2S,8S,8aS)-1,2,8-trihydroxyoctahydrothieno[1,2-a]thiopyranium (non-preferred name)"
NK1 "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 (1R,2S,4R,8S,8aS)-1,2,3,5,6,7,8,8a-octahydrothieno[1,2-a]thiopyran-4-ium-1,2,8-triol
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
NK1 'Create component' 2007-03-08 RCSB
NK1 'Modify descriptor' 2011-06-04 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
NK1 O7 O -1.745 2.169 1
NK1 C7 C -1.280 0.742 2
NK1 C6 C 0.147 0.280 3
NK1 C5 C 1.445 1.031 4
NK1 O5 O 1.444 2.531 5
NK1 C4 C 2.745 0.282 6
NK1 C3 C 2.746 -1.218 7
NK1 C2 C 1.448 -1.969 8
NK1 S1 S 0.148 -1.220 9
NK1 C9 C -1.278 -1.685 10
NK1 C8 C -2.161 -0.472 11
NK1 O8 O -3.661 -0.473 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
NK1 C7 O7 SINGLE BEGINWEDGE 1
NK1 C7 C6 SINGLE NONE 2
NK1 C7 C8 SINGLE NONE 3
NK1 C6 C5 SINGLE NONE 4
NK1 C6 S1 SINGLE NONE 5
NK1 C5 O5 SINGLE BEGINWEDGE 6
NK1 C5 C4 SINGLE NONE 7
NK1 C4 C3 SINGLE NONE 8
NK1 C3 C2 SINGLE NONE 9
NK1 S1 C2 SINGLE BEGINDASH 10
NK1 S1 C9 SINGLE NONE 11
NK1 C9 C8 SINGLE NONE 12
NK1 C8 O8 SINGLE BEGINWEDGE 13
#
_pdbe_chem_comp_substructure.comp_id NK1
_pdbe_chem_comp_substructure.substructure_name MurckoScaffold
_pdbe_chem_comp_substructure.id S1
_pdbe_chem_comp_substructure.substructure_type scaffold
_pdbe_chem_comp_substructure.substructure_smiles 'C1CC[S@+]2CCC[C@@H]2C1'
_pdbe_chem_comp_substructure.substructure_inchis InChI=1S/C8H15S/c1-2-6-9-7-3-5-8(9)4-1/h8H,1-7H2/q+1/t8-,9+/m0/s1
_pdbe_chem_comp_substructure.substructure_inchikeys QZXHSDYOQIPRDL-DTWKUNHWSA-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
NK1 C7 S1 1
NK1 C6 S1 1
NK1 C5 S1 1
NK1 C4 S1 1
NK1 C3 S1 1
NK1 C2 S1 1
NK1 S1 S1 1
NK1 C9 S1 1
NK1 C8 S1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id NK1
_pdbe_chem_comp_rdkit_properties.exactmw 191.074
_pdbe_chem_comp_rdkit_properties.amw 191.272
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 3
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 3
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 3
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 12
_pdbe_chem_comp_rdkit_properties.NumAtoms 27
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 4
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 0
_pdbe_chem_comp_rdkit_properties.FractionCSP3 1
_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 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 96.091
_pdbe_chem_comp_rdkit_properties.tpsa 60.690
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.137
_pdbe_chem_comp_rdkit_properties.CrippenMR 48.141
_pdbe_chem_comp_rdkit_properties.chi0v 6.449
_pdbe_chem_comp_rdkit_properties.chi1v 4.199
_pdbe_chem_comp_rdkit_properties.chi2v 2.821
_pdbe_chem_comp_rdkit_properties.chi3v 2.821
_pdbe_chem_comp_rdkit_properties.chi4v 2.049
_pdbe_chem_comp_rdkit_properties.chi0n 20.633
_pdbe_chem_comp_rdkit_properties.chi1n 10.199
_pdbe_chem_comp_rdkit_properties.chi2n 1.347
_pdbe_chem_comp_rdkit_properties.chi3n 1.347
_pdbe_chem_comp_rdkit_properties.chi4n 0.848
_pdbe_chem_comp_rdkit_properties.hallKierAlpha 0.230
_pdbe_chem_comp_rdkit_properties.kappa1 1.935
_pdbe_chem_comp_rdkit_properties.kappa2 3.178
_pdbe_chem_comp_rdkit_properties.kappa3 1.267
_pdbe_chem_comp_rdkit_properties.Phi 0.513
#
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
NK1 UniChem PDBe NK1
NK1 UniChem ZINC ZINC000139824259
#
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
NK1 O7 -2.316 1.362 -1.261 ETKDGv3 1
NK1 C7 -1.439 0.291 -1.012 ETKDGv3 2
NK1 C6 -0.450 0.594 0.136 ETKDGv3 3
NK1 C5 0.823 1.333 -0.352 ETKDGv3 4
NK1 O5 0.527 2.678 -0.635 ETKDGv3 5
NK1 C4 1.963 1.237 0.684 ETKDGv3 6
NK1 C3 2.573 -0.183 0.813 ETKDGv3 7
NK1 C2 1.645 -1.340 0.400 ETKDGv3 8
NK1 S1 -0.045 -0.986 0.832 ETKDGv3 9
NK1 C9 -1.192 -1.997 -0.061 ETKDGv3 10
NK1 C8 -2.193 -1.023 -0.694 ETKDGv3 11
NK1 O8 -3.290 -0.804 0.162 ETKDGv3 12
NK1 HO7 -2.771 1.594 -0.410 ETKDGv3 13
NK1 H7 -0.865 0.105 -1.947 ETKDGv3 14
NK1 H6 -0.948 1.183 0.937 ETKDGv3 15
NK1 H5 1.190 0.871 -1.295 ETKDGv3 16
NK1 HO5 0.255 3.112 0.215 ETKDGv3 17
NK1 H41 1.579 1.560 1.677 ETKDGv3 18
NK1 H42 2.773 1.946 0.405 ETKDGv3 19
NK1 H31 3.492 -0.241 0.191 ETKDGv3 20
NK1 H32 2.889 -0.335 1.868 ETKDGv3 21
NK1 H21 1.964 -2.281 0.895 ETKDGv3 22
NK1 H22 1.705 -1.489 -0.699 ETKDGv3 23
NK1 H91 -0.650 -2.554 -0.854 ETKDGv3 24
NK1 H92 -1.693 -2.717 0.620 ETKDGv3 25
NK1 H8 -2.582 -1.461 -1.639 ETKDGv3 26
NK1 HO8 -2.943 -0.454 1.024 ETKDGv3 27
#