data_SKD
#
_chem_comp.id SKD
_chem_comp.name "2-ACETYLAMINO-7-(1,2-DIHYDROXY-ETHYL)-3-HYDROXY-6,8-DIOXA-BICYCLO[3.2.1]OCTANE-5-CARBOXYLIC ACID"
_chem_comp.type NON-POLYMER
_chem_comp.pdbx_type HETAIN
_chem_comp.formula "C11 H17 N O8"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms 2,7-ANHYDRO-NEU5AC
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 1999-07-08
_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 291.255
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code SKD
_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 2SLI
_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
SKD C1 C1 C 0 1 N N N N N N 1.768 7.427 36.092 -2.791 -0.223 -0.843 C1 SKD 1
SKD C2 C2 C 0 1 N N S N N N 3.053 7.223 36.906 -1.404 0.067 -0.330 C2 SKD 2
SKD C3 C3 C 0 1 N N N N N N 4.256 6.883 36.005 -1.440 1.038 0.860 C3 SKD 3
SKD C4 C4 C 0 1 N N S N N N 5.534 7.444 36.673 -0.004 1.434 1.219 C4 SKD 4
SKD C5 C5 C 0 1 N N R N N N 5.465 7.266 38.209 0.842 0.167 1.389 C5 SKD 5
SKD C6 C6 C 0 1 N N R N N N 4.137 7.877 38.760 0.669 -0.712 0.141 C6 SKD 6
SKD C7 C7 C 0 1 N N R N N N 3.337 6.637 39.152 0.772 0.207 -1.099 C7 SKD 7
SKD C8 C8 C 0 1 N N R N N N 2.176 6.953 40.107 1.315 -0.574 -2.297 C8 SKD 8
SKD C9 C9 C 0 1 N N N N N N 2.682 7.498 41.445 1.342 0.333 -3.528 C9 SKD 9
SKD C10 C10 C 0 1 N N N N N N 7.168 7.272 39.930 0.953 -0.314 3.775 C10 SKD 10
SKD C11 C11 C 0 1 N N N N N N 8.412 7.911 40.514 0.492 -1.070 4.995 C11 SKD 11
SKD N5 N5 N 0 1 N N N N N N 6.642 7.835 38.846 0.394 -0.567 2.575 N5 SKD 12
SKD O1A O1A O 0 1 N N N N N N 1.694 6.937 34.939 -3.082 0.044 -1.984 O1A SKD 13
SKD O1B O1B O 0 1 N N N N N N 0.807 8.035 36.612 -3.703 -0.782 -0.031 O1B SKD 14
SKD O4 O4 O 0 1 N N N N N N 6.703 6.806 36.158 0.545 2.238 0.173 O4 SKD 15
SKD O6 O6 O 0 1 N N N N N N 3.397 8.389 37.646 -0.722 -1.129 0.105 O6 SKD 16
SKD O7 O7 O 0 1 N N N N N N 2.808 6.184 37.882 -0.575 0.643 -1.356 O7 SKD 17
SKD O8 O8 O 0 1 N N N N N N 1.303 7.902 39.508 2.640 -1.026 -2.009 O8 SKD 18
SKD O9 O9 O 0 1 N N N N N N 3.049 8.861 41.291 1.850 -0.396 -4.647 O9 SKD 19
SKD O10 O10 O 0 1 N N N N N N 6.661 6.301 40.494 1.826 0.521 3.874 O10 SKD 20
SKD H31 1H3 H 0 1 N N N N N N 4.330 5.793 35.780 -1.910 0.552 1.714 H31 SKD 21
SKD H32 2H3 H 0 1 N N N N N N 4.124 7.243 34.958 -2.007 1.929 0.587 H32 SKD 22
SKD H4 H4 H 0 1 N N N N N N 5.595 8.532 36.437 -0.004 2.000 2.150 H4 SKD 23
SKD H5 H5 H 0 1 N N N N N N 5.460 6.178 38.453 1.891 0.440 1.503 H5 SKD 24
SKD H6 H6 H 0 1 N N N N N N 4.309 8.643 39.551 1.365 -1.550 0.103 H6 SKD 25
SKD H7 H7 H 0 1 N N N N N N 3.967 5.892 39.692 1.412 1.062 -0.883 H7 SKD 26
SKD H8 H8 H 0 1 N N N N N N 1.627 6.002 40.303 0.672 -1.432 -2.492 H8 SKD 27
SKD H91 1H9 H 0 1 N N N N N N 1.943 7.350 42.267 0.332 0.678 -3.748 H91 SKD 28
SKD H92 2H9 H 0 1 N N N N N N 3.511 6.882 41.864 1.985 1.191 -3.333 H92 SKD 29
SKD H111 1H11 H 0 0 N N N N N N 8.853 7.439 41.422 1.055 -0.732 5.866 H111 SKD 30
SKD H112 2H11 H 0 0 N N N N N N 9.193 7.989 39.722 -0.569 -0.887 5.156 H112 SKD 31
SKD H113 3H11 H 0 0 N N N N N N 8.212 8.989 40.717 0.659 -2.137 4.846 H113 SKD 32
SKD HN5 HN5 H 0 1 N N N N N N 7.123 8.671 38.515 -0.304 -1.235 2.497 HN5 SKD 33
SKD HOB1 1HOB H 0 0 N N N N N N 0.011 8.161 36.108 -4.593 -0.969 -0.361 HOB1 SKD 34
SKD HO4 HO4 H 0 1 N N N N N N 7.487 7.150 36.568 -0.015 3.022 0.099 HO4 SKD 35
SKD HO8 HO8 H 0 1 N N N N N N 0.585 8.097 40.098 3.174 -0.238 -1.843 HO8 SKD 36
SKD HO9 HO9 H 0 1 N N N N N N 3.363 9.199 42.121 1.850 0.210 -5.400 HO9 SKD 37
#
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
SKD C1 C2 SING N N 1
SKD C1 O1A DOUB N N 2
SKD C1 O1B SING N N 3
SKD C2 C3 SING N N 4
SKD C2 O6 SING N N 5
SKD C2 O7 SING N N 6
SKD C3 C4 SING N N 7
SKD C3 H31 SING N N 8
SKD C3 H32 SING N N 9
SKD C4 C5 SING N N 10
SKD C4 O4 SING N N 11
SKD C4 H4 SING N N 12
SKD C5 C6 SING N N 13
SKD C5 N5 SING N N 14
SKD C5 H5 SING N N 15
SKD C6 C7 SING N N 16
SKD C6 O6 SING N N 17
SKD C6 H6 SING N N 18
SKD C7 C8 SING N N 19
SKD C7 O7 SING N N 20
SKD C7 H7 SING N N 21
SKD C8 C9 SING N N 22
SKD C8 O8 SING N N 23
SKD C8 H8 SING N N 24
SKD C9 O9 SING N N 25
SKD C9 H91 SING N N 26
SKD C9 H92 SING N N 27
SKD C10 C11 SING N N 28
SKD C10 N5 SING N N 29
SKD C10 O10 DOUB N N 30
SKD C11 H111 SING N N 31
SKD C11 H112 SING N N 32
SKD C11 H113 SING N N 33
SKD N5 HN5 SING N N 34
SKD O1B HOB1 SING N N 35
SKD O4 HO4 SING N N 36
SKD O8 HO8 SING N N 37
SKD O9 HO9 SING N N 38
#
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
SKD SMILES ACDLabs 10.04 O=C(NC1C(O)CC2(OC1C(O2)C(O)CO)C(=O)O)C
SKD SMILES_CANONICAL CACTVS 3.341 CC(=O)N[C@@H]1[C@@H](O)C[C@]2(O[C@H]([C@H](O)CO)[C@@H]1O2)C(O)=O
SKD SMILES CACTVS 3.341 CC(=O)N[CH]1[CH](O)C[C]2(O[CH]([CH](O)CO)[CH]1O2)C(O)=O
SKD SMILES_CANONICAL "OpenEye OEToolkits" 1.5.0 CC(=O)N[C@@H]1[C@H](C[C@@]2(O[C@H]1[C@H](O2)[C@@H](CO)O)C(=O)O)O
SKD SMILES "OpenEye OEToolkits" 1.5.0 CC(=O)NC1C(CC2(OC1C(O2)C(CO)O)C(=O)O)O
SKD InChI InChI 1.03 InChI=1S/C11H17NO8/c1-4(14)12-7-5(15)2-11(10(17)18)19-8(6(16)3-13)9(7)20-11/h5-9,13,15-16H,2-3H2,1H3,(H,12,14)(H,17,18)/t5-,6+,7+,8+,9+,11+/m0/s1
SKD InChIKey InChI 1.03 NCMJSVDTRDLWJE-YRMXFSIDSA-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
SKD "SYSTEMATIC NAME" ACDLabs 10.04 "(1R,2R,3S,5S,7R)-2-(acetylamino)-7-[(1R)-1,2-dihydroxyethyl]-3-hydroxy-6,8-dioxabicyclo[3.2.1]octane-5-carboxylic acid (non-preferred name)"
SKD "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.5.0 "(1S,3S,4R,5R,6R)-4-acetamido-6-[(1R)-1,2-dihydroxyethyl]-3-hydroxy-7,8-dioxabicyclo[3.2.1]octane-1-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
SKD 'Create component' 1999-07-08 RCSB
SKD 'Modify descriptor' 2011-06-04 RCSB
SKD 'Modify synonyms' 2020-06-05 PDBE
#
_pdbx_chem_comp_synonyms.ordinal 1
_pdbx_chem_comp_synonyms.comp_id SKD
_pdbx_chem_comp_synonyms.name 2,7-ANHYDRO-NEU5AC
_pdbx_chem_comp_synonyms.provenance ?
_pdbx_chem_comp_synonyms.type ?
#
_pdbe_chem_comp_synonyms.comp_id SKD
_pdbe_chem_comp_synonyms.name 2,7-ANHYDRO-NEU5AC
_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
SKD C1 C -0.553 3.028 1
SKD C2 C -0.161 1.546 2
SKD C3 C 1.102 2.036 3
SKD C4 C 2.138 0.516 4
SKD C5 C 1.098 -1.000 5
SKD C6 C -0.156 -0.511 6
SKD C7 C -1.634 -0.251 7
SKD C8 C -2.857 -1.173 8
SKD C9 C -4.251 -0.538 9
SKD C10 C 3.188 -2.373 10
SKD C11 C 3.948 -3.657 11
SKD N5 N 1.654 -2.348 12
SKD O1A O 0.520 4.091 13
SKD O1B O -2.000 3.436 14
SKD O4 O 3.639 0.510 15
SKD O6 O 0.226 0.517 16
SKD O7 O -1.640 1.277 17
SKD O8 O -2.708 -2.664 18
SKD O9 O -5.496 -1.387 19
SKD O10 O 3.944 -1.054 20
#
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
SKD C2 C1 SINGLE BEGINWEDGE 1
SKD C1 O1A DOUBLE NONE 2
SKD C1 O1B SINGLE NONE 3
SKD C2 C3 SINGLE NONE 4
SKD C2 O6 SINGLE NONE 5
SKD C2 O7 SINGLE NONE 6
SKD C3 C4 SINGLE NONE 7
SKD C4 C5 SINGLE NONE 8
SKD C4 O4 SINGLE BEGINDASH 9
SKD C5 C6 SINGLE NONE 10
SKD C5 N5 SINGLE BEGINWEDGE 11
SKD C6 C7 SINGLE NONE 12
SKD C6 O6 SINGLE NONE 13
SKD C7 C8 SINGLE NONE 14
SKD C7 O7 SINGLE BEGINWEDGE 15
SKD C8 C9 SINGLE NONE 16
SKD C8 O8 SINGLE BEGINDASH 17
SKD C9 O9 SINGLE NONE 18
SKD C10 C11 SINGLE NONE 19
SKD C10 N5 SINGLE NONE 20
SKD C10 O10 DOUBLE NONE 21
#
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
SKD MurckoScaffold S1 scaffold 'C1CC2OC[C@@H](C1)O2' InChI=1S/C6H10O2/c1-2-5-4-7-6(3-1)8-5/h5-6H,1-4H2/t5-,6?/m1/s1 DYXJGWLSYLPWMO-LWOQYNTDSA-N
SKD amide F1 fragment CC(N)=O InChI=1S/C2H5NO/c1-2(3)4/h1H3,(H2,3,4) DLFVBJFMPXGRIB-UHFFFAOYSA-N
SKD pyranose F2 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
SKD C2 S1 1
SKD C3 S1 1
SKD C4 S1 1
SKD C5 S1 1
SKD C6 S1 1
SKD C7 S1 1
SKD O6 S1 1
SKD O7 S1 1
SKD N5 F1 1
SKD C10 F1 1
SKD O10 F1 1
SKD C11 F1 1
SKD C5 F2 1
SKD C6 F2 1
SKD O6 F2 1
SKD C2 F2 1
SKD C3 F2 1
SKD C4 F2 1
SKD O7 F2 1
#
_pdbe_chem_comp_rdkit_properties.comp_id SKD
_pdbe_chem_comp_rdkit_properties.exactmw 291.095
_pdbe_chem_comp_rdkit_properties.amw 291.256
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 9
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 5
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 8
_pdbe_chem_comp_rdkit_properties.NumHBD 5
_pdbe_chem_comp_rdkit_properties.NumHBA 8
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 20
_pdbe_chem_comp_rdkit_properties.NumAtoms 37
_pdbe_chem_comp_rdkit_properties.NumHeteroatoms 9
_pdbe_chem_comp_rdkit_properties.NumAmideBonds 1
_pdbe_chem_comp_rdkit_properties.FractionCSP3 0.818
_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 2
_pdbe_chem_comp_rdkit_properties.NumAtomStereoCenters 6
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 137.943
_pdbe_chem_comp_rdkit_properties.tpsa 145.550
_pdbe_chem_comp_rdkit_properties.CrippenClogP -2.826
_pdbe_chem_comp_rdkit_properties.CrippenMR 61.434
_pdbe_chem_comp_rdkit_properties.chi0v 9.213
_pdbe_chem_comp_rdkit_properties.chi1v 4.738
_pdbe_chem_comp_rdkit_properties.chi2v 2.187
_pdbe_chem_comp_rdkit_properties.chi3v 2.187
_pdbe_chem_comp_rdkit_properties.chi4v 1.453
_pdbe_chem_comp_rdkit_properties.chi0n 26.213
_pdbe_chem_comp_rdkit_properties.chi1n 12.819
_pdbe_chem_comp_rdkit_properties.chi2n 2.187
_pdbe_chem_comp_rdkit_properties.chi3n 2.187
_pdbe_chem_comp_rdkit_properties.chi4n 1.453
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -1.260
_pdbe_chem_comp_rdkit_properties.kappa1 4.369
_pdbe_chem_comp_rdkit_properties.kappa2 5.261
_pdbe_chem_comp_rdkit_properties.kappa3 2.380
_pdbe_chem_comp_rdkit_properties.Phi 1.149
#
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
SKD UniChem PDBe SKD
SKD UniChem ChEBI 28695
SKD UniChem PubChem 449401
SKD UniChem Nikkaji J384.431E
#
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
SKD C1 -2.290 -0.919 -2.258 ETKDGv3 1
SKD C2 -1.264 -0.845 -1.164 ETKDGv3 2
SKD C3 -0.499 -2.193 -1.024 ETKDGv3 3
SKD C4 1.005 -1.948 -0.739 ETKDGv3 4
SKD C5 1.233 -0.697 0.160 ETKDGv3 5
SKD C6 0.193 0.424 -0.180 ETKDGv3 6
SKD C7 -1.039 0.345 0.717 ETKDGv3 7
SKD C8 -1.731 1.722 0.874 ETKDGv3 8
SKD C9 -3.062 1.625 1.639 ETKDGv3 9
SKD C10 3.181 0.742 0.922 ETKDGv3 10
SKD C11 4.582 1.219 0.720 ETKDGv3 11
SKD N5 2.600 -0.188 -0.003 ETKDGv3 12
SKD O1A -3.436 -1.386 -2.020 ETKDGv3 13
SKD O1B -1.958 -0.527 -3.552 ETKDGv3 14
SKD O4 1.580 -3.078 -0.135 ETKDGv3 15
SKD O6 -0.339 0.181 -1.445 ETKDGv3 16
SKD O7 -1.903 -0.546 0.062 ETKDGv3 17
SKD O8 -0.879 2.652 1.498 ETKDGv3 18
SKD O9 -2.857 1.101 2.923 ETKDGv3 19
SKD O10 2.525 1.142 1.922 ETKDGv3 20
SKD H31 -0.582 -2.799 -1.954 ETKDGv3 21
SKD H32 -0.946 -2.793 -0.201 ETKDGv3 22
SKD H4 1.498 -1.764 -1.724 ETKDGv3 23
SKD H5 1.120 -1.022 1.219 ETKDGv3 24
SKD H6 0.663 1.432 -0.154 ETKDGv3 25
SKD H7 -0.795 -0.053 1.726 ETKDGv3 26
SKD H8 -1.966 2.112 -0.142 ETKDGv3 27
SKD H91 -3.772 0.978 1.077 ETKDGv3 28
SKD H92 -3.509 2.641 1.718 ETKDGv3 29
SKD H111 5.288 0.384 0.911 ETKDGv3 30
SKD H112 4.709 1.573 -0.325 ETKDGv3 31
SKD H113 4.814 2.056 1.412 ETKDGv3 32
SKD HN5 3.200 -0.540 -0.783 ETKDGv3 33
SKD HOB1 -2.634 -0.591 -4.304 ETKDGv3 34
SKD HO4 1.634 -3.780 -0.835 ETKDGv3 35
SKD HO8 -0.610 2.274 2.376 ETKDGv3 36
SKD HO9 -3.752 1.067 3.352 ETKDGv3 37
#