data_Z5J
#
_chem_comp.id Z5J
_chem_comp.name beta-L-Olivopyranose
_chem_comp.type "L-saccharide, beta linking"
_chem_comp.pdbx_type ATOMS
_chem_comp.formula "C6 H12 O4"
_chem_comp.mon_nstd_parent_comp_id ?
_chem_comp.pdbx_synonyms
;beta-L-Olivose; 2,6-dideoxy-beta-L-arabino-hexopyranose; 2,6-dideoxy-beta-L-glucopyranose;
2,6-dideoxy-beta-L-mannopyranose; 2-deoxy-beta-L-quinovopyranose; 2-deoxy-beta-L-rhamnoopyranose; L-Olivose; Olivose
;
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2012-12-18
_chem_comp.pdbx_modified_date 2020-07-17
_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 148.157
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code Z5J
_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 1Q0Z
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site RCSB
#
loop_
_pdbx_chem_comp_synonyms.ordinal
_pdbx_chem_comp_synonyms.comp_id
_pdbx_chem_comp_synonyms.name
_pdbx_chem_comp_synonyms.provenance
_pdbx_chem_comp_synonyms.type
1 Z5J beta-L-Olivose PDB ?
2 Z5J 2,6-dideoxy-beta-L-arabino-hexopyranose PDB ?
3 Z5J 2,6-dideoxy-beta-L-glucopyranose PDB ?
4 Z5J 2,6-dideoxy-beta-L-mannopyranose PDB ?
5 Z5J 2-deoxy-beta-L-quinovopyranose PDB ?
6 Z5J 2-deoxy-beta-L-rhamnoopyranose PDB ?
7 Z5J L-Olivose PDB ?
8 Z5J Olivose PDB ?
#
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
Z5J O4 O1 O 0 1 N N N N N N 19.478 8.593 14.223 2.478 -0.322 0.242 O4 Z5J 1
Z5J C4 C1 C 0 1 N N R N N N 18.969 9.089 12.953 1.142 -0.140 -0.229 C4 Z5J 2
Z5J C5 C2 C 0 1 N N S N N N 18.075 8.023 12.243 0.257 -1.277 0.289 C5 Z5J 3
Z5J C6 C3 C 0 1 N N N N N N 18.854 6.835 11.662 0.760 -2.609 -0.268 C6 Z5J 4
Z5J O5 O2 O 0 1 N N N N N N 17.324 8.803 11.298 -1.091 -1.061 -0.135 O5 Z5J 5
Z5J C3 C4 C 0 1 N N S N N N 18.179 10.383 13.322 0.596 1.196 0.284 C3 Z5J 6
Z5J O3 O3 O 0 1 N N N N N N 19.019 11.528 13.529 1.372 2.268 -0.254 O3 Z5J 7
Z5J C2 C5 C 0 1 N N N N N N 17.232 10.849 12.236 -0.862 1.345 -0.162 C2 Z5J 8
Z5J C1 C6 C 0 1 N N S N N N 16.589 9.648 11.583 -1.670 0.151 0.354 C1 Z5J 9
Z5J O1 O4 O 0 1 N Y N N N N 15.210 9.594 11.186 -3.019 0.254 -0.106 O1 Z5J 10
Z5J HO1 H4O H 0 1 N Y N N N N 14.758 10.366 11.505 -3.589 -0.472 0.183 HO1 Z5J 11
Z5J H4 H11 H 0 1 N N N N N N 19.801 9.357 12.286 1.136 -0.142 -1.319 H4 Z5J 12
Z5J H5 H21 H 0 1 N N N N N N 17.383 7.625 13.000 0.296 -1.300 1.378 H5 Z5J 13
Z5J H61 H31 H 0 1 N N N N N N 18.153 6.136 11.183 1.788 -2.773 0.055 H61 Z5J 14
Z5J H62 H32 H 0 1 N N N N N N 19.576 7.199 10.916 0.130 -3.419 0.101 H62 Z5J 15
Z5J H63 H33 H 0 1 N N N N N N 19.392 6.318 12.471 0.721 -2.586 -1.357 H63 Z5J 16
Z5J H3 H41 H 0 1 N N N N N N 17.597 10.180 14.233 0.649 1.218 1.373 H3 Z5J 17
Z5J HO3 H3O H 0 1 N Y N N N N 18.482 12.280 13.749 1.081 3.146 0.030 HO3 Z5J 18
Z5J H21 H51 H 0 1 N N N N N N 16.453 11.488 12.677 -1.276 2.267 0.246 H21 Z5J 19
Z5J H22 H52 H 0 1 N N N N N N 17.792 11.421 11.482 -0.909 1.373 -1.250 H22 Z5J 20
Z5J H1 H61 H 0 1 N N N N N N 16.366 9.191 12.558 -1.656 0.146 1.444 H1 Z5J 21
Z5J HO4 H1O H 0 1 N Y N N N N 20.017 9.261 14.631 3.095 0.363 -0.049 HO4 Z5J 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
Z5J O4 C4 SING N N 1
Z5J C4 C5 SING N N 2
Z5J C4 C3 SING N N 3
Z5J C4 H4 SING N N 4
Z5J C5 C6 SING N N 5
Z5J C5 O5 SING N N 6
Z5J C5 H5 SING N N 7
Z5J C6 H61 SING N N 8
Z5J C6 H62 SING N N 9
Z5J C6 H63 SING N N 10
Z5J O5 C1 SING N N 11
Z5J C3 O3 SING N N 12
Z5J C3 C2 SING N N 13
Z5J C3 H3 SING N N 14
Z5J O3 HO3 SING N N 15
Z5J C2 C1 SING N N 16
Z5J C2 H21 SING N N 17
Z5J C2 H22 SING N N 18
Z5J C1 O1 SING N N 19
Z5J C1 H1 SING N N 20
Z5J HO1 O1 SING N N 21
Z5J O4 HO4 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
Z5J SMILES ACDLabs 12.01 OC1C(OC(O)CC1O)C
Z5J InChI InChI 1.03 InChI=1S/C6H12O4/c1-3-6(9)4(7)2-5(8)10-3/h3-9H,2H2,1H3/t3-,4-,5-,6-/m0/s1
Z5J InChIKey InChI 1.03 FDWRIIDFYSUTDP-BXKVDMCESA-N
Z5J SMILES_CANONICAL CACTVS 3.370 C[C@@H]1O[C@H](O)C[C@H](O)[C@H]1O
Z5J SMILES CACTVS 3.370 C[CH]1O[CH](O)C[CH](O)[CH]1O
Z5J SMILES_CANONICAL "OpenEye OEToolkits" 1.7.6 C[C@H]1[C@@H]([C@H](CC(O1)O)O)O
Z5J SMILES "OpenEye OEToolkits" 1.7.6 CC1C(C(CC(O1)O)O)O
#
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
Z5J "SYSTEMATIC NAME" ACDLabs 12.01 2,6-dideoxy-beta-L-arabino-hexopyranose
Z5J "SYSTEMATIC NAME" "OpenEye OEToolkits" 1.7.6 (4S,5R,6S)-6-methyloxane-2,4,5-triol
Z5J "CONDENSED IUPAC CARBOHYDRATE SYMBOL" GMML 1.0 LOlib
Z5J "COMMON NAME" GMML 1.0 b-L-Olivopyranose
Z5J "SNFG CARBOHYDRATE SYMBOL" GMML 1.0 Oli
Z5J "IUPAC CARBOHYDRATE SYMBOL" PDB-CARE 1.0 b-L-2,6-deoxy-Glcp
#
loop_
_pdbx_chem_comp_feature.comp_id
_pdbx_chem_comp_feature.type
_pdbx_chem_comp_feature.value
_pdbx_chem_comp_feature.source
_pdbx_chem_comp_feature.support
Z5J "CARBOHYDRATE ISOMER" L PDB ?
Z5J "CARBOHYDRATE RING" pyranose PDB ?
Z5J "CARBOHYDRATE ANOMER" beta PDB ?
Z5J "CARBOHYDRATE PRIMARY CARBONYL GROUP" aldose PDB ?
#
loop_
_pdbx_chem_comp_audit.comp_id
_pdbx_chem_comp_audit.action_type
_pdbx_chem_comp_audit.date
_pdbx_chem_comp_audit.processing_site
Z5J 'Create component' 2012-12-18 RCSB
Z5J 'Other modification' 2019-08-12 RCSB
Z5J 'Other modification' 2019-12-19 RCSB
Z5J 'Other modification' 2020-06-03 RCSB
Z5J 'Other modification' 2020-06-10 RCSB
Z5J 'Other modification' 2020-07-03 RCSB
Z5J 'Modify atom id' 2020-07-17 RCSB
Z5J 'Modify component atom id' 2020-07-17 RCSB
Z5J 'Initial release' 2020-07-29 RCSB
#
loop_
_pdbe_chem_comp_synonyms.comp_id
_pdbe_chem_comp_synonyms.name
_pdbe_chem_comp_synonyms.provenance
_pdbe_chem_comp_synonyms.type
Z5J beta-L-Olivose wwPDB ?
Z5J 2,6-dideoxy-beta-L-arabino-hexopyranose wwPDB ?
Z5J 2,6-dideoxy-beta-L-glucopyranose wwPDB ?
Z5J 2,6-dideoxy-beta-L-mannopyranose wwPDB ?
Z5J 2-deoxy-beta-L-quinovopyranose wwPDB ?
Z5J 2-deoxy-beta-L-rhamnoopyranose wwPDB ?
Z5J L-Olivose wwPDB ?
Z5J Olivose wwPDB ?
#
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
Z5J O4 O 3.805 -0.983 1
Z5J C4 C 5.104 -0.233 2
Z5J C5 C 5.104 1.268 3
Z5J C6 C 3.805 2.018 4
Z5J O5 O 6.404 2.018 5
Z5J C3 C 6.404 -0.983 6
Z5J O3 O 6.404 -2.482 7
Z5J C2 C 7.702 -0.233 8
Z5J C1 C 7.702 1.268 9
Z5J O1 O 9.002 2.018 10
#
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
Z5J C4 O4 SINGLE BEGINWEDGE 1
Z5J C4 C5 SINGLE NONE 2
Z5J C4 C3 SINGLE NONE 3
Z5J C5 C6 SINGLE BEGINDASH 4
Z5J C5 O5 SINGLE NONE 5
Z5J O5 C1 SINGLE NONE 6
Z5J C3 O3 SINGLE BEGINDASH 7
Z5J C3 C2 SINGLE NONE 8
Z5J C2 C1 SINGLE NONE 9
Z5J C1 O1 SINGLE BEGINDASH 10
#
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
Z5J MurckoScaffold S1 scaffold C1CCOCC1 InChI=1S/C5H10O/c1-2-4-6-5-3-1/h1-5H2 DHXVGJBLRPWPCS-UHFFFAOYSA-N
Z5J 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
Z5J C4 S1 1
Z5J C5 S1 1
Z5J O5 S1 1
Z5J C3 S1 1
Z5J C2 S1 1
Z5J C1 S1 1
Z5J C4 F1 1
Z5J C5 F1 1
Z5J O5 F1 1
Z5J C1 F1 1
Z5J C2 F1 1
Z5J C3 F1 1
Z5J O1 F1 1
#
_pdbe_chem_comp_rdkit_properties.comp_id Z5J
_pdbe_chem_comp_rdkit_properties.exactmw 148.074
_pdbe_chem_comp_rdkit_properties.amw 148.158
_pdbe_chem_comp_rdkit_properties.lipinskiHBA 4
_pdbe_chem_comp_rdkit_properties.lipinskiHBD 3
_pdbe_chem_comp_rdkit_properties.NumRotatableBonds 4
_pdbe_chem_comp_rdkit_properties.NumHBD 3
_pdbe_chem_comp_rdkit_properties.NumHBA 4
_pdbe_chem_comp_rdkit_properties.NumHeavyAtoms 10
_pdbe_chem_comp_rdkit_properties.NumAtoms 22
_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 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 4
_pdbe_chem_comp_rdkit_properties.NumUnspecifiedAtomStereoCenters 0
_pdbe_chem_comp_rdkit_properties.labuteASA 76.174
_pdbe_chem_comp_rdkit_properties.tpsa 69.920
_pdbe_chem_comp_rdkit_properties.CrippenClogP -1.165
_pdbe_chem_comp_rdkit_properties.CrippenMR 33.184
_pdbe_chem_comp_rdkit_properties.chi0v 4.633
_pdbe_chem_comp_rdkit_properties.chi1v 2.271
_pdbe_chem_comp_rdkit_properties.chi2v 0.823
_pdbe_chem_comp_rdkit_properties.chi3v 0.823
_pdbe_chem_comp_rdkit_properties.chi4v 0.417
_pdbe_chem_comp_rdkit_properties.chi0n 16.633
_pdbe_chem_comp_rdkit_properties.chi1n 7.995
_pdbe_chem_comp_rdkit_properties.chi2n 0.823
_pdbe_chem_comp_rdkit_properties.chi3n 0.823
_pdbe_chem_comp_rdkit_properties.chi4n 0.417
_pdbe_chem_comp_rdkit_properties.hallKierAlpha -0.160
_pdbe_chem_comp_rdkit_properties.kappa1 1.612
_pdbe_chem_comp_rdkit_properties.kappa2 2.837
_pdbe_chem_comp_rdkit_properties.kappa3 1.462
_pdbe_chem_comp_rdkit_properties.Phi 0.457
#
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
Z5J UniChem PDBe Z5J
Z5J UniChem ZINC ZINC000002046819
Z5J UniChem 'PubChem TPHARMA' 16178370
Z5J UniChem PubChem 11105517
#
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
Z5J O4 -0.093 -0.241 2.171 ETKDGv3 1
Z5J C4 0.470 0.390 1.048 ETKDGv3 2
Z5J C5 1.083 -0.696 0.105 ETKDGv3 3
Z5J C6 2.518 -0.334 -0.283 ETKDGv3 4
Z5J O5 0.334 -0.875 -1.090 ETKDGv3 5
Z5J C3 -0.613 1.204 0.315 ETKDGv3 6
Z5J O3 -0.005 1.984 -0.684 ETKDGv3 7
Z5J C2 -1.664 0.265 -0.314 ETKDGv3 8
Z5J C1 -1.036 -1.062 -0.795 ETKDGv3 9
Z5J O1 -1.687 -1.504 -1.956 ETKDGv3 10
Z5J HO1 -2.587 -1.819 -1.678 ETKDGv3 11
Z5J H4 1.264 1.095 1.396 ETKDGv3 12
Z5J H5 1.141 -1.671 0.643 ETKDGv3 13
Z5J H61 2.939 -1.122 -0.944 ETKDGv3 14
Z5J H62 2.539 0.635 -0.826 ETKDGv3 15
Z5J H63 3.156 -0.260 0.623 ETKDGv3 16
Z5J H3 -1.116 1.876 1.050 ETKDGv3 17
Z5J HO3 -0.650 2.700 -0.923 ETKDGv3 18
Z5J H21 -2.165 0.787 -1.159 ETKDGv3 19
Z5J H22 -2.449 0.035 0.440 ETKDGv3 20
Z5J H1 -1.154 -1.844 -0.003 ETKDGv3 21
Z5J HO4 -0.225 0.460 2.863 ETKDGv3 22
#