data_J5B
#
_chem_comp.id J5B
_chem_comp.name "(3R)-3-hydroxybutyl alpha-D-glucopyranoside"
_chem_comp.type D-saccharide
_chem_comp.pdbx_type ATOMS
_chem_comp.formula "C10 H20 O7"
_chem_comp.mon_nstd_parent_comp_id GLC
_chem_comp.pdbx_synonyms
;(2~{R},3~{S},4~{S},5~{R},6~{S})-2-(hydroxymethyl)-6-[(3~{R})-3-oxidanylbutoxy]oxane-3,4,5-triol; reacted
3,4-EPOXYBUTYL-ALPHA-D-GLUCOPYRANOSIDE; (3R)-3-hydroxybutyl alpha-D-glucoside; (3R)-3-hydroxybutyl D-glucoside;
(3R)-3-hydroxybutyl glucoside
;
_chem_comp.pdbx_formal_charge 0
_chem_comp.pdbx_initial_date 2019-01-26
_chem_comp.pdbx_modified_date 2024-09-27
_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 252.262
_chem_comp.one_letter_code ?
_chem_comp.three_letter_code J5B
_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 2XGI
_chem_comp.pdbx_subcomponent_list ?
_chem_comp.pdbx_processing_site EBI
_chem_comp.pdbx_pcm Y
#
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 J5B "(2~{R},3~{S},4~{S},5~{R},6~{S})-2-(hydroxymethyl)-6-[(3~{R})-3-oxidanylbutoxy]oxane-3,4,5-triol" PDB ?
2 J5B "reacted 3,4-EPOXYBUTYL-ALPHA-D-GLUCOPYRANOSIDE" PDB ?
3 J5B "(3R)-3-hydroxybutyl alpha-D-glucoside" PDB ?
4 J5B "(3R)-3-hydroxybutyl D-glucoside" PDB ?
5 J5B "(3R)-3-hydroxybutyl glucoside" 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
J5B C1 C1 C 0 1 N N S N N N 14.124 7.119 28.143 -0.507 -0.740 1.185 C1 J5B 1
J5B O1 O1 O 0 1 N N N N N N 14.253 7.812 26.895 0.509 -0.983 0.209 O1 J5B 2
J5B C2 C2 C 0 1 N N R N N N 12.646 6.880 28.463 -1.789 -1.471 0.780 C2 J5B 3
J5B O2 O2 O 0 1 N N N N N N 11.954 6.157 27.425 -1.520 -2.867 0.643 O2 J5B 4
J5B C3 C3 C 0 1 N N S N N N 11.958 8.229 28.704 -2.286 -0.911 -0.557 C3 J5B 5
J5B O3 O3 O 0 1 N N N N N N 10.586 8.002 28.982 -3.522 -1.536 -0.907 O3 J5B 6
J5B C4 C4 C 0 1 N N S N N N 12.630 8.978 29.846 -2.496 0.600 -0.419 C4 J5B 7
J5B O4 O4 O 0 1 N N N N N N 11.997 10.264 30.038 -2.890 1.144 -1.680 O4 J5B 8
J5B C5 C5 C 0 1 N N R N N N 14.117 9.141 29.501 -1.186 1.250 0.033 C5 J5B 9
J5B O5 O5 O 0 1 N N N N N N 14.715 7.856 29.223 -0.764 0.663 1.265 O5 J5B 10
J5B C6 C6 C 0 1 N N N N N N 14.934 9.806 30.589 -1.404 2.752 0.231 C6 J5B 11
J5B O6 O6 O 0 1 N N N N N N 14.956 8.987 31.757 -0.157 3.378 0.539 O6 J5B 12
J5B C7 C7 C 0 1 N N N N N N 15.605 8.189 26.554 1.809 -0.536 0.600 C7 J5B 13
J5B C8 C8 C 0 1 N N N N N N 15.710 8.761 25.151 2.810 -0.846 -0.515 C8 J5B 14
J5B C9 C9 C 0 1 N N R N N N 15.938 10.259 24.938 4.202 -0.368 -0.097 C9 J5B 15
J5B C10 C10 C 0 1 N N N N N N 15.059 10.698 23.788 5.225 -0.788 -1.154 C10 J5B 16
J5B O9 O9 O 0 1 N N N N N N 15.880 10.976 26.196 4.201 1.056 0.025 O9 J5B 17
J5B H1 H1 H 0 1 N N N N N N 14.616 6.138 28.064 -0.172 -1.104 2.157 H1 J5B 18
J5B H2 H2 H 0 1 N N N N N N 12.592 6.303 29.398 -2.552 -1.319 1.544 H2 J5B 19
J5B HO2 H3 H 0 1 N Y N N N N 11.045 6.037 27.674 -1.197 -3.287 1.452 HO2 J5B 20
J5B H3 H4 H 0 1 N N N N N N 12.056 8.833 27.790 -1.546 -1.108 -1.332 H3 J5B 21
J5B HO3 H5 H 0 1 N Y N N N N 10.151 8.833 29.133 -3.464 -2.496 -1.004 HO3 J5B 22
J5B H4 H6 H 0 1 N N N N N N 12.545 8.378 30.764 -3.274 0.793 0.320 H4 J5B 23
J5B HO4 H7 H 0 1 N Y N N N N 12.423 10.724 30.752 -3.712 0.773 -2.029 HO4 J5B 24
J5B H5 H8 H 0 1 N N N N N N 14.184 9.766 28.598 -0.421 1.091 -0.727 H5 J5B 25
J5B H61 H9 H 0 1 N N N N N N 15.963 9.956 30.231 -1.811 3.184 -0.683 H61 J5B 26
J5B H62 H10 H 0 1 N N N N N N 14.486 10.780 30.836 -2.103 2.912 1.051 H62 J5B 27
J5B HO6 H11 H 0 1 N Y N N N N 15.470 9.412 32.433 -0.219 4.332 0.678 HO6 J5B 28
J5B H12 H12 H 0 1 N N N N N N 16.248 7.299 26.622 1.785 0.539 0.779 H12 J5B 29
J5B H13 H13 H 0 1 N N N N N N 15.952 8.947 27.271 2.111 -1.050 1.513 H13 J5B 30
J5B H14 H14 H 0 1 N N N N N N 14.771 8.509 24.637 2.834 -1.921 -0.693 H14 J5B 31
J5B H15 H15 H 0 1 N N N N N N 16.547 8.242 24.661 2.509 -0.333 -1.427 H15 J5B 32
J5B H16 H16 H 0 1 N N N N N N 16.972 10.351 24.575 4.467 -0.814 0.862 H16 J5B 33
J5B H17 H17 H 0 1 N N N N N N 15.200 11.774 23.608 4.960 -0.342 -2.113 H17 J5B 34
J5B H18 H18 H 0 1 N N N N N N 15.332 10.136 22.883 6.217 -0.448 -0.857 H18 J5B 35
J5B H19 H19 H 0 1 N N N N N N 16.486 10.583 26.813 3.973 1.520 -0.793 H19 J5B 36
J5B H20 H20 H 0 1 N N N N N N 14.005 10.502 24.037 5.227 -1.874 -1.247 H20 J5B 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
J5B C10 C9 SING N N 1
J5B C9 C8 SING N N 2
J5B C9 O9 SING N N 3
J5B C8 C7 SING N N 4
J5B C7 O1 SING N N 5
J5B O1 C1 SING N N 6
J5B O2 C2 SING N N 7
J5B C1 C2 SING N N 8
J5B C1 O5 SING N N 9
J5B C2 C3 SING N N 10
J5B C3 O3 SING N N 11
J5B C3 C4 SING N N 12
J5B O5 C5 SING N N 13
J5B C5 C4 SING N N 14
J5B C5 C6 SING N N 15
J5B C4 O4 SING N N 16
J5B C6 O6 SING N N 17
J5B C1 H1 SING N N 18
J5B C2 H2 SING N N 19
J5B O2 HO2 SING N N 20
J5B C3 H3 SING N N 21
J5B O3 HO3 SING N N 22
J5B C4 H4 SING N N 23
J5B O4 HO4 SING N N 24
J5B C5 H5 SING N N 25
J5B C6 H61 SING N N 26
J5B C6 H62 SING N N 27
J5B O6 HO6 SING N N 28
J5B C7 H12 SING N N 29
J5B C7 H13 SING N N 30
J5B C8 H14 SING N N 31
J5B C8 H15 SING N N 32
J5B C9 H16 SING N N 33
J5B C10 H17 SING N N 34
J5B C10 H18 SING N N 35
J5B O9 H19 SING N N 36
J5B C10 H20 SING N N 37
#
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
J5B InChI InChI 1.03 "InChI=1S/C10H20O7/c1-5(12)2-3-16-10-9(15)8(14)7(13)6(4-11)17-10/h5-15H,2-4H2,1H3/t5-,6-,7-,8+,9-,10+/m1/s1"
J5B InChIKey InChI 1.03 IQTXPPTUXXJFDH-JQRWTQJCSA-N
J5B SMILES_CANONICAL CACTVS 3.385 "C[C@@H](O)CCO[C@H]1O[C@H](CO)[C@@H](O)[C@H](O)[C@H]1O"
J5B SMILES CACTVS 3.385 "C[CH](O)CCO[CH]1O[CH](CO)[CH](O)[CH](O)[CH]1O"
J5B SMILES_CANONICAL "OpenEye OEToolkits" 2.0.6 "C[C@H](CCO[C@@H]1[C@@H]([C@H]([C@@H]([C@H](O1)CO)O)O)O)O"
J5B SMILES "OpenEye OEToolkits" 2.0.6 "CC(CCOC1C(C(C(C(O1)CO)O)O)O)O"
#
_pdbx_chem_comp_identifier.comp_id J5B
_pdbx_chem_comp_identifier.type "SYSTEMATIC NAME"
_pdbx_chem_comp_identifier.program "OpenEye OEToolkits"
_pdbx_chem_comp_identifier.program_version 2.0.6
_pdbx_chem_comp_identifier.identifier "(2~{R},3~{S},4~{S},5~{R},6~{S})-2-(hydroxymethyl)-6-[(3~{R})-3-oxidanylbutoxy]oxane-3,4,5-triol"
#
_pdbx_chem_comp_related.comp_id J5B
_pdbx_chem_comp_related.related_comp_id GLC
_pdbx_chem_comp_related.relationship_type "Carbohydrate core"
_pdbx_chem_comp_related.details ?
#
loop_
_pdbx_chem_comp_atom_related.ordinal
_pdbx_chem_comp_atom_related.comp_id
_pdbx_chem_comp_atom_related.atom_id
_pdbx_chem_comp_atom_related.related_comp_id
_pdbx_chem_comp_atom_related.related_atom_id
_pdbx_chem_comp_atom_related.related_type
1 J5B C1 GLC C1 "Carbohydrate core"
2 J5B C2 GLC C2 "Carbohydrate core"
3 J5B C3 GLC C3 "Carbohydrate core"
4 J5B C4 GLC C4 "Carbohydrate core"
5 J5B C5 GLC C5 "Carbohydrate core"
6 J5B C6 GLC C6 "Carbohydrate core"
7 J5B O1 GLC O1 "Carbohydrate core"
8 J5B O2 GLC O2 "Carbohydrate core"
9 J5B O3 GLC O3 "Carbohydrate core"
10 J5B O4 GLC O4 "Carbohydrate core"
11 J5B O5 GLC O5 "Carbohydrate core"
12 J5B O6 GLC O6 "Carbohydrate core"
13 J5B H1 GLC H1 "Carbohydrate core"
14 J5B H62 GLC H62 "Carbohydrate core"
15 J5B HO6 GLC HO6 "Carbohydrate core"
16 J5B H2 GLC H2 "Carbohydrate core"
17 J5B HO2 GLC HO2 "Carbohydrate core"
18 J5B H3 GLC H3 "Carbohydrate core"
19 J5B HO3 GLC HO3 "Carbohydrate core"
20 J5B H4 GLC H4 "Carbohydrate core"
21 J5B HO4 GLC HO4 "Carbohydrate core"
22 J5B H5 GLC H5 "Carbohydrate core"
23 J5B H61 GLC H61 "Carbohydrate core"
#
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
J5B "CARBOHYDRATE ISOMER" D PDB ?
J5B "CARBOHYDRATE RING" pyranose PDB ?
J5B "CARBOHYDRATE ANOMER" alpha PDB ?
J5B "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
J5B "Create component" 2019-01-26 EBI
J5B "Initial release" 2019-02-06 RCSB
J5B "Other modification" 2020-07-03 RCSB
J5B "Modify parent residue" 2020-07-17 RCSB
J5B "Modify name" 2020-07-17 RCSB
J5B "Modify synonyms" 2020-07-17 RCSB
J5B "Modify atom id" 2020-07-17 RCSB
J5B "Modify component atom id" 2020-07-17 RCSB
J5B "Modify leaving atom flag" 2020-07-17 RCSB
J5B "Modify PCM" 2024-09-27 PDBE
#
_pdbx_chem_comp_pcm.pcm_id 1
_pdbx_chem_comp_pcm.comp_id J5B
_pdbx_chem_comp_pcm.modified_residue_id GLU
_pdbx_chem_comp_pcm.type None
_pdbx_chem_comp_pcm.category Carbohydrate
_pdbx_chem_comp_pcm.position "Amino-acid side chain"
_pdbx_chem_comp_pcm.polypeptide_position "Any position"
_pdbx_chem_comp_pcm.comp_id_linking_atom C10
_pdbx_chem_comp_pcm.modified_residue_id_linking_atom OE2
_pdbx_chem_comp_pcm.uniprot_specific_ptm_accession ?
_pdbx_chem_comp_pcm.uniprot_generic_ptm_accession ?
#